U.S. patent application number 11/555519 was filed with the patent office on 2007-06-28 for methods for producing members of specific binding pairs.
This patent application is currently assigned to MEDICAL RESEARCH COUNCIL. Invention is credited to Timothy Peter Bonnert, David John Chiswell, Timothy Piers Clackson, Andrew David Griffiths, Kasper Philipp Holliger, Ronald Henry Jackson, Kevin Stuart Johnson, James David Marks, Hendricus Renerus Jacobus Mattheus Hoogenboom, John McCafferty, Anthony Richard Pope, Gregory Paul Winter.
Application Number | 20070148774 11/555519 |
Document ID | / |
Family ID | 27516982 |
Filed Date | 2007-06-28 |
United States Patent
Application |
20070148774 |
Kind Code |
A1 |
McCafferty; John ; et
al. |
June 28, 2007 |
METHODS FOR PRODUCING MEMBERS OF SPECIFIC BINDING PAIRS
Abstract
A member of a specific binding pair (sbp) is identified by
expressing DNA encoding a genetically diverse population of such
sbp members in recombinant host cells in which the sbp members are
displayed in functional form at the surface of a secreted
recombinant genetic display package (rgdp) containing DNA encoding
the sbp member or a polypeptide component thereof, by virtue of the
sbp member or a polypeptide component thereof being expressed as a
fusion with a capsid component of the rgdp. The displayed sbps may
be selected by affinity with a complementary sbp member, and the
DNA recovered from selected rgdps for expression of the selected
sbp members. Antibody sbp members may be thus obtained, with the
different chains thereof expressed, one fused to the capsid
component and the other in free form for association with the
fusion partner polypeptide. A phagemid may be used as an expression
vector, with said capsid fusion helping to package the phagemid
DNA. Using this method libraries of DNA encoding respective chains
of such multimeric sbp members may be combined, thereby obtaining a
much greater genetic diversity in the sbp members than could easily
be obtained by conventional methods.
Inventors: |
McCafferty; John;
(Cambridgeshire, GB) ; Pope; Anthony Richard;
(Cambridge, GB) ; Johnson; Kevin Stuart;
(Cambridgeshire, GB) ; Mattheus Hoogenboom; Hendricus
Renerus Jacobus; (Cambridge, GB) ; Griffiths; Andrew
David; (Cambridge, GB) ; Jackson; Ronald Henry;
(Cambridge, GB) ; Holliger; Kasper Philipp;
(Cambridge, GB) ; Marks; James David; (Cambridge,
GB) ; Clackson; Timothy Piers; (Cambridge, GB)
; Chiswell; David John; (Buckingham, GB) ; Winter;
Gregory Paul; (Cambridge, GB) ; Bonnert; Timothy
Peter; (Cambridge, GB) |
Correspondence
Address: |
HOWREY LLP
C/O IP DOCKETING DEPARTMENT
2941 FAIRVIEW PARK DR, SUITE 200
FALLS CHURCH
VA
22042-2924
US
|
Assignee: |
MEDICAL RESEARCH COUNCIL
London
GB
CAMBRIDGE ANTIBODY TECHNOLOGY LIMITED
Cambridge
GB
|
Family ID: |
27516982 |
Appl. No.: |
11/555519 |
Filed: |
November 1, 2006 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
09417479 |
Oct 13, 1999 |
|
|
|
11555519 |
Nov 1, 2006 |
|
|
|
08484893 |
Jun 7, 1995 |
6172197 |
|
|
09417479 |
Oct 13, 1999 |
|
|
|
07971857 |
Jan 8, 1993 |
5969108 |
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08484893 |
Jun 7, 1995 |
|
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Current U.S.
Class: |
435/456 ;
435/472; 977/802 |
Current CPC
Class: |
B01J 2219/00718
20130101; C07K 2319/41 20130101; C07K 16/468 20130101; G01N 33/6857
20130101; C07K 2317/55 20130101; C07K 2319/735 20130101; C07K 16/40
20130101; Y10S 530/867 20130101; C07K 19/00 20130101; C07K 16/44
20130101; C12N 15/62 20130101; C07K 2317/34 20130101; C07K 2319/02
20130101; C12N 15/73 20130101; G01N 33/53 20130101; C07K 2317/21
20130101; C07K 2317/622 20130101; C07K 2317/92 20130101; C07K
2319/00 20130101; C07K 16/34 20130101; C07K 2317/24 20130101; C07K
2317/62 20130101; C07K 16/005 20130101; C07K 16/26 20130101; C07K
16/462 20130101; C40B 40/02 20130101; C12N 15/1037 20130101; C07K
16/00 20130101; C07K 16/18 20130101 |
Class at
Publication: |
435/456 ;
435/472; 977/802 |
International
Class: |
C12N 15/86 20060101
C12N015/86; C12N 15/74 20060101 C12N015/74 |
Foreign Application Data
Date |
Code |
Application Number |
Jul 10, 1991 |
GB |
PCT/GB91/01134 |
Jul 10, 1990 |
GB |
9015198.6 |
Oct 19, 1990 |
GB |
9022845.3 |
Nov 12, 1990 |
GB |
9024503.6 |
Mar 6, 1991 |
GB |
9104744.9 |
May 15, 1991 |
GB |
9110549.4 |
Claims
1. A phagemid comprising a DNA encoding a single-chain
antibody-coliphage pIII fusion protein, wherein the fusion protein
contains a contiguous full length coliphage pIII protein.
2. The phagemid according to claim 1, wherein the fusion protein
contains a protease-sensitive region between the antibody and the
coliphage pIII protein.
3. The phagemid according to either claim 1 or claim 2, wherein the
phagemid comprises the genetic elements and DNA sequences (SEQ ID
NOS: 7-17) of FIGS. 1(a)-1(c).
4. A process of producing the phagemid according to claim 1,
comprising fusing a DNA encoding the single-chain antibody to a DNA
encoding the contiguous full length coliphage pIII protein and
inserting the resulting DNA into a phagemid vector.
5. The process according to claim 4, further comprising inserting a
DNA encoding a protease-sensitive region between the DNA encoding
the single-chain antibody and the DNA encoding the coliphage pIII
protein.
6. A method of selecting antibodies from an antibody library,
comprising screening said antibody library with an antigen, wherein
said antibody library consists of phagemids according to either
claim 1 or claim 2.
7. A method of presenting a peptide or protein at the surface of a
phagemid viral particle, comprising producing said phagemid viral
particle, wherein said phagemid viral particle comprises a DNA
sequence encoding said peptide or protein fused to a DNA sequence
encoding a contiguous full length coliphage pIII protein.
8. A filamentous bacteriophage particle displaying on its surface
as a fusion with a gene III coat protein surface component a member
of a specific binding pair in functional form comprising a binding
domain for a complementary specific binding pair member, the
particle containing a phagemid genome which is plasmid nucleic acid
containing a single stranded phage replication origin and a
nucleotide sequence encoding said fusion, and the particle having a
coat partially derived from a helper phage and partly from said
fusion.
9. A particle according to claim 8 wherein the displayed specific
binding pair member comprises a binding domain of an
immunoglobulin.
10. A particle according to claim 9 wherein the specific binding
pair member is a scFv molecule.
Description
[0001] This application is a continuation of U.S. Ser. No.
09/417,479, (filed on Oct. 13, 1999), which is a division of U.S.
Ser. No. 08/484,893 (now U.S. Pat. No. 6,172,197), filed on Jun. 7,
1995, which is a continuation of U.S. Ser. No. 07/971,857 (now U.S.
Pat. No. 5,969,108) filed on Jan. 8, 1993, which is a U.S. National
Stage of PCT/GB91/01134 filed on Jul. 10, 1991, which claims
priority to U.K. Applications 9015198.6 (filed Jul. 10, 1990),
9022845.3 (filed Oct. 19, 1990), 9024503.6 (filed Nov. 20, 1990),
9104744.9 (filed Mar. 6, 1991), and 9110549.4 (filed May 15, 1991).
Each of these applications is hereby incorporated by reference
herein.
[0002] The present invention relates to methods for producing
members of specific binding pairs. The present invention also
relates to the biological binding molecules produced by these
methods. Owing to their high specificity for a given antigen, the
advent of monoclonal antibodies (Kohler, G. and Milstein C; 1975
Nature 256: 495) represented a significant technical break-through
with important consequences both scientifically and commercially.
Monoclonal antibodies are traditionally made by establishing an
immortal mammalian cell line which is derived from a single
immunoglobulin producing cell secreting one form of a biologically
functional antibody molecule with a particular specificity. Because
the antibody-secreting mammalian cell line is immortal, the
characteristics of the antibody are reproducible from batch to
batch. The key properties of monoclonal antibodies are their
specificity for a particular antigen and the reproducibility with
which they can be manufactured.
[0003] Structurally, the simplest antibody (IgG) comprises four
polypeptide chains, two heavy (H) chains and two light (L) chains
inter-connected by disulphide bonds (see FIG. 1). The light chains
exist in two distinct forms called kappa (K) and lambda (.lamda.).
Each chain has a constant region (C) and a variable region (V).
Each chain is organized into a series of domains. The light chains
have two domains, corresponding to the C region and the other to
the V region. The heavy chains have four domains, one corresponding
to the V region and three domains (1, 2 and 3) in the C region. The
antibody has two arms (each arm being a Fab region), each of which
has a VL and a VH region associated with each other. It is this
pair of v regions (VL and VH) that differ from one antibody to
another (owing to amino acid sequence variations), and which
together are responsible for recognising the antigen and providing
an antigen binding site (ABS). In even more detail, each V region
is made up from three complementarity determining regions (CDR)
separated by four framework regions (FR). The CDR's are the most
variable part of the variable regions, and they perform the
critical antigen binding function. The CDR regions are derived from
many potential germ line sequences via a complex process involving
recombination, mutation and selection.
[0004] It has been shown that the function of binding antigens can
be performed by fragments of a whole antibody. Example binding
fragments are (i) the Fab fragment consisting of the VL, VH, CL and
CH1 domains; (ii) the Fd fragment consisting of the VH and CH1
domains; (iii) the Fv fragment consisting of the VL and VH domains
of a single arm of an antibody, (iv) the dAb fragment (Ward, E. S.
et al., Nature 341, 544-546 (1989) which consists of a VH domain;
(v) isolated CDR regions; and (vi) F(ab').sub.2 fragments, a
bivalent fragment comprising two Fab fragments linked by a
disulphide bridge at the hinge region.
[0005] Although the two domains of the Fv fragment are coded for by
separate genes, it has proved possible to make a synthetic linker
that enables them to be made as a single protein chain (known as
single chain Fv (scFv); Bird, R. E. et al., Science 242, 423-426
(1988) Huston, J. S. et al., Proc. Natl. Acad. Sci., USA 85,
5879-5883 (1988)) by recombinant methods. These scFv fragments were
assembled from genes from monoclonals that had been previously
isolated. In this application, the applicants describe a process to
assemble scFv fragments from VH and VL domains that are not part of
an antibody that has been previously isolated.
[0006] Whilst monoclonal antibodies, their fragments and
derivatives have been enormously advantageous, there are
nevertheless a number of limitations associated with them.
[0007] Firstly, the therapeutic applications of monoclonal
antibodies produced by human immortal cell lines holds great
promise for the treatment of a wide range of diseases (Clinical
Applications of Monoclonal Antibodies. Edited by E. S. Lennox.
British Medical Bulletin 1984. Publishers Churchill Livingstone).
Unfortunately, immortal antibody-producing human cell lines are
very difficult to establish and they give low yields of antibody
(approximately 1 .mu.g/ml). In contrast, equivalent rodent cell
lines yield high amounts of antibody (approximately 100 .mu.g/ml).
However, the repeated administration of these foreign rodent
proteins to humans can lead to harmful hypersensitivity reactions.
In the main therefore, these rodent-derived monoclonal antibodies
have limited therapeutic use.
[0008] Secondly, a key aspect in the isolation of monoclonal
antibodies is how many different clones of antibody producing cells
with different specificities, can be practically established and
sampled compared to how many theoretically need to be sampled in
order to isolate a cell producing antibody with the desired
specificity characteristics (Milstein, C., Royal Soc. Croonian
Lecture, Proc. R. Soc. London B. 239; 1-16, (1990)). For example,
the number of different specificities expressed at any one time by
lymphocytes of the murine immune system is thought to be
approximately 10.sup.7 and this is only a small proportion of the
potential repertoire of specificities. However, during the
isolation of a typical antibody producing cell with a desired
specificity, the investigator is only able to sample 10.sup.3 to
10.sup.4 individual specificities. The problem is worse in the
human, where one has approximately 10.sup.12 lymphocyte
specificities, with the limitation on sampling of 10.sup.3 or
10.sup.4 remaining.
[0009] This problem has been alleviated to some extent in
laboratory animals by the use of immunisation regimes. Thus, where
one wants to produce monoclonal antibodies having a specificity
against a particular epitope, an animal is immunised with an
immunogen expressing that epitope. The animal will then mount an
immune response against the immunogen and there will be a
proliferation of lymphocytes which have specificity against the
epitope. Owing to this proliferation of lymphocytes with the
desired specificity, it becomes easier to detect them in the
sampling procedure. However, this approach is not successful in all
cases, as a suitable immunogen may not be available. Furthermore,
where one wants to produce human monoclonal antibodies (e.g., for
therapeutic administration as previously discussed), such an
approach is not practically, or ethically, feasible.
[0010] In the last few years, these problems have in part, been
addressed by the application of recombinant DNA methods to the
isolation and production of, e.g., antibodies and fragments of
antibodies with antigen binding ability, in bacteria such as E.
coli.
[0011] This simple substitution of immortalised cells with
bacterial cells as the `factory`, considerably simplifies
procedures for preparing large amounts of binding molecules.
Furthermore, a recombinant production system allows scope for
producing tailor-made antibodies and fragments thereof. For
example, it is possible to produce chimeric molecules with new
combinations of binding and effector functions, humanised
antibodies (e.g., murine variable regions combined with human
constant domains or murine-antibody CDRs grafted onto a human FR)
and novel antigen-binding molecules. Furthermore, the use of
polymerase chain reaction (PCR) amplification (Saiki, R. K., et
al., Science 239, 487-491 (1988)) to isolate antibody producing
sequences from cells (e.g., hybridomas and B cells) has great
potential for speeding up the timescale under which specificities
can be isolated. Amplified VH and VL genes are cloned directly into
vectors for expression in bacteria or mammalian cells (Orlandi, R.,
et al., 1989, Proc. Natl. Acad. Sci., USA 86, 3833-3837; Ward, E.
S., et al., 1989 supra; Larrick, J. W., et al., 1989, Biochem.
Biophys. Res. Commun. 160, 1250-1255; Sastry, L. et al., 1989,
Proc. Natl. Acad. Sci., USA., 86, 5728-5732). Soluble antibody
fragments secreted from bacteria are then screened for binding
activities.
[0012] However, like the production system based upon immortalised
cells, the recombinant production system still suffers from the
selection problems previously discussed and therefore relies on
animal immunization to increase the proportion of cells with
desired specificity. Furthermore, some of these techniques can
exacerbate the screening problems. For example, large separate H
and L chain libraries have been produced from immunized mice and
combined together in a random combinatorial manner prior to
screening (Huse, W. D. et al., 1989, Science 246, 1275-1281,
WO90/14443; WO90/14424 and WO90/14430). Crucially, however, the
information held within each cell, namely the original pairing of
one L chain with one H chain, is lost. This loses some, of the
advantage gained by using immunization protocols in the animal.
Currently, only libraries derived from single VH domains (dAbs;
Ward, E. S., et al., 1989, supra.) do not suffer this drawback.
However, because not all antibody VH domains are capable of binding
antigen, more have to be screened. In addition, the problem of
directly screening many different specificities in prokaryotes
remains to be solved.
[0013] Thus, there is a need for a screening system which
ameliorates or overcomes one or more of the above or other
problems. The ideal system would allow the sampling of very large
numbers of specificities (e.g., 10.sup.6 and higher), rapid sorting
at each cloning round, and rapid transfer of the genetic material
coding for the binding molecule from one stage of the production
process, to the next stage.
[0014] The most attractive candidates for this type of screening,
would be prokaryotic organisms (because they grow quickly, are
relatively simple to manipulate and because large numbers of clones
can be created) which express and display at their surface a
functional binding domain, e.g., an antibody, receptor, enzyme,
etc. In the UK patent GB 2137631B methods for the co-expression in
a single host cell of the variable H and L chain genes of
immunoglobulins were disclosed. However, the protein was expressed
intracellularly and was insoluble. Further, the protein required
extensive processing to generate antibody fragments with binding
activity and this generated material with only a fraction of the
binding activity expected for antibody fragments at this
concentration. It has already been shown that antibody fragments
can be secreted through bacterial membranes with the appropriate
signal peptide (Skerra, A. and Pluckthun, A. 1988 Science 240
1038-1040; Better, M et al 1988, Science 240 1041-1043) with a
consequent increase in the binding activity of antibody fragments.
These methods require screening of individual clones for binding
activity in the same way as do mouse monoclonal antibodies.
[0015] It has not been shown however, how a functional binding
domain, e.g., an antibody, antibody fragment, receptor, enzyme,
etc., can be held on the bacterial surface in a configuration which
allows sampling of say its antigen binding properties and selection
for clones with desirable properties. In large part, this is
because the bacterial surface is a complex structure, and in the
gram-negative organisms there is an outer wall which further
complicates the position. Further, it has not been shown that,
e.g., an antibody domain will fold correctly when expressed as a
fusion with a surface protein of bacteria or bacteriophage.
[0016] Bacteriophage are attractive prokaryote related organisms
for this type of screening. In general, their surface is a
relatively simple structure, they can be grown easily in large
numbers, they are amenable to the practical handling involved in
many potential mass screening programmes, and they carry genetic
information for their own synthesis within a small, simple package.
The difficulty has been to practically solve the problem of how to
use bacteriophages in this manner. A Genex Corporation patent
application number WO88/06630 has proposed that the bacteriophage
lambda would be a suitable vehicle for the expression of antibody
molecules, but they do not provide a teaching which enables the
general idea to be carried out.
[0017] For example, WO88/06630 does not demonstrate that any
sequences: (a) have been expressed as a fusion with gene V; (b)
have been expressed on the surface of lambda; and (c) have been
expressed so that the protein retains biological activity.
Furthermore there is no teaching on how to screen for suitable
fusions. Also, since the lambda virions are assembled within the
cell, the fusion protein would be expressed intracellularly and
would be predicted to be inactive. Bass et al., in December 1990
(after the earliest priority date for the present application)
describe deleting part of gene III of the filamentous bacteriophage
M13 and inserting the coding sequence for human growth hormone
(hGH) into the N-terminal site of the gene. The growth hormone
displayed by M13 was shown to be functional. (Bass, S., et al.
Proteins, Structure, Function and Genetics (1990) 8: 309-314). A
functional copy of gene III was always present in addition, when
this fusion was expressed. A Protein Engineering Corporation patent
application WO90/02809 proposes the insertion of the coding
sequence for bovine pancreatic trypsin inhibitor (BPTI) into gene
VIII of M13. However, the proposal was not shown to be operative.
For example, there is no demonstration of the expression of BPTI
sequences as fusions with protein VIII and display on the surface
of M13. Furthermore this document teaches that when a fusion is
made with gene III, it is necessary to use a second synthetic copy
of gene III, so that some unaltered gene III protein will be
present. The embodiments of the present application do not do this.
In embodiments where phagemid is rescued with M13K07 gene III
deletion phage, there is no unaltered gene III present.
[0018] WO90/02809 also teaches that phagemids that do not contain
the full genome of M13 and require rescue by coinfection with
helper phage are not suitable for these purposes because
coinfection could lead to recombination.
[0019] In all embodiments where the present applicants have used
phagemids, they have used a helper phage and the only sequences
derived from filamentous bacteriophage in the phagemids are the
origin of replication and gene III sequences.
[0020] WO90/02809 also teaches that their process needed
information such as nucleotide sequence of the starting molecule
and its three-dimensional structure. The use of a pre-existing
repertoire of binding molecules to select for a binding member,
such as is disclosed herein, for example, using an immunoglobulin
gene repertoire of animals, was not disclosed. Further, they do not
discuss favouring variegation of their binding molecules in natural
blocks of variation such as CDRs of immunoglobulins, in order to
favour generation of improved molecules and prevent unfavourable
variations. WO90/02809 also specifically excluded the application
of their process to the production of scFv molecules.
[0021] In each of the above discussed patents (WO88/06630 and
WO90/02809), the protein proposed for display is a single
polypeptide chain. There is no disclosure of a method for the
display of a dimeric molecule by expression of one monomer as a
fusion with a capsid protein and the other protein in a free
form.
[0022] Another disclosure published in May 1991 (after the earliest
priority date for the present application) describes the insertion
into gene VIII of M13, the coding sequences for one of the two
chains of the Fab portion of an antibody with co-expression of the
other from a plasmid.
[0023] The two chains were demonstrated as being expressed as a
functional Fab fragment on the surface of the phage (Kang A. S. et
al., (1991) Proc. Natl. Acad. Sci, USA, 88 p 4363-4366). No
disclosure was made of the site of insertion into gene VIII and the
assay for pAb binding activity by ELISA used a reagent specific for
antibody L chain rather than for phage. A further disclosure
published in March 1991 (after the earliest priority date for the
present application) describes the insertion of a fragment of the
AIDS virus protein gag into the N-terminal portion of gene III of
the bacteriophage fd. The expression of the gag protein fragment
was detected by immunological methods, but it was not shown whether
or not the protein was expressed in a functional form
(Tsunetsugu-Yokota Y et al. (1991) Gene 99 p 261-265).
[0024] The problem of how to use bacteriophages in this way is in
fact a difficult one. The protein must be inserted into the phage
in such a way that the integrity of the phage coat is not
undermined, and the protein itself should be functional retaining
its biological activity with respect to antigen binding. Thus,
where the protein of choice is an antibody, it should fold
efficiently and correctly and be presented for antigen binding.
Solving the problem for antibody molecules and fragments would also
provide a general method for any biomolecule which is a member of a
specific binding pair, e.g., receptor molecules and enzymes.
[0025] Surprisingly, the applicants have been able to construct a
bacteriophage that expresses and displays at its surface a large
biologically functional binding molecule (e.g., antibody fragments,
and enzymes and receptors) and which remains intact and infectious.
The applicants have called the structure which comprises a virus
particle and a binding molecule displayed at the viral surface a
`package`. Where the binding molecule is an antibody, an antibody
derivative or fragment, or a domain that is homologous to an
immunoglobulin domain, the applicants call the package a `phage
antibody` (pAb). However, except where the context demands
otherwise, where the term phage antibody is used generally, it
should also be interpreted as referring to any package comprising a
virus particle and a biologically functional binding molecule
displayed at the viral surface.
[0026] pAbs have a range of applications in selecting antibody
genes encoding antigen binding activities. For example, pAbs could
be used for the cloning and rescue of hybridomas (Orlandi, R., et
al (1989) PNAS 86 p 3833-3837), and in the screening of large
combinatorial libraries (such as found in Huse, W. D. et al., 1989,
Science 246, 1275-1281). In particular, rounds of selection using
pAbs may help in rescuing the higher affinity antibodies from the
latter libraries. It may be preferable to screen small libraries
derived from antigen-selected cells (Casali, P., et al., (1986)
Science 234 p 476-479) to rescue the original VH/VL pairs
comprising the Fv region of an antibody. The use of pAbs may also
allow the construction of entirely synthetic antibodies.
Furthermore, antibodies may be made which have some synthetic
sequences, e.g., CDRs, and some naturally derived sequences. For
example, V-gene repertoires could be made in vitro by combining
un-rearranged V genes, with D and J segments. Libraries of pAbs
could then be selected by binding to antigen, hypermutated in vitro
in the antigen-binding loops or V domain framework regions, and
subjected to further rounds of selection and mutagenesis.
[0027] As previously discussed, separate H and L chain libraries
lose the original pairing between the chains. It is difficult to
make and screen a large enough library for a particularly
advantageous combination of H and L chains.
[0028] For example, in a mouse there are approximately 10.sup.7
possible H chains and 10.sup.7 possible L chains. Therefore, there
are 10.sup.14 possible combinations of H and L chains, and to test
for anything like this number of combinations one would have to
create and screen a library of about 10.sup.14 clones. This has not
previously been a practical possibility.
[0029] The present invention provides a number of approaches which
ameliorate this problem.
[0030] In a first approach, (a random combinatorial approach, see
examples 20 and 21) as large a library as is practically possible
is created which expresses as many of the 10.sup.14 potential
combinations as possible. However, by virtue of the expression of
the H and L chains on the surface of the phage, it is reasonably
practicable to select the desired combination, from all the
generated combinations by affinity techniques (see later for
description of selection formats).
[0031] In a second approach (called a dual combinatorial approach
by the present applicants, see example 26), a large library is
created from two smaller libraries for selection of the desired
combination. This ameliorates the problems still further. The
approach involves the creation of: (i) a first library of say
10.sup.7, e.g., H chains which are displayed on a bacteriophage (as
a fusion with the protein encoded by gene III) which is resistant
to, e.g., tetracycline; and (ii) a second library of say 10.sup.7,
e.g., L chains in which the coding sequences for these light chains
are within a plasmid vector containing an origin of replication for
a bacteriophage (a phagemid) which is resistant to, e.g.,
ampicillin (i.e., a different antibiotic) and are expressed in the
periplasmic space of a host bacterium. The first library is then
used to infect the bacteria containing the second library to
provide 10.sup.14 combinations of H and L chains on the surface of
the resulting phage in the bacterial supernatant.
[0032] The advantage of this approach is that two separate
libraries of, e.g., 10.sup.7 are created in order to produce
10.sup.14 combinations. Creating a 10.sup.7 library is a practical
possibility.
[0033] The 10.sup.14 combinations are then subjected to selection
(see later for description of selection formats) as disclosed by
the present application. This selection will then produce a
population of phages displaying a particular combination of H and L
chains having the desired specificity. The phages selected,
however, will only contain DNA encoding one partner of the paired H
and L chains (deriving from either the phage or phagemid). The
sample eluate containing the population is then divided into two
portions. A first portion is grown on, e.g., tetracycline plates to
select those bacteriophage containing DNA encoding H chains which
are involved in the desired antigen binding. A second portion is
grown on, e.g., ampicillin plates to select those bacteriophage
containing phagemid DNA encoding L chains which are involved in the
desired antigen binding. A set of colonies from individually
isolated clones, e.g., from the tetracycline plates are then used
to infect specific colonies, e.g., from the ampicillin plates. This
results in bacteriophage expressing specific combinations of H and
L chains which can then be assayed for antigen binding.
[0034] In a third approach (called a hierarchical dual
combinational approach by the present applicants), an individual
colony from either the H or L chain clone selected by growth on the
antibiotic plates, is used to infect a complete library of clones
encoding the other chain (H or L). Selection is as described above.
This favours isolation of the most favourable combination.
[0035] In a fourth approach (called a hierarchrical approach by the
present applicants, see examples 22 and 46) both chains are cloned
into the same vector. However, one of the chains which is already
known to have desirable properties is kept fixed. A library of the
complementary chain is inserted into the same vector. Suitable
partners for the fixed chain are selected following display on the
surface of bacteriophage.
[0036] In a fifth approach (see example 48), to improve the chances
of recovering original pairs, the complexity of the combinatorial
libraries can be reduced by using small B populations of
B-lymphocytes selected for binding to a desired antigen. The cells
provide, e.g., mRNA or DNA, for preparing libraries of antibody
genes for display on phage. This technique can be used in
combination with the above mentioned four approaches for selection
of antibody specificities.
[0037] Phagemids have been mentioned above. The applicants have
realised and demonstrated that in many cases phagemids will be
preferred to phage for cloning antibodies because it is easier to
use them to generate more comprehensive libraries of the immune
repertoire. This is because the phagemid DNA is approximately 100
times more efficient than bacteriophage DNA in transforming
bacteria (see example 19). Also, the use of phagemids gives the
ability to vary the number of gene III binding molecule fusion
proteins displayed on the surface of the bacteriophage (see example
17). For example, in a system comprising a bacterial cell
containing a phagemid encoding a gene III fusion protein and
infected with a helper phage, induction of expression of the gene
III fusion protein to different extents, will determine the number
of gene III fusion proteins present in the space defined between
the inner and outer bacterial membranes following superinfection.
This will determine the ratio of gene III fusion protein to native
gene III protein displayed by the assembled phage.
[0038] Expressing a single fusion protein per virion may aid
selection of antibody specificities on the basis of affinity by
avoiding the `avidity` effect where a phage expressing two copies
of a low affinity antibody would have the same apparent affinity as
a phage expressing one copy of a higher affinity antibody. In some
cases however, it will be important to display all the gene III
molecules derived by superinfection of cells containing phagemids
to have fusions (e.g., for selecting low affinity binding molecules
or improving sensitivity on ELISA). One way to do this is to
superinfect with a bacteriophage which contains a defective gene
III. The applicants have, therefore, developed and used a phage
which is deleted in gene III. This is completely novel.
[0039] The demonstration that a functional antigen-binding domain
can be displayed on the surface of phage, has implications beyond
the construction of novel antibodies. For example, if other protein
domains can be displayed at the surface of a phage, phage vectors
could be used to clone and select genes by the binding properties
of the displayed protein. Furthermore, variants of proteins,
including epitope libraries built into the surface of the protein,
could be made and readily selected for binding activities. In
effect, other protein architectures might serve as "nouvelle"
antibodies.
[0040] The technique provides the possibility of building
antibodies from first principles, taking advantage of the
structural framework on which the antigen binding loops fold. In
general, these loops have a limited number of conformations which
generate a variety of binding sites by alternative loop
combinations and by diverse side chains. Recent successes in
modelling antigen binding sites augurs well for de novo design. In
any case, a high resolution structure of the antigen is needed.
However, the approach is attractive for making, e.g., catalytic
antibodies, particularly for small substrates. Here side chains or
binding sites for prosthetic groups might be introduced, not only
to bind selectively to the transition state of the substrate, but
also to participate directly in bond making and breaking. The only
question is whether the antibody architecture, specialised for
binding, is the best starting point for building catalysts. Genuine
enzyme architectures, such as the triose phosphate isomerase (TIM)
barrel, might be more suitable. Like antibodies, TIM enzymes also
have a framework structure (a barrel of .beta.-strands and
.alpha.-helices) and loops to bind substrate. Many enzymes with a
diversity of catalytic properties are based on this architecture
and the loops might be manipulated independently on the frameworks
for design of new catalytic and binding properties. The phage
selection system as provided by the present disclosure can be used
to select for antigen binding activities and the CDR loops thus
selected, used on either an antibody framework or a TIM barrel
framework. Loops placed on a, e.g., a TIM barrel framework could be
further modified by mutagenesis and subjected to further selection.
Thus, there is no need to select for high affinity binding
activities in a single step. The strategy of the immune system, in
which low affinity evolves to high affinity seems more realistic
and can be mimicked using this invention.
[0041] One class of molecules that could be useful in this type of
application are receptors. For example, a specific receptor could
be displayed on the surface of the phage such that it would bind
its ligand. The receptor could then be modified by, for example, in
vitro mutagenesis and variants having higher binding affinity for
the ligand selected. The selection may be carried out according to
one or more of the formats described below with reference to FIG. 2
(which refers particularly to pAbs) in which the pAb antibody is
replaced with a phage receptor and the antigen with a ligand 1.
[0042] Alternatively, the phage-receptor could be used as the basis
of a rapid screening system for the binding of ligands, altered
ligands, or potential drug candidates. The advantages of this
system namely of simple cloning, convenient expression, standard
reagents and easy handling makes the drug screening application
particularly attractive. In the context of this discussion,
receptor means a molecule that binds a specific, or group of
specific, ligand(s). The natural receptor could be expressed on the
surface of a population of cells, or it could be the extracellular
domain of such a molecule (whether such a form exists naturally or
not), or a soluble molecule performing a natural binding function
in the plasma, or within a cell or organ.
[0043] Another possibility, is the display of an enzyme molecule or
active site of an enzyme molecule on the surface of a phage (see
examples 11, 12, 30, 31, 32 and 36). Once the phage enzyme is
expressed, it can be selected by affinity chromatography, for
instance on columns derivatized with transition state analogues. If
an enzyme with a different or modified specificity is desired, it
may be possible to mutate an enzyme displayed as a fusion on
bacteriophage and then select on a column derivatised with an
analogue selected to have a higher affinity for an enzyme with the
desired modified specificity.
[0044] Although throughout this application, the applicants discuss
the possibility of screening for higher affinity variants of pAbs,
they recognise that in some applications, for example low affinity
chromatography (Ohlson, S. et al Anal. Biochem., 169, pp. 204-208
(1988)), it may be desirable to isolate lower affinity
variants.
[0045] Examples 21 and 23 show that the present invention provides
a way of producing antibodies with low affinities (as seen in the
primary immune response or in unimmunised animals). This is made
possible by displaying multiple copies of the antibody on the phage
surface in association with gene III protein. Thus, pAbs allow
genes for these antibodies to be isolated and if necessary, mutated
to provide improved antibodies.
[0046] pAbs also allow the selection of antibodies for improved
stability. It has been noted for many antibodies, that yield and
stability are improved when the antibodies are expressed at
30.degree. C. rather than 37.degree. C. If pAbs are displayed at
37.degree. C., only those which are stable will be available for
affinity selection. When antibodies are to be used in vivo for
therapeutic or diagnostic purposes, increased stability would
extend the half-life of antibodies in circulation.
[0047] Although stability is important for all antibodies and
antibody domains selected using phage, it is particularly important
for the selection of Fv fragments which are formed by the
non-covalent association of VH and VL fragments. Fv fragments have
a tendency to dissociate and have a much reduced half-life in
circulation compared to whole antibodies. Fv fragments are
displayed on the surface of phage, by the association of one chain
expressed as a gene III protein fusion with the complementary chain
expressed as a soluble fragment. If pairs of chains have a high
tendency to dissociate, they will be much less likely to be
selected as pAbs. Therefore, the population will be enriched for
pairs which do associate stably. Although dissociation is less of a
problem with Fab fragments, selection would also occur for Fab
fragments which associate stably. pAbs allow selection for
stability to protease attack, only those pAbs that are not cleaved
by proteases will be capable of binding their ligand and therefore
populations of phage will be enriched for those displaying stable
antibody domains.
[0048] The technique of displaying binding molecules on the phage
surface can also be used as a primary cloning system. For example,
a cDNA library can be constructed and inserted into the
bacteriophage and this phage library screened for the ability to
bind a ligand. The ligand/binding molecule combination could
include any pair of molecules with an ability to specifically bind
to one another, e.g., receptor/ligand, enzyme/substrate (or
analogue), nucleic acid binding protein/nucleic acid, etc. If one
member of the complementary pair is available, this may be a
preferred way of isolating a clone for the other member of the
pair.
[0049] It will often be necessary to increase the diversity of a
population of genes cloned for the display of their proteins on
phage or to mutate an individual nucleotide sequence. Although in
vitro or in vivo mutagenesis techniques could be used for either
purpose, a particularly suitable method would be to use mutator
strains. A mutator strain is a strain which contains a genetic
defect which causes DNA replicated within it to be mutated with
respect to its parent DNA. Hence if a population of genes as gene
III fusions is introduced into these strains it will be further
diversified and can then be transferred to a non-mutator strain, if
desired, for display and selection. Example 38 covers the use of
mutator strains with phage antibodies (an example of in vitro
mutagenesis and selection of phage antibodies is given in example
45).
Targeted Gene Transfer
[0050] A useful and novel set of applications makes use of the
binding protein on the phage to target the phage genome to a
particular cell or group of cells. For example, a pAb specific for
a cell surface molecule could be used to bind to the target cell
via the surface molecule. The phage could then be internalised,
either through the action of the receptor itself or as the result
of another event (e.g. an electrical discharge such as in the
technique of electroporation). The phage genome would then be
expressed if the relevant control signals (for transcription and
translation and possibly replication) were present. This would be
particularly useful if the phage genome contained a sequence whose
expression was desired in the target cell (along with the
appropriate expression control sequences). A useful sequence might
confer antibiotic resistance to the recipient cell or label the
cell by the expression of its product (e.g. if the sequence
expressed a detectable gene product such as a luciferase, see
White, M, et al, Techniques 2(4), p 194-201 (1990)), or confer a
particular property on the target cell (e.g., if the target cell
was a tumour cell and the new sequence directed the expression of a
tumour suppressing gene), or express an antisense construct
designed to turn off a gene or set of genes in the target cell, or
a gene or gene product designed to be toxic to the target cell.
Alternatively, the sequence whose expression is desired in the
target cell can be encoded on a phagemid. The phagemid DNA may then
be incorporated into a phage displaying an antibody specific for a
cell surface receptor. For example, incorporation may be by
superinfection of bacteria containing the phagemid, with a helper
phage whose genome encodes the antibody fragment specific for the
target cell. The package is then used to direct the phagemid to the
target cell.
[0051] This technique of "targeted gene transfer" has a number of
uses in research and also in therapy and diagnostics. For example,
gene therapy often aims to target the replacement gene to a
specific cell type that is deficient in its activity. Targetting
pAbs provide a means of achieving this.
[0052] In diagnostics, phage specific for particular bacteria or
groups of bacteria have been used to target marker genes, e.g.,
luciferase, to the bacterial host (sec, for example, Ulitzer, S.,
and Kuhn, J., EPA 85303913.9). If the host range of the phage is
appropriate, only those bacteria that are being tested for, will be
infected by the phage, express the luciferase gene and be detected
by the light they emit. This system has been used to detect the
presence of Salmonella. One major problem with this approach is the
initial isolation of a bacteriophage with the correct host range
and then the cloning of a luciferase gene cassette into that phage,
such that it is functional. The pAb system allows the luciferase
cassette to be cloned into a well characterised system (filamentous
phage) and allows simple selection of an appropriate host range, by
modifying the antibody (or other binding molecule) specificity that
the pAb encodes.
[0053] The present applicants have also been able to develop novel
selection systems and assay formats which depend on the unique
properties of these replicable genetic display packages, e.g.,
pAbs.
Terminology
[0054] Much of the terminology discussed in this section has been
mentioned in the text where appropriate.
Specific Binding Pair
[0055] This describes a pair of molecules (each being a member of a
specific binding pair) which are naturally derived or synthetically
produced. One of the pair of molecules, has an area on its surface,
or a cavity which specifically binds to, and is therefore defined
as complementary with a particular spatial and polar organisation
of the other molecule, so that the pair have the property of
binding specifically to each other. Examples of types of specific
binding pairs are antigen-antibody, biotin-avidin, hormone-hormone
receptor, receptor-ligand, enzyme-substrate, IgG-protein A.
Multimeric Member
[0056] This describes a first polypeptide which will associate with
at least a second polypeptide, when the polypeptides are expressed
in free form and/or on the surface of a substrate. The substrate
may be provided by a bacteriophage. Where there are two associated
polypeptides, the associated polypeptide complex is a dimer, where
there are three, a trimer, etc. The dimer, trimer, multimer, etc.,
or the multimeric member may comprise a member of a specific
binding pair.
[0057] Example multimeric members are heavy domains based on an
immunoglobulin molecule, light domains based on an immunoglobulin
molecule, T-cell receptor subunits.
Replicable Genetic Display Package (Rgdp)
[0058] This describes a biological particle which has genetic
information providing the particle with the ability to replicate.
The particle can display on its surface at least part of a
polypeptide. The polypeptide can be encoded by genetic information
native to the particle and/or artificially placed into the particle
or an ancestor of it. The displayed polypeptide may be any member
of a specific binding pair e.g., heavy or light chain domains based
on an immunoglobulin molecule, an enzyme or a receptor, etc.
[0059] The particle may be a virus e.g., a bacteriophage such as fd
or M13.
Package
[0060] This describes a replicable genetic display package in which
the particle is displaying a member of a specific binding pair at
its surface. The package may be a bacteriophage which displays an
antigen binding domain at its surface. This type of package has
been called a phage antibody (pAb).
Antibody
[0061] This describes an immunoglobulin whether natural or partly
or wholly synthetically produced. The term also covers any protein
having a binding domain which is homologous to an immunoglobulin
binding domain. These proteins can be derived from natural sources,
or partly or wholly synthetically produced.
[0062] Example antibodies are the immunoglobulin isotypes and the
Fab, F(ab.sup.1).sub.2, scFv, Fv, dAb, Fd fragments.
Immunoglobulin Superfamily
[0063] This describes a family of polypeptides, the members of
which have at least one domain with a structure related to that of
the variable or constant domain of immunoglobulin molecules. The
domain contains two S-sheets and usually a conserved disulphide
bond (see A. F. Williams and A. N. Barclay 1988 Ann. Rev Immunol. 6
381-405).
[0064] Example members of an immunoglobulin superfamily are CD4,
platelet derived growth factor receptor (PDGFR), intercellular
adhesion molecule. (ICAM). Except where the context otherwise
dictates, reference to immunoglobulins and immunoglobulin homologs
in this application includes members of the immunoglobulin
superfamily and homologs thereof.
Homologs
[0065] This term indicates polypeptides having the same or
conserved residues at a corresponding position in their primary,
secondary or tertiary structure. The term also extends to two or
more nucleotide sequences encoding the homologous polypeptides.
[0066] Example homologous peptides are the immunoglobulin
isotypes.
Functional
[0067] In relation to a sbp member displayed on the surface of a
rgdp, means that the sbp member is presented in a folded form in
which its specific binding domain for its complementary sbp member
is the same or closely analogous to its native configuration,
whereby it exhibits similar specificity with respect to the
complementary sbp member. In this respect, it differs from the
peptides of Smith et al, supra, which do not have a definite folded
configuration and can assume a variety of configurations determined
by the complementary members with which they may be contacted.
Genetically Diverse Population
[0068] In connection with sbp members or polypeptide components
thereof, this is referring not only to diversity that can exist in
the natural population of cells or organisms, but also diversity
that can be created by artificial mutation in vitro or in vivo.
[0069] Mutation in vitro may for example, involve random
mutagenesis using oligonucleotides having random mutations of the
sequence desired to be varied. In vivo mutagenesis may for example,
use mutator strains of host microorganisms to harbour the DNA (see
Example 38 below).
Domain
[0070] A domain is a part of a protein that is folded within itself
and independently of other parts of the same protein and
independently of a complementary binding member.
Folded Unit
[0071] This is a specific combination of an .alpha.-helix and/or
.beta.-strand and/or .beta.-turn structure. Domains and folded
units contain structures that bring together amino acids that are
not adjacent in the primary structure.
Free Form
[0072] This describes the state of a polypeptide which is not
displayed by a replicable genetic display package.
Conditionally Defective
[0073] This describes a gene which does not express a particular
polypeptide under one set of conditions, but expresses it under
another set of conditions. An example, is a gene containing an
amber mutation expressed in non-suppressing or suppressing hosts
respectively.
[0074] Alternatively, a gene may express a protein which is
defective under one set of conditions, but not under another set.
An example is a gene with a temperature sensitive mutation.
Suppressible Translational Stop Codon
[0075] This describes a codon which allows the translation of
nucleotide sequences downstream of the codon under one set of
conditions, but under another set of conditions translation ends at
the codon. Example of suppressible translational stop codons are
the amber, ochre and opal codons.
Mutator Strain
[0076] This is a host cell which has a genetic defect which causes
DNA replicated within it to be mutated with respect to its parent
DNA. Example mutator strains are NR9046mutD5 and NR9046 mut T1 (see
Example 38).
Helper Phage
[0077] This is a phage which is used to infect cells containing a
defective phage genome and which functions to complement the
defect. The defective phage genome can be a phagemid or a phage
with some function encoding gene sequences removed. Examples of
helper phages are M13KO7, M13K07 gene III no. 3; and phage
displaying or encoding a binding molecule fused to a capsid
protein.
Vector
[0078] This is a DNA molecule, capable of replication in a host
organism, into which a gene is inserted to construct a recombinant
DNA molecule.
Phage Vector
[0079] This is a vector derived by modification of a phage genome,
containing an origin of replication for a bacteriophage, but not
one for a plasmid.
Phagemid Vector
[0080] This is a vector derived by modification of a plasmid
genome, containing an origin of replication for a bacteriophage as
well as the plasmid origin of replication.
Secreted
[0081] This describes a rgdp or molecule that associates with the
member of a sbp displayed on the rgdp, in which the sbp member
and/or the molecule, have been folded and the package assembled
externally to the cellular cytosol.
Repertoire of Rearranged Immunoglobulin Genes
[0082] A collection of naturally occurring nucleotides, e.g., DNA
sequences which encoded expressed immunoglobulin genes in an
animal. The sequences are generated by the in vivo rearrangement
of, e.g., V, D and J segments for H chains and, e.g., the V and J
segments for L chains. Alternatively the sequences may be generated
from a cell line immunized in vitro and in which the rearrangement
in response to immunization occurs intracellularly.
Library
[0083] A collection of nucleotide, e.g., DNA, sequences within
clones.
Repertoire of Artificially Rearranged Immunoglobulin Genes
[0084] A collection of nucleotide, e.g., DNA, sequences derived
wholly or partly from a source other than the rearranged
immunoglobulin sequences from an animal. This may include, for
example, DNA sequences encoding VH domains by combining
unrearranged V segments with D and J segments and DNA sequences
encoding VL domains by combining V and J segments.
[0085] Part or all of the DNA sequences may be derived by
oligonucleotide synthesis.
Secretory Leader Peptide
[0086] This is a sequence of amino acids joined to the N-terminal
end of a polypeptide and which directs movement of the polypeptide
out of the cytosol.
Eluant
[0087] This is a solution used to breakdown the linkage between two
molecules. The linkage can be a non-covalent or covalent bond(s).
The two molecules can be members of a sbp.
Derivative
[0088] This is a substance which derived from a polypeptide which
is encoded by the DNA within a selected rgdp. The derivative
polypeptide may differ from the encoded polypeptide by the
addition, deletion, substitution or insertion of amino acids, or by
the linkage of other molecules to the encoded polypetide. These
changes may be made at the nucleotide or protein level. For
example, the encoded polypeptide may be a Fab fragment which is
then linked to an Fc tail from another source. Alternatively
markers such as enzymes, flouresceins, etc., may be linked to,
e.g., Fab, scFv fragments.
SUMMARY OF THE INVENTION
[0089] The present invention provides a method for producing a
replicable genetic display package or population such rgdps of
which method comprises the steps of: [0090] a) inserting a
nucleotide sequence encoding a member of a specific binding pair
e.g., a binding molecule within a viral genome; [0091] b) culturing
the virus containing said nucleotide sequence, so that said binding
molecule is expressed and displayed by the virus at its
surface.
[0092] The present invention also provides a method for selecting a
rgdp specific for a particular epitope which comprises producing a
population of such rgdps as described above and the additional step
of selecting for said binding molecule by contacting the population
with said epitope so that individual rgdps with the desired
specificity may bind to said epitope. The method may comprise one
or more of the additional steps of: (i) separating any bound rgdps
from the epitope; (ii) recovering any separated rgdps and (iii)
using the inserted nucleotide sequences from any separated rgdps in
a recombinant system to produce the binding molecule separate from
virus. The selection step may isolate the nucleotide sequence
encoding the binding molecule of desired specificity, by virtue of
said binding molecule being expressed in association with the
surface of the virus in which said encoding nucleic acid is
contained.
[0093] The present invention also provides a method of producing a
multimeric member of a specific binding pair (sbp), which method
comprises:
[0094] expressing in a recombinant host organism a first
polypeptide chain of said sbp member or a genetically diverse
population of said sbp member fused to a component of a secreted
replicable genetic display package (rgdp) which thereby displays
said polypeptide at the surface of the package, and expressing in a
recombinant host organism a second polypeptide chain of said
multimer and causing or allowing the polypeptide chains come
together to form said multimer as part of said rgdp at least one of
said polypeptide chains being expressed from nucleic acid that is
capable of being packaged using said component therefor, whereby
the genetic material of each said rgdp encodes a said polypeptide
chain. Both said chains may be expressed in the same host
organism.
[0095] The first and second chains of said multimer may be
expressed as separate chains from a single vector containing their
respective nucleic acid.
[0096] At least one of said polypeptide chains may be expressed
from a phage vector.
[0097] At least one of said polypeptide chains may be expressed
from a phagemid vector, the method including using a helper phage,
or a plasmid expressing complementing phage genes, to help package
said phagemid genome, and said component of the rgdp is a capsid
protein therefor. The capsid protein may be absent, defective or
conditionally defective in the helper phage.
[0098] The method may comprise introducing a vector capable of
expressing said first polypeptide chain, into a host organism which
expresses said second polypeptide chain in free form, or
introducing a vector capable of expressing said second polypeptide
in free form into a host organism which expresses said first
polypeptide chain.
[0099] Each of the polypeptide chain may be expressed from nucleic
acid which is capable of being packaged as a rgdp using said
component fusion product, whereby encoding nucleic acid for both
said polypeptide chains are packaged in respective rgdps.
[0100] The nucleic acid encoding at least one of said first and
second polypeptide chains may be obtained from a library of nucleic
acid including nucleic acid encoding said chain or a population of
variants of said chain. Both the first and second polypeptide
chains may be obtained from respective said libraries of nucleic
acid.
[0101] The present invention also provides a method of producing a
member of a specific binding pair (sbp), from a nucleic acid
library including nucleic acid encoding said sbp member or a
genetically diverse population of said type of sbp members, which
method comprises: [0102] expressing in recombinant host cells
polypeptides encoded by said library nucleic acid fused to a
component of a secreted replicable genetic display package (rgdp)
or in free form for association with a polypeptide component of
said sbp member which is expressed as a fusion to said rgdp
component so that the rgdp displays said sbp member in functional
form at the surface of the package, said library nucleic acid being
contained within the host cells in a form that is capable of being
packaged using said rgdp component, whereby the genetic material of
an rgdp displaying an sbp member contains nucleic acid encoding
said sbp member or a polypeptide component thereof.
[0103] The nucleotide sequences for the libraries may be derived
from, e.g., animal spleen cells or peripheral blood lymphocytes.
Alternatively the nucleotide sequence may be derived by the in
vitro mutagenesis of an existing antibody coding sequence.
[0104] The present invention also provides a method of producing a
member of a specific binding pair (sbp), which method comprises:
[0105] expressing in recombinant host cells nucleic acid encoding
said sbp member or a genetically diverse population of said type of
sbp member wherein the or each said sbp member or a polypeptide
component thereof is expressed as a fusion with a component of a
secreted replicable genetic display package (rgdp) which displays
said sbp member at the surface of the package, nucleic acid
encoding said sbp member or a polypeptide component thereof being
contained within the host cell in a form that is capable of being
packaged using said rgdp component whereby the genetic material of
the rgdp displaying said sbp member encodes said sbp member or a
polypeptide component thereof, said host organism being a mutator
strain which introduces genetic diversity into the sbp member to
produce said mixed population.
[0106] The present invention also provides a method of producing a
member of a specific binding pair (sbp), which method comprises:
[0107] expressing in recombinant host cells nucleic acid encoding
said sbp member or a genetically diverse population of said type of
sbp member wherein the or each said sbp member or a polypeptide
component thereof is expressed as a fusion with a component of a
secreted replicable genetic display package (rgdp) which displays
said sbp member in functional form at the surface of the package,
nucleic acid encoding said sbp member or a polypeptide component
thereof being contained within the host cell in a form that is
capable of being packaged using said rgdp component whereby the
genetic material of the rgdp displaying an sbp member encodes said
sbp member or a polypeptide component thereof, said fusions being
with bacteriophage capsid protein and the rgdps being formed with
said fusions in the absence of said capsid expressed in wild-type
form.
[0108] The present invention also provides a method of producing a
member of a specific binding pair (sbp) which method comprises:
[0109] expressing in recombinant host cells nucleic acid encoding
said sbp member or a genetically diverse population of said type of
sbp member or a polypeptide component thereof fused to a component
of a secreted replicable genetic display package (rgdp) which
displays said sbp member in functional form at the surface of the
package, nucleic acid encoding said sbp member or a polypeptide
component thereof being contained within the host cell in a form
that is capable of being packaged using said rgdp component whereby
the genetic material of the rgdp displaying an sbp member or a
polypeptide component thereof encodes said sbp member or a
polypeptide component thereof, said sbp member or polypeptide
component thereof being expressed from a phagemid as a capsid
fusion, and a helper phage, or a plasmid expressing complementing
phage genes, is used along with said capsid fusions to package the
phagemid nucleic acid.
[0110] The library or genetically diverse population may be
obtained from: [0111] (i) the repertoire of rearranged
immunoglobulin genes of an animal immunised with complementary sbp
member, [0112] (ii) the repertoire of rearranged immunoglobulin
genes of an animal not immunised with complementary sbp member,
[0113] (iii) a repertoire of artificially rearranged immunoglobulin
gene or genes [0114] (iv) a repertoire of immunoglobulin homolog
gene or genes; or [0115] (v) a mixture of any of (i), (ii), (iii)
and (iv).
[0116] The capsid protein may be absent, defective or conditionally
defective in the helper phage.
[0117] The host cell may be a mutator strain which introduces
genetic diversity into the sbp member nucleic acid.
[0118] The sbp member may comprise a domain which is, or is
homologous to, an immunoglobulin domain.
[0119] The rgdp may be a bacteriophage, the host a bacterium, and
said component of the rgdp a capsid protein for the bacteriophage.
The phage may be a filamentous phage. The phage may be selected
from the class I phages fd, M13, f1, If1, lke, ZJ/Z, Ff and the
class II phages Xf, Pf1 and Pf3. The phage may be fd or a
derivative of fd. The derivative may be tetracycline resistant. The
said sbp member or polypeptide chain thereof may be expressed as a
fusion with the gene III capsid protein of phage fd or its
counterpart in another filamentous phage. The sbp member or
polypeptide chain thereof may be inserted in the N-terminal region
of the mature capsid protein downstream of a secretory leader
peptide. The sequence may be inserted after amino acid +1 of the
mature protein. The site for insertion may be flanked by short
sequences corresponding to sequences which occur at each end of the
nucleic acid to be inserted. For example, where 4 the protein
domain is an immunoglobulin domain, the insertion site in the phage
may be flanked by nucleotide sequences which code for the first
five amino acids and the last five amino acids of the Ig domain.
Such flanking nucleotide sequences are shown in FIGS. 4B and C,
wherein the site-flanking nucleotide sequences encode amino acid
sequences QVQLQ (SEQ ID NO:1) and VTVSS (SEQ ID NO:2) which occur
at either end of the VH domain, or QVQLQ (SEQ ID NO:1) and LEIKR
(SEQ ID NO:3) which occur at either end of the Fv (combined VH+VL)
domain. Each of these sequences flanking the insertion site may
include a suitable cleavage site, as shown in FIG. 4A and FIG.
4B.
[0120] Alternatively, the flanking nucleotide sequences shown in
FIGS. 4B and C as described above, may be used to flank the
insertion site for any nucleic acid to be inserted, whether or not
that nucleic acid codes an immunoglobulin.
[0121] The host may be E. coli.
[0122] Nucleic acid encoding an sbp member polypeptide may be
linked downstream to a viral capsid protein through a suppressible
translational stop codon.
[0123] As previously mentioned, the present invention also provides
novel selection systems and assay formats. In these systems and
formats, the gene sequence encoding the binding molecule (e.g., the
antibody) of desired specificity is separated from a general
population of rgdps having a range of specifies, by the fact of its
binding to a specific target (e.g., the antigen or epitope). Thus
the rgdps formed by said expression may be selected or screened to
provide an individual sbp member or a selected mixed population of
said sbp members associated in their respective rgdps with nucleic
acid encoding said sbp member or a polypeptide chain thereof. The
rgdps may be selected by affinity with a member complementary to
said sbp member.
[0124] Any rgdps bound to said second member may be recovered by
washing with an eluant. The washing conditions may be varied in
order to obtain rgdps with different binding affinities for said
epitope. Alternatively, to obtain, e.g., high affinity rgdps, the
complementary member (e.g., an epitope) may be presented to the
population of rgdps (e.g., pAbs) already bound to a binding member
in which case pAbs with a higher affinity for the epitope will
displace the already bound binding member. Thus the eluant may
contain a molecule which competes with said rgdp for binding to the
complementary sbp member. The rgdp may be applied to said
complementary sbp member in the presence of a molecule which
competes with said package for binding to said complementary sbp
member. Nucleic acid derived from a selected or screened rgdp may
be used to express said sbp member or a fragment or derivative
thereof in a recombinant host organism. Nucleic acid from one or
more rgdps may be taken and used to provide encoding nucleic acid
in a further said method to obtain an individual sbp member or a
mixed population of sbp members, or encoding nucleic acid therefor.
The expression end product may be modified to produce a derivative
thereof.
[0125] The expression end product or derivative thereof may be used
to prepare a therapeutic or prophylactic medicament or a diagnestic
product.
[0126] The present invention also provides recombinant host cells
harbouring a library of nucleic acid fragments comprising fragments
encoding a genetically diverse population of a type of member of a
specific binding pair (sbp), each sbp member or a polypeptide
component thereof being expressed as a fusion with a component of a
secretable replicable genetic display package (rgdp), so that said
sbp members are displayed on the surface of the rgdps in functional
form and the genetic material of the rgdps encode the associated
sbp member or a polypeptide component thereof. The type of sbp
members may be immunoglobulins or immunoglobulin homologs, a first
polypeptide chain of which is expressed as a said fusion with a
component of the rgdp and a second polypeptide chain of which is
expressed in free form and associates with the fused first
polypeptide chain in the rgdp.
[0127] The present invention also provides a helper phage whose
genome lacks nucleic acid encoding one of its capsid proteins, or
whose encoding nucleic acid therefor is conditionally defective, or
which encodes said capsid protein in defective or conditionally
defective form.
[0128] The present invention also provides a bacterial host cell
containing a filamentous phage genome defective for a capsid
protein thereof and wherein the host cell is capable of expressing
capsid protein complementing said defect such that infectious phage
particles can be obtained therefrom. The complementing capsid
protein may be expressed in said host from another vector contained
therein. The defective capsid protein may be gene III of phage fd
or its counterpart in another filamentous phage.
[0129] The present invention also provides recombinant E. coli TG1
M13KO7 gIII No. 3 (NCTC 12478).
[0130] The present invention also provides a phage antibody having
the form of a replicable genetic display package displaying on its
surface in functional form a member of a specific binding pair or a
specific binding domain thereof.
[0131] In the above methods, the binding molecule may be an
antibody, or a domain that is homologous to an immunoglobulin. The
antibody and/or domain may be either naturally derived or synthetic
or a combination of both. The domain may be a Fab, scFv, Fv dAb or
Fd molecule. Alternatively, the binding molecule may be an enzyme
or receptor or fragment, derivative or analogue of any such enzyme
or receptor. Alternatively, the binding molecule may be a member of
an immunoglobulin superfamily and which has a structural form based
on an immunoglobulin molecule.
[0132] The present invention also provides rgdps as defined above
and members of specific binding pairs e.g., binding molecules such
as antibodies, enzymes, receptors, fragments and derivatives
thereof, obtainable by use of any of the above defined methods. The
derivatives may comprise members of the specific binding pairs
fused to another molecule such as an enzyme or a Fc tail.
[0133] The invention also includes kits for carrying out the
methods hereof. The kits will include the necessary vectors. One
such vector will typically have an origin of replication for single
stranded bacteriophage and either contain the sbp member nucleic
acid or have a restriction site for its insertion in the 5' end
region of the mature coding sequence of a phage capsid protein, and
with a secretory leader coding sequence upstream of said site which
directs a fusion of the capsid protein exogenous polypeptide to the
periplasmic space.
[0134] The restriction sites in the vectors are preferably those of
enzymes which cut only rarely in protein coding sequences.
[0135] The kit preferably includes a phagemid vector which may have
the above characteristics, or may contain, or have a site for
insertion, of sbp member nucleic acid for expression of the encoded
polypeptide in free form.
[0136] The kits will also contain ancillary components required for
carrying out the method, the nature of such components depending of
course on the particular method employed.
[0137] Useful ancillary components may comprise helper phage, PCR
primers, and buffers and enzymes of various kinds.
[0138] PCR primers and associated reagents for use where the sbp
members are antibodies may have the following characteristics:
[0139] (i) primers having homology to the 51 end of the sense or
anti-sense strand of sequences encoding domains of antibodies; and
[0140] (ii) primers including tag sequences 5' to these homologous
sequences which incorporate restriction sites to allow insertion
into vectors; together with sequences to allow assembly of
amplified VH and VL regions to enable expression as Fv, scFv or Fab
fragments.
[0141] Buffers and enzymes are typically used to enable preparation
of nucleotide sequences encoding Fv, scFv or Fab fragments derived
from rearranged or unrearranged immunoglobulin genes according to
the strategies described herein.
[0142] The applicants have chosen the filamentous F-specific
bacteriophages as an example of the type of phage which could
provide a vehicle for the display of binding molecules, e.g.,
antibodies and antibody fragments and derivatives thereof, on their
surface and facilitate subsequent selection and manipulation.
[0143] The F-specific phages (e.g. fl, fd and M13) have evolved a
method of propagation which does not kill the host cell and they
are used commonly as vehicles for recombinant DNA (Kornberg, A.,
DNA Replication, W.H. Freeman and Co., San Francisco, 1980). The
single stranded DNA genome (approximately 6.4 Kb) of fd is extruded
through the bacterial membrane where it sequesters capsid
sub-units, to produce mature virions. These virions are 6 nm in
diameter, 1 .mu.m in length and each contain approximately 2,800
molecules of the major coat protein encoded by viral gene VIII and
four molecules of the adsorption molecule gene III protein (g3p)
the latter is located at one end of the virion. The structure has
been reviewed by Webster et al., 1978 in The Single Stranded DNA
Phages, 557-569, Cold Spring Harbor Laboratory Press. The gene III
product is involved in the binding of the phage to the bacterial
F-pilus.
[0144] Although these phages do not kill their host during normal
replication, disruption of some of their genes can lead to cell
death (Kornberg, A., 1980 supra.) This places some restraint on
their use. The applicants have recognized that gene III of phage fd
is an attractive possibility for the insertion of biologically
active foreign sequences. There are, however, other candidate sites
including for example gene VIII and gene VI.
[0145] The protein itself is only a minor component of the phage
coat and disruption of the gene does not lead to cell death (Smith,
G. 1988, Virology 167: 156-165). Furthermore, it is possible to
insert some foreign sequences (with no biological function) into
various positions within this gene (Smith, G. 1985 Science 228:
1315-1317, Parmley, S. F. and Smith, G. P. Gene: 73 (1988) p.
305-318, and de la Cruz, V. F., et al., 1988, J. Biol. Chem., 263:
4318-4322). Smith et al described the display of peptides on the
outer surface of phage but they did not describe the display of
protein domains. Peptides can adopt a range of structures which can
be different when in free solution, than when bound to, for
example, an antibody, or when forming part of a protein (Stanfield,
R. I. et al., (1990) Science 248, p 712-719). Proteins in general
have a well defined tertiary structure and perform their biological
function only when adopting this structure. For example, the
structure of the antibody D1.3 has been solved in the free form and
when bound to antigen (Bhat, T. N. et al., (1990) Nature 347, p
483-485). The gross structure of the protein is identical in each
instance with only minor variations around the binding site for the
antigen. Other proteins have more substantial conformation changes
on binding of ligand, for instance the enzymes hexokinase and
pyruvate dehydrogenase during their catalytic cycle, but they still
retain their overall pattern of folding. This structural integrity
is not confined to whole proteins, but is exhibited by protein
domains. This leads to the concept of a folded unit which is part
of a protein, often a domain, which has a well defined primary,
secondary and tertiary structure and which retains the same overall
folding pattern whether binding to a binding partner or not. The
only gene sequence that Smith et al., described that was of
sufficient size to encode a domain (a minimum of perhaps 50 amino
acids) was a 335 bp fragment of a .beta.-galctrosidase
corresponding to nucleotides 861-1195 in the .beta.-galactosidase
gene sequence (Parmley, S.+Smith, G. P. 1988 supra. This would
encode 112 amino acids of a much larger 380 amino acid domain.
Therefore, prior to the present application, no substantially
complete domain or folded unit had been displayed on phage. In
these cases, although the infectivity of the virion was disrupted,
the inserted sequences could be detected on the phage surface by
use of, e.g., antibodies.
[0146] The protein encoded by gene III has several domains (Pratt,
D., et al., 1969 Virology 39:42-53, Grant, R. A., et al., 1981, J.
Biol. Chem. 256: 539-546 and Armstrong, J., et al., FEBS Lett. 135:
167-172 1981.) including: (i) a signal sequence that directs the
protein to the cell membrane and which is then cleaved off; (ii) a
domain that anchors the mature protein into the bacterial cell
membrane (and also the phage coat); and (iii) a domain that
specifically binds to the phage receptor, the F-pilus of the host
bacterium. Short sequences derived from protein molecules have been
inserted into two places within the mature molecule (Smith, G.,
1985 supra., and Parmley, S.F. and Smith G. P., 1988 supra).
Namely, into an inter-domain region and also between amino acids 2
and 3 at the N-terminus. The insertion sites at the N-terminus were
more successful in maintaining the structural integrity of the gene
III protein and displaying the peptides on the surface of the
phage. By use of antisera specific for the peptides, the peptides
inserted into this position were shown to be on the surface of the
phage. These authors were also able to purify the phage, using this
property. However, the peptides expressed by the phage, did not
possess measurable biological functions of their own.
[0147] Retaining the biological function of a molecule when it is
expressed in a radically different context to its natural state is
difficult. The demands on the structure of the molecule are heavy.
In contrast, retaining the ability to be bound by specific antisera
is a passive process which imposes far less rigorous demands on the
structure of the molecule. For example, it is the rule rather than
the exception that polyclonal antisera will recognise totally
denatured, and biologically inactive, proteins on Western blots
(see for example, Harlow, E. and Lane, D., Antibodies, a Laboratory
Manual, Cold Spring Harbor Laboratory Press 1988). Therefore, the
insertion of peptides into a region that allows their structure to
be probed with antisera teaches only that the region allows the
inserted sequences to be exposed and does not teach that the region
is suitable for the insertion of large sequences with demanding
structural constraints for the display of a molecule with a
biological or binding function. In particular, it does not teach
that domains or folded units of proteins can be displayed from
sequences inserted in this region.
[0148] This experience with Western blots is a graphic practical
demonstration which shows that retaining the ability to be bound by
specific antisera imposes far less rigorous demands on the
structure of a polypeptide, than does folding for the retention of
a biological function.
[0149] Studies have been carried out, in which E. coli have been
manipulated to express the protein .beta.-adrenergic receptor as a
fusion with the outer membrane protein lamB. The s-adrenergic
receptor was expressed in a functional form as determined by the
presence of binding activity. However, when an equivalent antibody
fusion was made with lamB, the antibody fusion was toxic to the
host cell.
[0150] The applicants have investigated the possibility of
inserting the gene coding sequence for biologically active antibody
fragments into the gene III region of fd to express a large fusion
protein. As is apparent from the previous discussion, this approach
makes onerous demands on the functionality of the fusion protein.
The insertion is large, encoding antibody fragments of at least
100-200 amino acids; the antibody derived domain must fold
efficiently and correctly to display antigen-binding; and most of
the functions of gene III must be retained. The applicants approach
to the construction of the fusion molecule was designed to minimise
the risk of disrupting these functions. In an embodiment of the
invention, the initial vector used was fd-tet (Zacher, A. N., et
al., 1980, Gene 9, 127-140) a tetracycline resistant version of fd
bacteriophage that can be propagated as a plasmid that confers
tetracycline resistance to the infected E. coli host. The
applicants chose to insert after the signal sequence of the fd gene
III protein for several reasons. In particular, the applicants
chose to insert after amino acid 1 of the mature protein to retain
the context for the signal peptidase cleavage. To retain the
structure and function of gene III itself, the majority of the
original amino acids are synthesized after the inserted
immunoglobulin sequences. The inserted immunoglobulin sequences
were designed to include residues from the switch region that links
VH-VL to CH1-CL (Lesk, A., and Chothia, C., Nature 335, 188-190,
1988).
[0151] Surprisingly, by manipulating gene III of bacteriophage fd,
the present applicants have been able to construct a bacteriophage
that displays on its surface large biologically functional
antibody, enzyme, and receptor molecules whilst remaining intact
and infectious. Furthermore, the phages bearing antibodies of
desired specificity, can be selected from a background of phages
not showing this specificity.
[0152] The sequences coding for a population of antibody molecules
and for insertion into the vector to give expression of antibody
binding functions on the phage surface can be derived from a
variety of sources. For example, immunised or non-immunised rodents
or humans, and from organs such as spleen and peripheral blood
lymphocytes. The coding sequences are derived from these sources by
techniques familiar to those skilled in the art (Orlandi, R., et
al., 1989 supra; Larrick, J. W., et al., 1989 supra; Chiang, Y. L.,
et al., 1989 Bio Techniques 7, p. 360-366; Ward, E. S, et al., 1989
supra; Sastry, L., et al., 1989 supra.) or by novel linkage
strategies described in examples 14, 33, 40 and 42. Novel
strategies are described in examples 7, 25, 33, 39 and 40 for
displaying dimeric molecules, e.g., Fab and Fv fragments on the
surface of a phage. Each individual pAb in the resulting library of
pAbs will express antibodies or antibody derived fragments that are
monoclonal with respect to their antigen-binding
characteristics.
[0153] The disclosure made by the present applicants is important
and provides a significant breakthrough in the technology relating
to the production of biological binding molecules, their fragments
and derivatives by the use of recombinant methods.
[0154] In standard recombinant techniques for the production of
antibodies, an expression vector containing sequences coding for
the antibody polypeptide chains is used to transform, e.g., E.
coli. The antibody polypeptides are expressed and detected by use
of standard screening systems. When the screen detects an antibody
polypeptide of the desired specificity, one has to return to the
particular transformed E. coli expressing the desired antibody
polypeptide. Furthermore, the vector containing the coding sequence
for the desired antibody polypeptide then has to be isolated for
use from E. coli in further processing steps.
[0155] In the present invention however, the desired antibody
polypeptide when expressed, is already packaged with its gene
coding sequence. This means that when the an antibody polypeptide
of desired specificity is selected, there is no need to return to
the original culture for isolation of that sequence. Furthermore,
in previous methods in standard recombinant techniques, each clone
expressing antibody needs to be screened individually. The present
application provides for the selection of clones expressing
antibodies with desired properties and thus only requires screening
of clones from an enriched pool.
[0156] Because a rgdp (e.g., a pAb) is a novel structure that
displays a member of a specific binding pair (e.g., an antibody of
monoclonal antigen-binding specificity) at the surface of a
relatively simple replicable structure also containing the genetic
information encoding the member, rgdps, e.g., pAbs, that bind to
the complementary member of the specific binding pair (e.g.,
antigen) can be recovered very efficiently by either eluting off
the complementary member using for example diethylamine, high salt,
etc., and infecting suitable bacteria, or by denaturing the
structure, and specifically amplifying the sequences encoding the
member using PCR. That is, there is no necessity to refer back to
the original bacterial clone that gave rise to the pAb.
[0157] For some purposes, for example immunoprecipitation and some
diagnostic tests, it is advantageous to use polyclonal antibodies
or antibody fragments. The present invention allows this to be
achieved by either selection of an enriched pool of pAbs with
desired properties or by mixing individually isolated clones with
desired properties. The antibodies or antibody fragments may then
be expressed in soluble form if desired. Such a selected polyclonal
pAb population can be grown from stocks of phage, bacteria
containing phagemids or bacteria expressing soluble fragments
derived from the selected polyclonal population. Thus a reagent
equivalent to a polyclonal antiserum is created which can be
replicated and routinely manufactured in culture without use of
animals.
Selection Formats and Affinity Maturation
[0158] Individual rgdps, e.g., pAbs expressing the desired
specificity, e.g., for an antigen, can be isolated from the complex
library using the conventional screening techniques (e.g. as
described in Harlow, E., and Lane, D., 1988, supra Gherardi, E et
al. 1990. J. Immunol. meth. 126 p 61-68).
[0159] The applicants have also devised a series of novel selection
techniques that are practicable only because of the unique
properties of rgdps. The general outline of some screening
procedures is illustrated in FIG. 2A and FIG. 2B using pAbs as an
example type of rgdp.
[0160] The population/library of pAbs to be screened could be
generated from immunised or other animals; or be created in vitro
by mutagenising pre-existing phage antibodies (using techniques
well-known in the art such as oligonucleotide directed mutagenesis
(Sambrook, J., et al., 1989 Molecular Cloning a Laboratory Manual,
Cold Spring Harbor Laboratory Press). This population can be
screened in one or more of the formats described below with
reference to FIG. 2A and FIG. 2B, to derive those individual pAbs
whose antigen binding properties are different from sample c.
Binding Elution
[0161] FIG. 2A shows antigen (ag) bound to a solid surface(s) the
solid surface (s) may be provided by a petri dish, chromatography
beads, magnetic beads and the like. The population/library of pAbs
is then passed over the ag, and those individuals p that bind are
retained after washing, and optionally detected with detection
system d. A detection system based upon anti-fd antisera is
illustrated in more detail below in example 4. If samples of bound
population p are removed under increasingly stringent conditions,
the binding affinity represented in each sample will increase.
Conditions of increased stringency can be obtained, for example, by
increasing the time of soaking or changing the pH of the soak
solution, etc.
Competition
[0162] Referring to FIG. 2B antigen ag can be bound to a solid
support s and bound to saturation by the original binding molecule
c. If a population of mutant pAb (or a set of unrelated pAbs) is
offered to the complex, only those that have higher affinity for
antigen ag than c will bind. In most examples, only a minority of
population c will be displaced by individuals from population p. If
c is a traditional antibody molecule, all bound material can be
recovered and bound p recovered by infecting suitable bacteria
and/or by use of standard techniques such as PCR.
[0163] An advantageous application is where ag is used as a
receptor and c the corresponding ligand. The recovered bound
population p is then related structurally to the receptor binding
site/and or ligand. This type of specificity is known to be very
useful in the pharmaceutical industry.
[0164] Another advantageous application is where ag is an antibody
and c its antigen. The recovered bound population p is then an
anti-idiotype antibody which have numerous uses in research and the
diagnostic and pharmaceutical industries.
[0165] At present it is difficult to select directly for
anti-idiotype antibodies. pAbs would give the ability to do this
directly by binding pAb libraries (e.g., a naive library) to B
cells (which express antibodies on their surface) and isolating
those phage that bound well.
[0166] In some instances it may prove advantageous to pre-select
population p. For example, in the anti-idiotype example above, p
can be absorbed against a related antibody that does not bind the
antigen.
[0167] However, if c is a pAb, then either or both c and p can
advantageously be marked in some way to both distinguish and select
for bound p over bound c. This marking can be physical, for
example, by pre-labelling p with biotin; or more advantageously,
genetic. For example, c can be marked with an EcoB restriction
site, whilst p can be marked with an EcoK restriction site (see
Carter, P. et al., 1985, Nucl. Acids Res. 13, 4431-4443). When
bound p+c are eluted from the antigen and used to infect suitable
bacteria, there is restriction (and thus no growth) of population c
(i.e. EcoB restricting bacteria in this example). Any phage that
grew, would be greatly enriched for those individuals from p with
higher binding affinities. Alternatively, the genetic marking can
be achieved by marking p with new sequences, which can be used to
specifically amplify p from the mixture using PCR.
[0168] Since the bound pAbs can be amplified using for example PCR
or bacterial infection, it is also possible to rescue the desired
specificity even when insufficient individuals are bound to allow
detection via conventional techniques.
[0169] The preferred method for selection of a phage displaying a
protein molecule with a desired specificity or affinity will often
be elution from an affinity matrix with a ligand (e.g., example
21). Elution with increasing concentrations of ligand should elute
phage displaying binding molecules of increasing affinity. However,
when, e.g., a pAb binds to its antigen with high affinity or
avidity (or another protein to its binding partner) it may not be
possible to elute the pAb from an affinity matrix with molecule
related to the antigen. Alternatively, there may be no suitable
specific eluting molecule that can be prepared in sufficiently high
concentration. In these cases it is necessary to use an elution
method which is not specific to, e.g., the antigen-antibody
complex. Some of the non-specific elution methods generally used
reduce phage viability for instance, phage viability is reduced
with time at pH12 (Rossomando, E. F. and Zinder N. D., J. Mol.
Biol. 36 387-399 1968). There may be interactions between, e.g.,
antibodies and affinity matrices which cannot be disrupted without
completely removing phage infectivity. In these cases a method is
required to elute phage which does not rely on disruption of, e.g.,
the antibody - antigen interaction. A method was therefore devised
which allows elution of bound pAbs under mild conditions (reduction
of a dithiol group with dithiothreitol) which do not disrupt phage
structure (example 47).
[0170] This elution procedure is just one example of an elution
procedure under mild conditions. A particularly advantageous method
would be to introduce a nucleotide sequence encoding amino acids
constituting a recognition site for cleavage by a highly specific
protease between the foreign gene inserted, in this instance a gene
for an antibody fragment, and the sequence of the remainder of gene
III. Examples of such highly specific proteases are Factor X and
thrombin. After binding of the phage to an affinity matrix and
elution to remove non-specific binding phage and weak binding
phage, the strongly bound phage would be removed by washing the
column with protease under conditions suitable for digestion at the
cleavage site. This would cleave the antibody fragment from the
phage particle eluting the phage. These phage would be expected to
be infective, since the only protease site should be the one
specifically introduced. Strongly binding phage could then be
recovered by infecting e.g., E. coli TG1 cells.
[0171] An alternative procedure to the above is to take the
affinity matrix which has retained the strongly bound pAb and
extract the DNA, for example by boiling in SDS solution. Extracted
DNA can then be used to directly transform E. coli host cells or
alternatively the antibody encoding sequences can be amplified, for
example using PCR with suitable primers such as those disclosed
herein, and then inserted into a vector for expression as a soluble
antibody for further study or a pAb for further rounds of
selection.
[0172] Another preferred method for selection according to affinity
would be by binding to an affinity matrix containing low amounts of
ligand.
[0173] If one wishes to select from a population of phages
displaying a protein molecule with a high affinity for its ligand,
a preferred strategy is to bind a population of phage to an
affinity matrix which contains a low amount of ligand. There is
competition between phage, displaying high affinity and low
affinity proteins, for binding to the ligand on the matrix. Phage
displaying high affinity protein is preferentially bound and low
affinity protein is washed away. The high affinity protein is then
recovered by elution with the ligand or by other procedures which
elute the phage from the affinity matrix (example 35 demonstrates
this procedure).
[0174] In summary then, for recovery of the packaged DNA from the
affinity step, the package can be simply eluted, it can be eluted
in the presence of a homologous sbp member which competes with said
package for binding to a complementary sbp member; it could be
removed by boiling, it could be removed by proteolytic cleavage of
the protein; and other methods will be apparent to those skilled in
the art e.g., destroying the link between the substrate and
complementary sbp member to release said packaged DNA and sbp
member. At any rate, the objective is to obtain the DNA from the
package so that it can be used directly or indirectly, to express
the sbp member encoded thereby.
[0175] The efficiency of this selection procedure for pAbs and the
ability to create very large libraries means that the immunisation
techniques developed to increase the proportion of screened cells
producing antibodies of interest will not be an absolute
requirement. The technique allows the rapid isolation of binding
specificities, e.g., antigen-binding specificities, including those
that would be difficult or even unobtainable by conventional
techniques, for example, catalytic or anti-idiotypic antibodies.
Removal of the animal altogether is now possible, once a complete
library of the immune repertoire has been constructed. The novel
structure of the pAb molecule can be used in a number of other
applications, some examples of which are:
Signal Amplification
[0176] Acting as a novel molecular entity in itself, rgdps, e.g.,
pAbs combine the ability to bind a specific molecule, e.g., antigen
with amplification, if the major coat protein is used to attach
another moiety. This moiety can be attached via immunological,
chemical, or any other means and can be used, for example, to label
the complex with detection reagents or cytotoxic molecules for use
in vivo or in vitro.
Physical Detection
[0177] The size of the rgdps, e.g., pAbs can be used as a marker
particularly with respect to physical methods of detection such as
electron microscopy and/or some biosensors, e.g., surface plasmon
resonance.
Diagnostic Assays
[0178] The rgdps, e.g., pAbs also have advantageous uses in
diagnostic assays, particularly where separation can be effected
using their physical properties for example centrifugation,
filtration, etc.
[0179] In order that the invention is more fully understood,
embodiments will now be described in more detail by way of example
only and not by way of limitation with reference to the figures
described below.
BRIEF DESCRIPTION OF THE DRAWINGS
[0180] FIG. 1 shows the basic structure of the simplest antibody
molecule IgG.
[0181] FIGS. 2A and 2B show schematically selection techniques
which utilise the unique properties of pAbs; 2A shows a
binding/elution system; and 2B shows a competition system (p=pAb;
ag=antigen to which binding by pAb is required; c=competitor
population, e.g., antibody, pAb, ligand; s=substrate (e.g. plastic
beads, etc.); d=detection system.
[0182] FIG. 3 shows the vector fd-tet and a scheme for the
construction of vectors, fdTPs/Bs (for insertion of VH coding
sequences) and fdTPs/Xh for the insertion of scFv coding
sequences.
[0183] FIGS. 4A-4B show the nucleotide sequences for the
oligonucleotides and vectors. All sequences are drawn 5' to 3' and
are numbered according to Beck et al., 1978, Nucl. Acid Res., 5:
4495-4503. 4a shows the sequences of the oligonucleotides used for
mutagenesis (oligo's 1 and 2) or sequencing (oligo 3). The
sequences shown were synthesized on an Applied Biosystems,
oligonucleotide synthesizer and are complementary to the single
stranded form of fd-tet (they are in the anti-sense form with
respect to gene III). 4B shows the sequences of the various
constructs around the gene III insertion site. These sequences are
drawn in the sense orientation with respect to gene III; (A) fd-tet
(and fdT.delta.Bst) (B) fdTPs/Bs and (C) fdTPs/Xh. The key
restriction enzyme sites are shown along with the immunoglobulin
amino acids contributed by the vectors, (amino acid single letter
code is used, see Harlow, E., and Lane, D., 1988 supra.).
[0184] FIGS. 5A-5B show the nucleotide and amino acid sequences for
scFv in the vector scFvD1.3 myc. This gives the sequence of the
anti-lysozyme single chain Fv and surrounding sequences in scFvD1.3
myc, showing the N-terminal pel B signal peptide sequence and the
C-terminal myc tag sequence (Ward, E. S., et al., 1989, supra.).
Also shown is the peptide sequence linking the VH and VL regions.
The amino acid sequence is represented above the nucleotide
sequence by the single letter code, see Harlow, E., and Lane D.,
1988 supra.
[0185] FIG. 6 shows the binding of pAbs to lysozyme and the effect
of varying the amount of supernatant. Each point is the average of
duplicate samples. Lysozyme was coated at 1 mg/ml in 50 mM
NaHCO.sub.3.
[0186] FIG. 7 shows the effect of varying the coating concentration
of lysozyme or bovine serum albumin on the binding of pAbs to
lysozyme in graphical form. Each point is the average of duplicate
samples.
[0187] FIG. 8 shows the sequence around the cloning site in gene
III of fd-CAT2. Restriction enzyme sites are shown as well as the
amino acids encoded by antibody derived sequences. These are
flanked at the 5' end by the gene III signal peptide and at the 3'
end by 3 alanine residues (encoded by the Not 1 restriction site)
and the remainder of the mature gene III protein. The arrow shows
the cleavage site for cutting of the signal peptide.
[0188] FIG. 9 shows the binding of pAb (1.3) to lysozymes. Binding
of phage as detected by ELISA to (a) hen egg-white lysozyme (HEL)
(b) turkey egg-white lysozyme (TEL), (c) human lysozyme (HUL), (d)
bovine serum albumin (BSA). A further control of (e) fdTPs/Bs to
HEL.
[0189] FIGS. 10A-11D show a map of FabD1.3 in pUC19.
[0190] FIG. 11 shows the ELISA results providing a comparison of
lysozyme-binding by phage-Fab and phage-scFv. Vector=fdCAT2
(example 5); fdscFv(OX)=pAbNQ11 (Example 9); fdVHCH1 (D1.3)=grown
in normal cells (i.e. no L chain, see example 7); fdFab(D1.3) i.e.
fdVHCH1 (D1.3) grown in cells containing D1.3 L chain; fdscFv
(D1.3)=pAbD1.3.
[0191] FIGS. 12A-12B show oligonucleotide probing of affinity
purified phage. 10.sup.12 phage in the ratio of 1 pAb (D1.3) in
4.times.10.sup.4 fdTPS/Bs phages were affinity purified and probed
with an oligonucleotide specific for pAb (D1.3) A is a filter after
one round of affinity purification (900 colonies total) and B is a
filter after two rounds (372 colonies total).
[0192] FIG. 13 shows the sequence of the anti-oxazolone antibody
fragment NQ11 scFv. The sequence contributed by the linker is shown
in the lower case. The sequence for VH is before the linker
sequence and the sequence for VL is after the linker.
[0193] FIG. 14 shows the ELISA results for binding pAb NQ11 and pAb
D1.3 and vector fdTPs/xh to specified antigens.
[0194] FIG. 15 shows the sequence surrounding the phoA insertion in
fd-phoAla166. The restriction sites used for cloning are shown, as
well as the amino acids encoded by phoA around the insertion site.
The first five amino acids of the mature fusion come from gene
III.
[0195] FIG. 16a shows the structure of gene III and the native
BamHI site into which a scFv coding sequence was inserted in
example 13 and FIG. 16b shows the natural peptide linker sites A
and B for possible insertion of scFv coding sequences.
[0196] FIG. 17 shows schematically the protocol for PCR assembly of
mouse VH and VLK repertoires for phage display described in example
14.
[0197] FIG. 18 shows examples of the final products obtained with
the procedure of example 14. Lanes a and b show the products of the
initial PCR using heavy and light chain primers respectively; lane
c shows the complete assembled 700 bp product before final
digestion with Not1 and ApaL1; M1, M2 markers .PHI.74 Hae III
digest and 123 base pair ladder (BRL Limited, P.O. Box 35,
Washington Road, Paisley, Scotland), respectively.
[0198] FIG. 19 shows the binding of .sup.125I-PDGF-BB to fd
h-PDGFB-R phage in immunoprecipitation assay and comparison to
fdTPs/Bs and no phage controls; binding is expressed as a
percentage of the total .sup.125I-PDGF-BB added to the
incubation.
[0199] FIG. 20 shows the displacement of .sup.125-PDGF-BB bound to
fd-h-PDGFB-R phage using unlabelled PDGF-BB measured using an
immunoprecipitation assay. Binding is expressed as a percentage of
the total .sup.125I-PDGF-BB added to the incubation.
[0200] FIG. 21 shows the displacement of .sup.125I-PDGF-BB bound to
fd-h-PDGFB-R phage using unlabelled PDGF-BB measured using an
immunoprecipitation assay. Non-specific binding of
.sup.125I-PDGF-BB to vector phage fdTPs/Bs in the absence of added
unlabelled PDGF was deducted from each point.
[0201] FIG. 22 shows the results of an ELISA of lysozyme binding by
pCAT-3 scFv D1.3 phagemid in comparison with pCAT-3 vector (both
rescued by M13K07) and fdCAT2 scFv D1.3 as described in example 17.
The ELISA was performed as described in example 6 with
modifications detailed in example 18.
[0202] FIGS. 23A-23B show the digestion pattern seen when
individual clones, selected at random from a library of single
chain Fv antibody genes derived from an immunised mouse; are
digested with BstN1.
[0203] FIGS. 24A-24B show VH and VK gene sequences derived from the
combinatorial library in example 21 and the hierarchical library in
example 22.
[0204] FIGS. 25A-26B show a matrix of ELISA signals for clones
derived from random combinatorial library. Designation of the
clones is as in FIG. 24. The number of clones found with each
combination is shown by the numerals.
[0205] FIG. 26A shows the phagemid pHEN1 a derivative of pUC119
described in example 24; and the cloning sites in the phagemid
pHEN.
[0206] FIG. 27. The antibody constructs cloned into fd-CAT2 and
pHEN1 for display on the surface of phage. Constructs I, II, III
and IV were cloned into both fd-CAT2 (as ApaLI-NotI fragments) and
pHEN1 (as SfiI-NotI fragments) and pHEN1 (as SfiI-NotI fragments).
All the constructs contained the heavy chain (VH) and light chain
(VK) variable regions of the mouse anti-phOx antibody NQ10.12.5.
The constant domains were human CK and CH1 (.gamma.1 isotype).
[0207] FIG. 28. Three ways of displaying antibody fragments on the
surface of phage by fusion to gene III protein.
[0208] FIG. 29. Western blot of supernatant taken from pHEN1-II(+)
or pHEN1(-) cultures in E. coli HB2151, showing secretion of Fab
fragment from pHEN1-II only. The anti-human Fab detects both H and
L chain. Due to the attached c-myc tag, the L chain, highlighted by
both anti-c-myc tag and anti-human CK antisera, is slightly larger
(calculated Mr 24625) than the H chain (calculated Mr23145).
[0209] FIG. 30 is a plot showing the effect of lysozyme dilution on
ratio of ELISA signals obtained using pAbD1.3 or soluble scFv
D1.3.
[0210] FIG. 31 is a plot showing the effect of lysozyme dilution on
ELISA signals obtained using fdTscFvD1.3 and soluble scFvD1.3.
[0211] FIG. 32 is a plot showing positive results from an ELISA
screen of phage displaying scFv fragments derived from the cell
line 013 which express a monoclonal antibody directed against
oestriol.
[0212] FIG. 33 is a plot showing positive results from an ELISA
screen of phage displaying scFv fragments derived from the cell
line 014 which express a monoclonal antibody directed against
oestriol.
[0213] FIG. 34 is a Western Blot showing expression of the alkaline
phosphatase-gene 3 fusion. 16 .mu.l of 50 fold concentrate of each
phage sample was detected on western blots with either anti-gene 3
antiserum (e-f) or with anti-alkaline phosphatase antiserum
(c-f):
a) fd-phoAla166 grown in TG1 cells
b) fd-phoAla166 grown in KS272 cells
c) fdCCAT2 grown in TG1 cells
d) fdCAT2 grown in TG1 cells, mixed with 13 ng of purified alkaline
phosphatase
e) fd-phoAla166 grown in TG1 cells
f) fdCAT2 grown in TG1 cells.
[0214] FIGS. 35A-35B are Western Blots showing ultrafiltration of
phage-enzyme 10 .mu.l of 50 fold concentrate of phage (representing
5 mls of culture supernatant) was centrifuged through
ultrafiltration membranes with nominal molecular weight retention
of 300,000 daltons. Western blots of flow through and retentate
fractions were detected with anti-alkaline phosphatase antiserum.
The equivalent of 800 .mu.l of original culture supernatant was run
on the gel.
[0215] FIG. 35A. Phage were grown in TG1 cells. a) fd-phoAla166
before ultrafiltration (short exposure). b) fd-phoAla166 before
ultrafiltration. c) fd-phoAla166 material retained on
ultrafiltration membrane.
[0216] FIG. 35B. Phage were grown in KS272 cells. a) fd-phoAla166
before ultrafiltration. b) fd-phoAla166 material retained on
ultrafiltration membrane. c) fdCAT2. d) fdCAT2 mixed with purified
alkaline phosphatase before ultrafiltration. e) Retentate from
sample d. f) Flow through from sample d.
[0217] FIG. 36 Electrophoresis of samples from stages of a Fab
assembly. Samples from different stages in the PCR Fab assembly
process described in example 33 were subjected to electrophoresis
on a 1% TAE-agarose gel. Samples from a comparable scFv assembly
process (as in example 14) are shown for comparison. Samples left
to right are: TABLE-US-00001 M = Markers VHCH1 = sequences encoding
VHCH1 domains amplified by PCR VKCK = sequences encoding VKCK
domains amplified by PCR -L = Fab assembly reaction performed in
absence of linker +L = Fab PCR assembly reaction product VHCH1 plus
VKCK plus linker M = Markers VK = sequences encoding VK domain
amplified by PCR VL = sequences encoding VH domains amplified by
PCR -L = scFv assembly reaction in absence of linker +L = scFv
assembly reaction in presence of linker M = Markers
[0218] FIG. 37. Comparison of ELISA signals with scFv D1.3 cloned
in fd-CAT2 (fd) or pCAT-3. pCAT-3 scFv1.3 has been rescued with
M13K07 (KO7). M13KO7.DELTA.gIII No 3 (gIII No 3) or M13KO7
gIII.DELTA.No 2 (g111No2). Phage antibodies are compared at 10
times (10.times.) 1 times (1.times.) or 0.1 times (0.1.times.)
concentrations relative to concentration in the supernatant after
overnight growth. The fdCAT2 and pCAT-3 non-recombinant vector
signals were <0.01 at 10.times. concentration. M13KO7
gIII.DELTA.No 1 did not rescue at all, as judged by no signal above
background in this ELISA.
[0219] FIGS. 38A-38B. Western blot of PEG precipitated phage used
in ELISA probed with anti-g3p. Free g3p and the g3p-scFvD1.3 fusion
bands are arrowed. [0220] Sample 2--pCAT3 vector [0221] Sample
3--pCAT3 scFvD1.3 rescued with M13KO7, no IPTG [0222] Sample
4--pCAT3 scFvD1.3 rescued with M13KO7, 50 .mu.M IPTG [0223] Sample
5--pCAT3 scFvD1.3 rescued with M13KO7, 100 .mu.M IPTG [0224] Sample
6--pCAT3 scFvD1.3 rescued with M13KO7 gIII.DELTA. No 3 (no IPTG)
[0225] Sample 7--pCAT3 scFvD1.3 rescued with M13KO7 gIII.DELTA. No
2 (no IPTG)
[0226] FIG. 38A samples contain the equivalent of 8 .mu.l of
phagemid culture supernatant per track, and 80 .mu.l of the fd
supernatant (10-fold lower phage yield than the phagemid). FIG. 38B
phagemid samples are those used in FIG. 38A at a five-fold higher
sample loading (equivalent to 40 .mu.l of culture supernatant per
track) to enable visualisation of the fusion band in samples
rescued with parental M13K07.
[0227] FIG. 39 is a graph showing fdCAT2scFvD1.3 enrichment
produced from a mixture of fdCAT2scFvD1.3 and fdCAT2TPB4 by one
round of panning.
[0228] FIG. 40 is a graph showing fdCAT2scFvD1.3 enrichment
produced from a mixture of fdCAT2scFvD1.3 and fdCAT2TPB1 by one
round of panning.
[0229] FIG. 41. Western blot of phage proteins of fdCAT2(1) and
fd-tet-SNase(2) with anti-g3p antiserum. Marker molecular weights
bands are indicated (kD).
[0230] FIG. 42. Nuclease assay of soluble SNase (3 ng)(A-1),
fd-tet-SNase(4.times.10.sup.9TU, (B-1), fd-CAT2
(2.times.10.sup.10TU) (C-1) and of a PEG-precipitated fdCAT2 and
SNase mixture(2.times.10.sup.10TU and 0.7 ug)(D-1) in a 10-fold
dilution series (1 to 3 or 4). Marker (M) is a HindIII digest of
.lamda.-DNA(New England Biolabs).
[0231] FIG. 43. ELISA signals obtained with fd-tet, fd-CD4-V1 and
fd-CD4-V1V2. In each group of three, the samples are left to right
phage concentrate(SN); phage concentrate plus soluble CD4(SN+sCD4);
phage concentrate plus gp120 (SN+gp120).
[0232] FIGS. 44A-44B show the DNA sequence of scfv B18
(anti-NP).
[0233] FIG. 45 shows a map of the insert of sequences encoding
FvD1.3 present in fd-tet FvD1.3 (example 39). rbs designates the
ribosome binding site. Gene III is now shown in its full
length.
[0234] FIG. 46. shows an ELISA assay of phages displaying FvD1.3 or
scFvD1.3 by binding to plates coated with lysogyme. Signals
obtained at various dilution factors are shown. FvD1.3
(.DELTA.S-Stuffer) which does not express Fv was used as a
control.
[0235] FIG. 47. shows a schematic representation of steps involved
in the PCR assembly of nucleotide sequences encoding human Fab
fragments. Details are in example 40.
[0236] FIG. 48A shows a map of plasmid pJM1-FabD1.3 which is used
for the expression of soluble human Fab fragments and as a template
for the synthesis of linker DNA for Fab assembly. FIG. 48B is a
schematic representation of sequences encoding a Fab construct.
FIG. 48C shows the sequence of DNA template for the synthesis of
linker DNA for Fab assembly.
[0237] FIG. 49. shows a schematic representation of steps involved
in the PCR assembly of nucleotide sequences encoding human scFv
fragments. Details are in example 42.
[0238] FIGS. 50A-50B. ELISA assay of phage antibodies using plates
coated with turkey egg lysozyme. Two clones B1 and A4 are shown
derived by mutagenesis and selection from pAbD1.3 (example 45).
Concentration (x axis) refers to the concentration of phage for
each sample relative to the concentration in culture supernatant.
B1 has raised binding to turkey egg lysogyme compared to D1.3. A4
has reduced binding to hen egg lysogyme compared to D1.3.
[0239] FIG. 51. ELISA of phage antibodies binding to HEL and TEL.
Clone 1 is fdCAT2scFvD1.3. Clones 2 to 10 were obtained from the
library (example 46) after selection. The background values as
defined by binding of these clones to BSA were subtracted.
[0240] FIG. 52. shows the DNA sequence of the light chains D1.3 M1F
and M21 derived by selection from a hierarchical library in example
46.
[0241] FIG. 53 shows a Fv lambda expression vector (example 48)
derived from pUC119. It contains the rearranged lambdal germ line
gene. The heavy and light chain cassettes each contain a ribosome
binding site upstream of the pel B leader (Restriction sites shown
as: H=Hind III; Sp=SphI; B=BamHI, E=EcoRI.
MATERIALS AND METHODS
[0242] The following procedures used by the present applicants are
described in Sambrook, J. et al., 1989 supra.: restriction
digestion, ligation, preparation of competent cells (Hanahan
method), transformation, analysis of restriction enzyme digestion
products on agarose gels, purification of DNA using
phenol/chloroform, 5'-end labelling of oligonucleotides, filter
screening of bacterial colonies, preparation of 2.times.TY medium
and plates, preparation of tetracycline stock solutions, PAGE of
proteins, preparation of phosphate buffered saline.
[0243] All enzymes were supplied by New England Biolabs (CP
Laboratories, PO Box 22, Bishop's Stortford, Herts., England) and
were used according to manufacturer's instructions unless otherwise
stated.
[0244] The vector fd-tet (Zacher, A. N. et al., 1980, supra) was
obtained from the American Type Culture Collection (ATCC No. 37000)
and transformed into competent TG1 cells (genotype: K12.delta.
(lac-pro), sup E, thi, hsdD5/F traD36, pro A+B+, Lac 1.sup.q, lac
.delta.M15).
[0245] Viral particles were prepared by growing TG1 cells
containing the desired construct in 10 to 100 mls 2.times.TY medium
with 15 .mu.g/ml tetracycline for 16-24 hours. The culture
supernatant was collected by centrifugation for 10 mins at 10,000
rpm in an 8.times.50 ml rotor, Sorval RC-5B centrifuge. Phage
particles were precipitated by adding 1/5th volume 20% polyethylene
glycol (PEG)/2.5M NaC1 and leaving at 4.degree. C. for 1 hour.
These were spun for 15 minutes as described above and the pellets
resuspended in 10 mM Tris/HCl pH 8, 1 mM EDTA to 1/100th of the
original volume. Residual bacteria and undissolved material were
removed by spinning for 2 minutes in a microcentrifuge. Single
stranded DNA for mutagenesis or sequencing was prepared from
concentrated phage according to Sambrook, J., et al., 1989,
supra.
INDEX OF EXAMPLES
Example 1
Design of Insertion Point Linkers and Construction of Vectors
[0246] This example covers the construction of two derivatives of
the phage vector fd-tet: a) fdTPs/Bs for the insertion of VH coding
sequences; and b) fdTPs/Xh for the insertion of scFv coding
sequences. The derivative vectors have a new BstEII site for
insertion of sequences.
Example 2
Insertion of Immunoglobulin Fv Domain into Phage
[0247] This example covers the insertion of scFv coding sequences
derived from an anti-lysozyme antibody D1.3 into fdTPs/Xh to give
the construct fdTscFvD1.3.
Example 3
Insertion of Immunoglobulin VH Domain into Phage
[0248] This example covers the insertion of VH coding sequences
derived from an anti-lysozyme antibody D1.3 into fdTPs/Bs to give
the construct fdTVHD1.3.
Example 4
Analysis of Binding Specificity of Phage Antibodies
[0249] This example investigates the binding specificities of the
constructs fdTscFvD1.3 and fdTVHD1.3.
Example 5
Construction of fdCAT2
[0250] This example covers the construction of the derivative
fdCAT2 of the phage vector fdTPs/Xh. The derivative has restriction
sites for enzymes that cut DNA infrequently.
Example 6
Specific Binding of Phage Antibody (pAb) to Antigen
[0251] This example shows the binding of pAb fdTscFvD1.3 to
lysozyme by ELISA.
Example 7
Expression of FabD1.3
[0252] This example concerns the display of an antibody Fab
fragment at the phage surface. The VH-CH1 chain is expressed by
fdCAT2. The VL-CL chain is expressed by pUC19 in a bacterial host
cell also infected with fdCAT2.
Example 8
Isolation of Specific, Desired Phage from a Mixture of Vector
Phage
[0253] This example shows how a phage (e.g. fdTscFvD1.3) displaying
a binding molecule can be isolated from vector phage by affinity
techniques.
Example 9
Construction of pAb Expressing Anti-Hapten Activity
[0254] This example concerns the insertion of scFv coding sequences
derived from the anti-oxazolone antibody NQ11 into fdTPs/Xh to
generate the construct pAbNQ11. The example shows the binding of
pAbNQ11 to oxazalone by ELISA.
Example 10
Enrichment of pAbD1.3 from Mixtures of Other pAbs by Affinity
Purification
[0255] This example shows how a phage (e.g., pAbD1.3) displaying
one sort of binding molecule can be isolated from phage (e.g.
pAbNQ11) displaying another sort of binding molecule by affinity
techniques.
Example 11
Insertion of a Gene Encoding an Enzyme (Alkaline Phosphate) into
fdCAT2
[0256] This example concerns the invention of coding sequences for
an enzyme into the vector fdCAT2 to give the phage enzyme,
fdphoAla116.
Example 12
Measuring Enzyme Activity Phage--Enzyme
[0257] This example shows the functionality of an enzyme (alkaline
phosphatase) when displayed at the phage surface (fdphoAla166).
Example 13
Insertion of Binding Molecules into Alternative Sites in the
Phage
[0258] This example covers the insertion of scfv coding sequences
derived from a) the anti-lysozyme antibody D1.3; and b) the
anti-oxazalone antibody NQ11 into a BamHI site of fdTPs/Xh to give
the constructs fdTBam1 having an NQ11 insert.
Example 14
PCR Assembly of Mouse VH and VLK Repertoires for Phage Display
[0259] This example concerns a system for the display on phage of
all VH and VLK repertoires encoded by a mouse. The system involves
the following steps. 1) Preparation of RNA from spleen. 2)
Preparation of cDNA from the RNA 3) Use of primers specific for
antibody sequences to PCR amplify all VH and VLK cDNA coding
sequences 4) Use of PCR to create a linker molecule from linking
pairs of VH and VLK sequences 5) Use of PCR to assemble continuous
DNA molecules each comprising a VH sequence, a linker and a VLK
sequence. The specific VH/VLK combination is randomly derived 6)
Use of PCR to introduce restriction sites.
Example 15
Insertion of the Extracellular Domain of a Human Receptor for
Platelet Derived Growth Factor (PDGF) Isoform BB into fdCAT2
[0260] This example concerns the insertion of coding sequences for
the extracellular domain of the human receptor for PDGF into the
vector fdCAT2 to give the construct fdhPDGFBR.
Example 16
Binding of .sup.125I-PDGF-BB to the Extracellular Domain of the
Human Receptor for PDGF Isoform BB Displayed on the Surface of fd
Phage. Measured Using an Immunoprecipitation Assay
[0261] This example shows that the human receptor PDGF Isoform BB
is displayed on the surface of the phage in a form which has the
ability to bind its ligand.
Example 17
Construction of Phagemid Containing Gene III Fused with the Coding
Sequence for a Binding Molecule
[0262] This example concerns the construction of two phagemids
based on pUC119 which separately contain gene III from fdCAT2 and
the gene III scFv fusion fdCAT2seFvDI.3 to generate pCAT2 and pCAT3
scFvDI.3 respectively.
Example 18
Rescue of Anti-Lysozyme Antibody Specificity from pCAT3scFvD1.3 by
M13KO7
[0263] This example describes the rescue of the coding sequence for
the gene IIIscFv fusion from pCAT3scFvD1.3 by M13MO7 helper phage
growth, phage were shown to be displaying scFv anti-lypozyme
activity by ELISA.
Example 19
Transformation Efficiency of PCAT-3 and pCAT-3 scFvD1.3
Phagemids
[0264] This example compared the efficiency of the phagemids
pVC119, pCAT-3 and pCAT3scFvD1.3 and the phage fdCAT2 to transform
E. coli.
Example 20 PCR Assembly of a Single Chain Fv Library from an
Immunised Mouse
[0265] This example concerns a system for the display on phage of
scFv (comprising VH and VL) from an immunised mouse using the basic
technique outlined in example 14 (cDNA preparation and PCR assembly
of the mouse VH and VLK repertoires) and ligating the PCR assembled
sequences into fdCAT2 to create a phage library of 10.sup.5 clones.
Testing of 500 clones showed that none showed specificity against
phox.
Example 21
Selection of Antibodies Specific for 2-phenyl-5-oxazolone from a
Repertoire from an Immunised Mouse
[0266] This example shows that phage grown from the library
established in example 20 can be subjected to affinity selection
using phOX to select those phage displaying scFv with the desired
specificity.
Example 22
Generation of Further Antibody Specificities by the Assembly of
Hierarchial Libraries
[0267] This example concerns the construction of hierarchial
libraries in which a given VH sequence is combined with the
complete VLK repertoire and a given VLK sequence is combined with
the complete VH repertoire and selection from these libraries of
novel VH and VL pairings.
Example 23
Selection of Antibodies Displayed on Bacteriophage with Different
Affinities for 2-phenyl-5-oxazolone Using Affinity
Chromatography
[0268] This example concerns the separation by affinity techniques
of phages displaying scFv fragments with differing binding
affinities for a given antigen.
Example 24
Construction of Phagemid pHEN1 for the Expression of Antibody
Fragments Expressed on the Surface of Bacteriophage Following
Superinfection
[0269] This example concerns the construction of the phagemid pHEN1
derived from pUC119. pHEN1 has the features shown in FIG. 26.
Example 25
Display of Single Chain Fv and Fab Fragments Derived from the
Anti-Oxazolone Antibody NQ 10.12.5 on Bacteriophage fd Using pHEN1
and fdCAT2
[0270] This example describes the display of scFv and Fab fragment
with a specificity against phOx on the surface of a bacteriophage.
For display of scFv the phagemid pHEN1 comprises the sequences
encoding scFv (VH and VL) for rescue by either the phages VSM13 or
fdCAT2. For display of Fab the phage fdCAT2 comprises the sequence
for either the H or L chain as a fusion with g3p and the phagemid
pHEN1 comprises the sequence for the appropriate H or L chain
partner.
Example 26
Rescue of Phagemid Encoding a Gene III Protein Fusion with Antibody
Heavy or Light Chains by Phage Encoding the Complementary Antibody
Displayed on Phage and the Use of this Technique to Make Dual
Combinatorial Libraries
[0271] This example covers the use of phage antibodies encoding the
antibody heavy or light chain to rescue a phagemid encoding a gene
3 protein fusion with the complementary chain and the assay of Fab
fragments displayed on phage in ELISA. The use of this technique in
the preparation of a dual combinatorial library is discussed.
Example 27
Induction of Soluble scFv and Fab Fragments Using Phagemid
pHEN1
[0272] This example covers the generation of soluble scFv and Fab
fragments from gene III fusions with sequences encoding these
fragments by expression of clones in pHEN1 in an E. coli strain
which does not suppress amber mutations.
Example 28
Increased Sensitivity in ELISA of Lysozyme Using fdTscFvD1.3 as
Primary Antibody Compared to Soluble scFvD1.3
[0273] This example covers the use of fdTscFvD1.3 in ELISA showing
that lower amounts of lysozyme can be detected with phage antibody
fdTscFvD1.3 than with soluble scFvD1.3.
Example 29
Direct Rescue and Expression of Mouse Monoclonal Antibodies as
Single Chain Fv Fragments on the Surface of Bacteriophage fd
[0274] This example covers the display on phage as functional scFv
fragments of two clones directly derived from cells expressing
monoclonal antibodies directed against oestriol.
[0275] Both clones were established to be functional using
ELISA.
Example 30
Kinetic Properties of Alkaline Phosphatase Displayed on the Surface
of Bacteriophage fd
[0276] This example concerns the demonstration that the kinetic
properties of an enzyme, alkaline phosphatase, displayed on phage
are qualitatively similar to those of the same enzyme when in
solution.
Example 31
Demonstration Using Ultrafiltration that Cloned Alkaline
Phosphatase Behaves as Part of the Virus Particle
[0277] This example concerns the construction of the phage enzyme
fdphoArg166 and the demonstration that both the fusion protein made
and the catalytic activity observed derive from the phage
particle.
Example 32
Affinity Chromatography of Phage Alkaline Phosphatase
[0278] This example concerns the binding of alkaline phosphatase
displayed on phage to an arsenate-Sepharose affinity column and
specific elution of these phage using the reaction product,
phosphate.
Example 33
PCR Assembly of DNA Encoding the Fab Fragment of an Antibody
Directed Against Oxazolone
[0279] This example covers the construction of a DNA insert
encoding a Fab fragment by separate amplification of heavy and
light chain DNA sequences followed by assembly. The construct was
then inserted into the phage vector fdCAT2 and the phagemid vector
pHEN1 and the Fab fragment displayed on the surface was shown to be
functional.
Example 34
Construction of a Gene III Deficient Helper Phage
[0280] This example describes the construction of a helper phage
derived from M13KO7 by deleting sequences in gene III. Rescue of
pCAT3-scFvD1.3 is described. The scFvD1.3 is expressed at a high
level as a fusion using the deletion phage, equivalent to
expression using fdCAT2-scFvD1.3.
Example 35
Selection of Bacteriophage Expressing scFv Fragments Directed
Against Lysozyme from Mixtures According to Affinity Using a
Panning Procedure
[0281] This example concerns the selection of bacteriophage
according to the affinity of the scFv fragment directed against
lysozyme which is expressed on their surface. The phage of
different affinities were bound to Petri dishes coated with
lysozyme and, following washing, bound phage eluted using
triethylamine. Conditions were found where substantial enrichment
could be obtained for a phage with a 5-fold higher affinity than
the phage with which it was mixed.
Example 36
Expression of Catalytically Active Staphylococcal Nuclease on the
Surface of Bacteriophage fd
[0282] This example concerns the construction of a phage enzyme
which expresses Staphylococcal nuclease and the demonstration that
the phage enzyme retains nuclease activity.
Example 37
Display of the Two Aminoterminal Domains of Human CD4 on the
Surface of fd Phage
[0283] This example covers the cloning of genes for domains of CD4,
a cell surface receptor and member of the immunoglobulin
superfamily, into bacteriophage fd. The receptor is shown to be
functional on the surface of phage by binding to the HIV protein
gp120.
Example 38
Generation and Selection of Mutants of an
Anti-4-hydroxy-3-nitrophenylacetic Acid (NP) Antibody Expressed on
Phage Using Mutator Strains
[0284] This example covers the introduction of mutations into a
gene for an antibody cloned in phage by growth of the phage in
strains which randomly mutate DNA due to defects in DNA
replication. Several mutations are introduced into phage which can
then be selected from parent phage.
Example 39
Expression of a Fv Fragment on the Surface of Bacteriophage by
Non-Covalent Association of VH and VL Domains
[0285] This example shows that functional Fv fragments can be
expressed on the surface of bacteriophage by non-covalent
association of VH and VL domains. The VH domain is expressed as a
gene III fusion and the VL domain as a soluble polypeptide.
Sequences allowing expression of these domains from the
anti-lysozyme antibody D1.3 in this form were introduced into phage
and the resulting displayed Fv fragment shown to be functional by
ELISA.
Example 40
A PCR Based Technique for One Step Cloning of Human V-Genes as Fab
Constructs
[0286] This example gives methods for the assembly of Fab fragments
from genes for antibodies. Examples are given for genes for
antibodies directed against Rhesus-D in a human hybridoma and a
polyclonal lymphoblastic cell line.
Example 41
Selection of Phage Displaying a Human Fab Fragment Directed Against
the Rhesus-D Antigen by Binding to Cells Displaying the Rhesus D
Antigen on their Surface
[0287] This example concerns the construction of, and display of
phage antibodies from, a phagemid encoding a human Fab fragment
directed against the Rhesus D antigen. Phage displaying this
antigen were then affinity selected from a background of phage
displaying scFvD1.3 anti-lysozyme on the basis of binding to
Rhesus-D positive red blood cells.
Example 42
A PCR Based Technique for One Step Cloning of Human scFv
Constructs
[0288] This example describes the generation of libraries of scFv
fragments derived from an unimmunized human. Examples are given of
the preparation for phage display of libraries in phagemids of scFv
fragments derived from IgG and IgM sequences.
Example 43
Isolation of Binding Activities from a Library of scFvs from an
Unimmunized Human
[0289] This example describes the isolation, from the library of
scFv fragments derived from IgM genes of an unimmunized human, of
clones for phage antibodies directed against BSA, lysozyme and
oxazolone. Selection was by panning or affinity chromatography and
analysis of binding specificity by ELISA. Sequencing of the clones
showed them to be of human origin.
Example 44
Rescue of Human IgM Library Using Helper Phage Lacking Gene 3
(g3)
[0290] This example covers the isolation, from the library of scFv
fragments of unimmunized human IgM genes, of clones of phage
antibodies of clones for phage antibodies specific for
thyroglobulin and oxazolone. In this example rescue was with
M13K07gIII No3 (NCTC12478), a helper phage defective in gene III.
Fewer rounds of selection appeared necessary for a phagemid library
rescued with this phage compared to one rescued with M13K07.
Example 45
Alteration of Fine Specificity of scFvD1.3 Displayed on Phage by
Mutagenesis and Selection on Immobilized Turkey Lysozyme
[0291] This example covers the in vitro mutagenesis of pCATscFvD1.3
by replacement, with random amino acids, of residues known to be of
importance in the preferential recognition of hen egg lysozyme over
turkey egg lysozyme by scFvD1.3. Following selection for phage
antibodies recognising turkey egg lysozyme by affinity
chromatography, clones were analysed for specificity by ELISA. Two
groups of clones were found with more equal recognition of hen and
turkey lysozymes, one with increased ELISA signal with the turkey
enzyme and one with reduced signal for the hen enzyme.
Example 46
Modification of the Specificity of an Antibody by Replacement of
the VLK Domain by a VLK Library Derived from an Unimmunised
Mouse
[0292] This example shows that replacement of the VL domain of
scFvD1.3 specific for hen eggwhite lysozyme (HEL) with a library of
VL domains allows selection of scFv fragments which bind also to
turkey eggwhite lysozyme (TEL). The scFv fragments were displayed
on phage and selection by panning on tubes coated with TEL.
Analysis by ELISA showed clones with enhanced binding to TEL
compared to HEL. Those with highest binding to TEL were
sequenced.
Example 47
Selection of a Phage Antibody Specificity by Binding to an Antigen
Attached to Magnetic Beads. Use of a Cleavable Reagent to Allow
Elution of Bound Phage Under Mild Conditions
[0293] This example covers the use of a cleavable bond in the
affinity selection method to allow release of bound phage under
mild conditions. pAbNQ11 was enriched approximately 600 fold from a
mixture with pAbD1.3 by selection using biotinylated Ox-BSA bound
to magnetic beads. The cleavage of a bond between BSA and the
biotin allows elution of the phage.
Example 48
Use of Cell Selection to Provide an Enriched Pool of Antigen
Specific Antibody Genes, Application to Reducing the Complexity of
Repertoires of Antibody Fragments Displayed on the Surface of
Bacteriophage
[0294] This example covers the use of cell selection to produce an
enriched pool of genes encoding antibodies directed against
4-hydroxy-3-nitrophenylacetic acid and describes how this technique
could be used to reduce the complexity of antibody repertoires
displayed on the surface of bacteriophage.
Example 1
Design of Insertion Point Linkers and Construction of Vectors
[0295] The vector fd-tet has two BstEII restriction sites flanking
the tetracycline resistance gene (FIG. 3). Since the strategy for
inserting the VH fragments was to ligate them into a newly inserted
BstEII site within gene III, it was advantageous to delete the
original BstEII sites from fd-tet. This was achieved by digesting
fd-tet with the restriction enzyme BstEII, filling-in the 5'
overhangs and re-ligating to generate the vector fdT.delta.Bst.
Digestion of fd-tet with BstEII (0.5 units/.mu.l) was carried out
in 1.times.KGB buffer (100 mM potassium glutamate, 23 mM
Tris-acetate (pH 7.5), 10 mM magnesium acetate, 50 .mu.g/ml bovine
serum albumin, 0.5 mM dithiothreitol (Sambrook, J., et al., 1989,
supra.) with DNA at a concentration of 25 ng/.mu.l. The 5' overhang
was filled in, using 2.times.KGB buffer, 250 .mu.M each dNTP's
(Pharmacia Ltd., Pharmacia House, Midsummer Boulevard, Milton
Keynes, Bucks., UK.) and Klenow Fragment (Amersham International,
Lincoln Place, Green End, Aylesbury, Bucks., UK) at 0.04
units/.mu.l. After incubating for 1 hour at room temperature, DNA
was extracted with phenol/chloroform and precipitated with
ethanol.
[0296] Ligations were carried out at a DNA concentration of 50
ng/.mu.l). Ligations were transformed into competent TG1 cells and
plated onto TY plates supplemented with 15 .mu.g/ml tetracycline.
This selects for vectors where the gene for tetracycline resistance
protein has reinserted into the vector during the ligation step.
Colonies were picked into 25 mls of 2.times.TY medium supplemented
with 15 .mu.g/ml tetracycline and grown overnight at 37.degree.
C.
[0297] Double stranded DNA was purified form the resulting clones
using the gene-clean II kit (Bio101 Inc., PO Box 2284, La Jolla,
Calif., 92038-2284, USA) and according to the small scale rapid
plasmid DNA isolation procedure described therein. The orientation
of 5 of the resulting clones was checked using the restriction
enzyme ClaI. A clone was chosen which gave the same pattern of
restriction by ClaI as fd-tet, but which had no BstE II sites.
[0298] In vitro mutagenesis of fdT.delta.Bst was used to generate
vectors having appropriate restriction sites that facilitate
cloning of antibody fragments downstream of the gene III signal
peptide and in frame with the gene III coding sequence. The
oligonucleotide directed mutagenesis system version 2 (Amersham
International) was used with oligo 1 (FIG. 4a) to create fdTPs/Bs
(to facilitate cloning of VH fragments). The sequence offdTPs/Bs
(FIG. 4a) was confirmed using the SEQUENASE version 2.0 kit (USB
Corp., PO Box 22400, Cleveland, Ohio, 44122, USA.) with oligo 3
(FIG. 4) as a primer.
[0299] A second vector fdTPs/Xh (to facilitate cloning of single
chain Fv fragments) was generated by mutagenising fdTPs/Bs with
oligo 2 according to the method of Venkitaraman, A. R., Nucl. Acid
Res. 17, p 3314. The sequence of fdTPs/Xh (FIG. 4) was confirmed
using the sequenase version 2.0 kit (USB Corp.) with oligo 3 as a
primer.
[0300] Clearly, alternative constructions will be apparent to those
skilled in the art. For example, M13 and/or its host bacteria could
be modified such that its gene III could be disrupted without the
onset of excessive cell death; the modified fd gene III, or other
modified protein, could be incorporated into a plasmid containing a
single stranded phage replication origin, such as pUC119,
superinfection with modified phage such as KO7 would then result in
the encapsulation of the phage antibody genome in a coat partially
derived from the helper phage and partly from the phage antibody
gene III construct.
[0301] The detailed construction of a vector such as fdTPs/Bs is
only one way of achieving the end of a phage antibody. For example,
techniques such as sticky feet cloning/mutagenesis (Clackson, T.
and Winter, G. 1989 Nucl. Acids. Res., 17, p 10163-10170) could be
used to avoid use of restriction enzyme digests and/or ligation
steps.
Example 2
Insertion of Immunoglobulin Fv Domain into Phage
[0302] The plasmid scFv D1.3 myc (gift from g. Winter and A.
Griffiths) contains VH and VL sequences from the antibody D1.3
fused via a peptide linker sequence to form a single chain Fv
version of antibody D1.3. The sequence of the scFv and surrounding
sequences in scFvD1.3 myc is shown in FIG. 5.
[0303] The D1.3 antibody is directed against hen egg lysozyme
(Harper, M. et al., 1987, Molec. Immunol. 24, 97-108) and the scFv
form expressed in E. coli has the same specificity (A. Griffiths
and G. Winter personal Communication).
[0304] Digestion of scFv D1.3 myc with Pstl and Xhol (these
restriction sites are shown on FIG. 5), excises a fragment of 693
bp which encodes the bulk of the scFv. Ligation of this fragment
into fdTPs/Xh cleaved with Pst1 and Xhol gave rise to the construct
fdTscFvD1.3 encoding the gene III signal peptide and first amino
acid fused to the complete D1.3 scFv, followed by the mature gene
III protein from amino acid 2.
[0305] The vector fdTPs/Xh was prepared for ligation by digesting
with the Pst1 and Xhol for 2 hours followed by digestion with calf
intestinal alkaline phosphatase (Boehringer Mannheim UK Ltd., Bell
Lane, Lewes, East Sussex, BN7 1LG) at one unit/ul for 30 minutes at
37.degree. C. Fresh calf intestinal alkaline phosphatase was added
to a final total concentration of 2 units/ul and incubated for a
further 30 minutes at 37.degree. C. The reaction was extracted
three times with phenol/chloroform, precipitated with ethanol and
dissolved in water. The insert from scFvD1.3 myc was excised with
the appropriate restriction enzymes (PstI and XhoI) extracted twice
with phenol/chloroform, precipitated with ethanol and dissolved in
water. Ligations were carried out as described in example 1, except
both vector and insert samples were at a final concentration of 5
ng/ul each. The formation of the correct construct was confirmed by
sequencing as described in example 1.
[0306] To demonstrate that proteins of the expected size were
produced, virions were concentrated by PEG precipitation as
described above. The samples were prepared for electrophoresis as
described in Sambrook J. et al 1989 supra. The equivalent of 2 mls
of supernatant was loaded onto an 18% SDS polyacrylamide gel. After
electrophoresis, the gel was soaked in gel running buffer (50 mM
tris, 380 mM Glycine, 0.1% SDS) with 20% methanol for 15 minutes.
Transfer to nitrocellulose filter was executed in fresh
1.times.running buffer/20% methanol using TE70 Semi Phor a semi-dry
blotting apparatus (Hoeffer, 654 Minnesota Street, Box 77387, San
Francisco, Calif. 94107, USA).
[0307] After transfer, the filter was blocked by incubation for 1
hour in a 2% solution of milk powder (Marvel) in phosphate buffered
saline (PBS). Detection of scFv and VH protein sequences in the
phage antibody fusion proteins was effected by soaking the filter
for 1 hour with a 1/1000 dilution (in 2% milk powder) of a rabbit
polyclonal antiserum raised against affinity purified, bacterially
expressed scFv fragment (gift from G. Winter). After washing with
PBS (3.times.5 minute washes), bound primary antibody was detected
using an anti-rabbit antibody conjugated to horseradish peroxidase
(sigma, Fancy Road, Poole, Dorset, BH17 7NH, UK.) for 1 hour. The
filter was washed in PBS/0.1% triton X-100 and developed with 0.5
mg/ml 3,3'-diaminobenzidine tetrahydrochloride (DAB), 0.02% cobalt
chloride, 0.03% hydrogen peroxide in PBS.
[0308] The results showed that with clones fdTVHD1.3 (from example
3 incorporating sequences coding for VH) and fdTscFvD1.3
(incorporating sequences coding for scFv) a protein of between
69,000 and 92,500 daltons is detected by the anti-Fv serum. This is
the expected size for the fusion proteins constructed. This product
is not observed in supernatants derived from fd-tet, fdT.delta.Bst
or fdTPs/Xh.
Example 3
Insertion of Immunoglobulin VH Domain into Phage Antibody
[0309] The VH fragment from D1.3 was generated from the plasmid
pSW1-VHD1.3-TAG1 (Ward, E. S. et al., 1989 supra.).
[0310] Digestion of this plasmid with Pst1 and BstEII generates the
fragment shown between positions 113 and 432 in FIG. 5. Cloning of
this fragment into the Pst1 and BstEII sites of fdTPs/Bs gave rise
to the construct fdTVHD1.3 which encodes a fusion protein with a
complete VH domain inserted between the first and third amino acids
of the mature gene III protein (amino acid two has been
deleted).
[0311] The methods used were exactly as in example 2 except that
the vector used was fdTPs/Bs digested with Pst1 and BstEII.
Example 4
Analysis of Binding Specificity of Phage Antibodies
[0312] The binding of the various phage antibodies to the specific
antigen, lysozyme, was analysed using ELISA techniques. Phage
antibodies (e.g. fdTVHD1.3 and fdTsc/FvD1.3) were grown in E. coli
and Phage antibody particles were precipitated with PEG as
described in the materials and methods. Bound phage antibody
particles were detected using polyclonal sheep serum raised against
the closely related phage M13.
[0313] ELISA plates were prepared by coating 96 well plates (Falcon
Microtest III flexible plate. Falcon: Becton Dickinson Labware,
1950 Williams Drive, Oxnard, Calif., 93030, USA.) with 200 ul of a
solution of lysozyme (1 mg/ml unless otherwise stated) in 50 mm
NaHCO3 for 16-24 hours. Before use, this solution was removed, the
plate rinsed several times in PBS and incubated with 200 ul of 2%
milk powder/PBS for 1 hour. After rinsing several times with PBS,
100 ul of the test samples were added and incubated for 1 hour.
Plates were washed (3 rinses in 0.05% Tween 20/PBS followed by 3
rinses in PBS alone). Bound phage antibodies were detected by
adding 200 ul/well of a 1/1000 dilution of sheep anti-M13
polyclonal antiserum (gift from G. Winter, although an equivalent
antibody can be readily made by one skilled in the art using
standard methodologies) in 2% milk powder/PBS and incubating for 1
hour. After washing as above, plates were incubated with
biotinylated anti-sheep antibody (Amersham International) for 30
minutes. Plates were washed as above, and incubated with
streptavidin-horseradish peroxidase complex (Amersham
International). After a final wash as above, 0.5 mg/ml ABTS
substrate in citrate buffer was added (ABTS=2'2'-azinobis
(3-ethylbenzthiazoline sulphonic acid); citrate buffer=50 mM citric
acid, 50 mM tri-sodium citrate at a ratio of 54:46. Hydrogen
peroxide was added to a final concentration of 0.003% and the
plates incubated for 1 hour. The optical density at 405 nm was read
in a Titertek multiskan plate reader.
[0314] FIG. 6 shows the effect of varying the amount of phage
antibody. 100 ul of various dilutions of PEG precipitated phage
were applied and the amount expressed in terms of the original
culture volume from which it was derived. Signals derived from both
the scFv containing phage antibody (fdTscFvD1.3) and the VH
containing phage antibody (fdTVHD1.3) and the VH containing phage
antibody were higher than that derived from the phage antibody
vector (fdTPs/Xh). The highest signal to noise ratio occurs using
the equivalent of 1.3 mls of culture.
[0315] FIG. 7 shows the results of coating the plates with varying
concentrations of lysozyme or bovine serum albumin (BSA). The
equivalent of 1 ml of the original phage antibody culture
supernatant was used. The signals from supernatants derived from
fdTscFvD1.3 were again higher than those derived from fdTPs/Xh when
lysozyme coated wells were used. There was no significant
difference between these two types of supernatant when the plates
were coated with BSA. Broadly speaking the level of signal on the
plates is proportional to the amount of lysozyme coated. These
results demonstrate that the binding detected is specific for
lysozyme as the antigen.
Example 5
Construction of fd CAT 2
[0316] It would be useful to design vectors that enable the use of
restriction enzymes that cut DNA infrequently, thus avoiding
unwanted digestion of the antibody gene inserts within their coding
sequence. Enzymes with an eight base recognition sequence are
particularly useful in this respect, for example Not1 and Sfil.
Chaudhary et al (PNAS 87 p 1066-1070, 1990) have identified a
number of restriction sites which occur rarely in antibody variable
genes. The applicant has designed and constructed a vector that
utilises two of these sites, as an example of how this type of
enzyme can be used. Essentially sites for the enzymes ApaL1 and
Not1 were engineered into fdTPs/Xh to create fdCAT2.
[0317] The oligonucleotide: 5'ACT TTC AAC AGT TTC TGC GGC CGC CCG
TTT GAT CTC GAG CTC CTG CAG TTG GAC CTG TGC ACT GTG AGA ATA GAA 3'
(SEQ ID NO:4) was synthesised (supra FIG. 4 legend) and used to
mutagenise fdTPs/Xh using an in vitro mutagenesis kit from Amersham
International as described in example 1, to create fd-CAT2. The
sequence of fd-CAT2 was checked around the site of manipulation by
DNA sequencing. The final sequence around the insertion point
within gene III is shown in FIG. 8. N.B. fdCAT2 is also referred to
herein by the alternative terminologies fd-tet-DOG1 and fdDOG1.
Example 6
Specific Binding of Phage-Antibody (pAb) to Antigen
[0318] The binding of pAb D1.3 (fdTscFvD1.3 of example 2) to
lysozyme was further analysed by ELISA.
Methods.
1. Phage Growth.
[0319] Cultures of phage transduced bacteria were prepared in
[0320] 10-100 mls 2.times.TY medium with 15 .mu.g/ml tetracycline
and grown with shaking at 37.degree. C. for 16-24 hrs. Phage
supernatant was prepared by centrifugation of the culture (10 min
at 10,000 rpm, 8.times.50 ml rotor, Sorval RC-5B centrifuge). At
this stage, the phage titre was 1-5.times.10.sup.10/ml transducing
units. The phage were precipitated by adding 1/5 volume 20% PEG 2.5
M NaCl, leaving for 1 hr at 4.degree. C., and centrifuging (supra).
The phage pellets were resuspended in 10 mM Tris-HC1, 1 mM EDTA pH
8.0 to 1/100th of the original volume, and residual bacteria and
aggregated phage removed by centrifugation for 2 min in a bench
microcentrifuge.
ELISA
[0321] Plates were coated with antigen (1 mg/ml antigen) and
blocked as described in example 4. 2.times.10.sup.10 phage
transducing units were added to the antigen coated plates in
phosphate buffered saline (PBS) containing 2% skimmed milk powder
(MPBS). Plates were washed between each step with three rinses of
0.5% Tween-20 in PBS followed by three rinses of PBS. Bound phage
was developed by incubating with sheep anti-M13 antisera and
detected with horseradish peroxidase (HRP) conjugated anti-goat
serum (Sigma, Poole, Dorset, UK) which also detects sheep
immunoglobulins and ABTS (212'-azinobis (3-ethylbenzthiazoline
sulphonic acid).
[0322] Readings were taken at 405 nm after a suitable period. The
results (FIG. 9) show that the antibody bearing-phage had the same
pattern of reactivity as the original D1.3 antibody (Harper, M.,
Lema, F., Boulot, C., and Poljak, F. J. (1987) Molec. Immunol. 24,
97-108), and bound to hen egg-white lysozyme, but not to turkey
egg-white lysozyme, human lysozyme or bovine serum albumin. The
specificity of the phage is particularly illustrated by the lack of
binding to the turkey egg-white lysozyme that differs from hen
egg-white lysozyme by only 7 amino acids.
Example 7
Expression of Fab D1.3
[0323] The aim of this example was to demonstrate that the scFv
format used in example 2 was only one way of displaying antibody
fragments in the pAb system. A more commonly used antibody fragment
is the Fab fragment (FIG. 1) and this example describes the
construction of a pAb that expresses a Fab-like fragment on its
surface and shows that it binds specifically to its antigen. The
applicant chose to express the heavy chain of the antibody fragment
consisting of the VH and CH1 domains from coding sequences within
the pAb itself and to co-express the light chain in the bacterial
host cell infected with the pAb. The VH and CH1 regions of
anti-lysozyme antibody D1.3 were cloned in fd CAT2, and the
corresponding light chain cloned in plasmid pUC19. The work of
Skerra and Pluckthun (Science 240, p 1038-1040 (1988) and Better et
al 1988 supra; demonstrated that multimeric antigen binding
fragments of the antibody molecule could be secreted into the
periplasm of the bacterial cell in a functional form using suitable
signal sequences. However, in these publications, special measures
were described as being needed to recover the binding protein from
the cell, for example Skerra and Pluckham needed to recover the Fv
fragment from the periplasm by affinity chromatography. The present
applicants have shown that it is possible to direct the binding
molecule to the outside of the cell on a phage particle, a process
that requires several events to occur: correct secretion and
folding of the binding molecule; association of the chains of the
binding molecule; correct assembly of the phage particle; and
export of the intact phage particle from the cell.
[0324] Alternatively, it is possible however, to express the light
chain from within the pAb genome by, for example, cloning an
expression cassette into a suitable place in the phage genome. Such
a suitable place would be the intergenic region which houses the
multicloning sites engineered into derivative of the related phage
M13 (see, for example, Yanisch-Perron, C. et al., Gene 33, p
103-119, (1985)).
[0325] The starting point for this example was the clone Fab D1.3
in pUC19, a map of which is shown in FIG. 10. The regions
hybridising with the oligonucleotides KSJ6 and 7 below are shown
underlined in FIG. 10. The sequence encoding the VH-CH1 region
(defined at the 5' and 3' edges by the oligonucleotides KSJ6 and 7
below) was PCR amplified from Fab D1.3 in pUC19 using
oligonucleotides KSJ 6 and 7, which retain the Pst I site at the 5'
end and introduce a Xho I site at the 3' end, to facilitate cloning
into fd CAT2. The sequences for the oligonucleotides KSJ6 and 7 are
shown below. The underlined region of KSJ7 shows the portion
hybridising with the sequence for D1.3. KSJ6:5' AGG TGC AGC TGC AGG
AGT CAG G 3' (SEQ ID NO:5) KSJ7: 5' GGT GAC CTC GAG TGA AGA TTT GGG
CTC AAC TTT C 3' (SEQ ID NO:6)
[0326] PCR conditions were as described in example II, except that
thirty cycles of PCR amplification were performed with denaturation
at 92.degree. C. for 45 seconds, annealing at 55.degree. C. for 1
minute and extension at 72.degree. C. for 1 minute. The template
used was DNA from TG1 cells containing Fab D1.3 in pUC19
resuspended in water and boiled. The template DNA was prepared from
the colonies by picking some colony material into 100 .mu.l of
distilled H.sub.2O and boiling for 10 mins. 1 .mu.l of this mixture
was used in a 20 .mu.l PCR. This regime resulted in amplification
of the expected fragment of approximately 600 bp. This fragment was
cut with Pst I and Xho I, purified from an agarose gel and ligated
into Pst 1/Xho 1-cut fdCAT2. The PCR mixture was extracted with
phenol/chloroform and ethanol precipitated (Sambrook et al. supra.)
before digestion with Pst1 and Xho1 (New England Biolabs according
to manufacturers recommendations. The fragment was resolved on 1%
Tris-Acetate EDTA agarose gel (Sambrook et al. supra) and purified
using GENECLEAN (BIO 101, GENECLEAN, La Jolla, San Diego, Calif.,
USA) according to manufacturers recommendations.
[0327] fd-CAT2 vector DNA was digested with Pst 1 and Xho 1 (New
England BioLabs) according to manufacturers recommendations,
extracted with phenol/chloroform and ethanol precipitated (Sambrook
et al. supra.).
[0328] 75 ng of Pst 1/Xho 1-digested vector DNA was ligated to 40
ng of PCR-amplified Pst1 /Xho I-digested hEGF-R fragment in 12
.mu.l of ligation buffer (66 mM Tris HC1 (pH7.6), 5 mM MgCl.sub.2,
5 mM dithiothreitol, (100 .mu.g/ml bovine serum albumin, 0.5 mM
ATP, 0.5 mM Spermidine) and 400 units T4 DNA ligase (New England
BioLabs) for 16 hours at 16.degree. C.
[0329] Two .mu.l of the ligation mixture was transformed into 200
.mu.l of competent E. coli MC1061 cells, plated on 2TY agar
containing 15 .mu.g/ml tetracycline and incubated at 30.degree. C.
for 20 hours. A portion of the ligation reaction mixture was
transformed into E. coli MC1061 (Available from, for example
Clontech Laboratories Inc, Palo Alto, Calif.) and colonies
identified by hybridisation with the oligonucleotide D1.3CDR3A as
described in example 10. The presence of the VHCH1 gene fragment
was likewise confirmed by PCR, using oligonucleotides KSJ6 and 7. A
representative clone was called fd CAT2VHCH1 D1.3. The heavy chain
was deleted from Fab D1.3 in pUC19 by Sph I cleavage of Fab D1.3
plasmid DNA. The pUC 19 2.7 Kb fragment containing the light chain
gene was purified from a TAE agarose gel, and long of this DNA
self-ligated and transformed into competent E. coli TG1. Cells were
plated on 2TY agar containing ampicillin (100 .mu.g/ml) and
incubated at 30.degree. C. overnight. The resulting colonies were
used to make miniprep DNA (Sambrook et al. supra), and the absence
of the heavy chain gene confirmed by digestion with Sph I and Hind
III. A representative clone was called LCD1.3 DHC.
[0330] An overnight culture of fd CAT2VHCH1 D1.3 cells was
microcentrifuged at 13,000.times.g for 10 minutes and 50 .mu.l of
the supernatant containing phage particles added to 50 .mu.l of an
overnight culture of LCD1.3 DHC cells. The cells were incubated at
37.degree. C. for 10 minutes and plated on 2TY agar containing
ampicillin (100 .mu.g/ml) and 15 .mu.g/ml tetracycline.
[0331] Phage were prepared from some of the resulting colonies and
assayed for their ability to bind lysozyme as described in example
6.
[0332] The results (FIG. 11) showed that when the heavy and light
chain Fab derivatives from the original antibody D1.3 were present,
the pAb bound to lysozyme. pAb expressing the fd VHCH1 fragment did
not bind to lysozyme unless grown in cells also expressing the
light chain. This shows that a functional Fab fragment was produced
by an association of the free light chain with VHCH1 fragment fused
to gene III and expressed on the surface of the pAb.
Example 8
Isolation of Specific, Desired Phage from a Mixture of Vector
Phage.
[0333] The applicant purified pAb (D1.3) (originally called
fdTscFvD1.3 in example 2) from mixtures using antigen affinity
columns. pAb (D1.3) was mixed with vector fd phage (see table 1)
and approximately 10.sup.12 phage passed over a column of
lysozyme-Sepharose (prepared from cyanogen bromide activated
sepharose 4B (Pharmacia, Milton Keynes, Bucks, UK.) according to
the manufacturers instructions. TG1 cells were infected with
appropriate dilutions of the elutes and the colonies derived, were
analysed by probing with an oligonucleotide that detects only the
pAb (D1.3) see Table 1 and FIGS. 12A and 12B. A thousand fold
enrichment of pAb(D1.3) was seen with a single column pass.
[0334] By growing the enriched phage and passing it down the column
again, enrichments of up to a million fold were seen.
[0335] Enrichment was also demonstrated using purely immunological
criteria. For example, 10.sup.12 phage (at a ratio of 1 pAb (D1.3)
to 4.times.10.sup.6 fdTPs/Bs) was subjected to two rounds of
affinity selection, and then 26 colonies picked and grown
overnight. The phage was then assayed for lysozyme binding by ELISA
(as example 6). Five colonies yielded phage with lysozyme binding
activities, see table 1, and these were shown to encode the scFv
(D1.3) by PCR screening (example 13, using 30 cycles of 1 minute at
92.degree. C., 1 minute at 60.degree. C., 1 minute at 72.degree. C.
using CDR3PCR1 and oligo 3 (FIG. 4A) as primers).
[0336] Thus very rare pAbs can be fished out of large populations,
by using antigen to select and then screen the phage.
[0337] In this example, affinity chromatography of pAbs and
oligonucleotide probing were carried out as described below.
[0338] Approximately 10.sup.12 phage particles in 1 ml MPBS were
loaded onto a 1 ml lysozyme-Sepharose affinity column which had
been prewashed in MPBS. The column was washed in turn with 10 ml
PBS; then 10 ml 50 mM Tris-HCl, 500 mM Nacl pH 7.5; then 10 ml 50
mM Tris-HCl 500 mM NaCl pH 8.5; then 5 mls 50 mM Tris-HCl, 500 mM
NaCl pH 9.5 (adjusted with triethylamine) and then eluted with 5 ml
100 mM triethylamine. The eluate was neutralised with 0.5 M sodium
phosphate buffer pH 6.8 and the phage plated for analysis. For a
second round of affinity chromatography, the first column eluate
was plated to about 30,000 colonies per petri dish. After overnight
growth, colonies were then scraped into 5 ml 2.times.TY medium, and
a 20 .mu.l aliquot diluted into 10 ml fresh medium and grown
overnight. The phage was PEG precipitated as described above,
resuspended in 1 ml MPBS and loaded onto the column, washed and
eluted as above.
[0339] Oligonucleotides Synthesised: TABLE-US-00002 CDR3PCR1 5' TGA
GGA C(A or T) C(A or (SEQ ID NO:7) T) GC CGT CTA CTA CTG TGC
3'.
[0340] 40 pmole of oligonucleotide VH1FOR (Ward, E. S., et al
(1989) Nature 341, 544-546), specific to pAb (D1.3) was
phosphorylated with 100 .mu.Ci .alpha.-32P ATP, hybridised (1
pmole/ml) to nitrocellulose filters at 67.degree. C. in 6.times.
saline sodium citrate (SSC) Sambrook et al., supra. buffer for 30
minutes and allowed to cool to room temperature for 30 mins, washed
3.times.1 min at 60.degree. C. in 0.1.times.SSC.
Example 9
Construction of pAb Expressing Anti-Hapten Activity
[0341] Oxazolone is a hapten that is commonly used for studying the
details of the immune response. The anti-oxazalone antibody, NQ11
has been described previously (E. Gherardi, R. Pannell, C.
Milstein, J. Immunol. Method 126 61-68). A plasmid containing the
VH and VL gene of NQ11 was converted to a scFv form by inserting
the BstEII/SacI fragment of scFvD1.3 myc (nucleotides 432-499 of
FIG. 5) between the VH and VL genes to generate pscFvNQ11, the
sequence of which is shown in FIG. 13. This scFv was cloned into
the Pst1/Xhol site of FdTPs/Xh (as described earlier) to generate
pAb NQ11 has an internal Pst1 site and so it was necessary to do a
complete digest of pscFvNQ11 with Xhol followed by a partial digest
with Pst1).
[0342] The specific binding of pAb NQ11 was confirmed using ELISA.
ELISA plates were coated at 37.degree. C. in 50 mM NaHCO3 at a
protein concentration of 200 .mu.g/ml. Plates were coated with
either hen egg lysozyme (HEL), bovine serum albumin (BSA), or BSA
conjugated to oxazolone (OX-BSA) (method of conjugation in Makela
O., Kartinen M., Pelkonen J. L. T., Karjalainen K. (1978) J. Exp.
Med. 148 1644). Preparation of phage, binding to ELISA plates,
washing and detection was as described in example 6. Samples were
assayed in duplicate and the average absorbance after 10 minutes
presented in FIG. 14. This result demonstrates that the pAb NQ11
binds the correct antigen. FIG. 14 also shows that pAb D1.3 and pAb
NQ11 bind only to the antigen against which the original antibodies
were raised.
Example 10
[0343] Enrichment of pAb D1.3 from Mixtures of Other pAb by
Affinity Purification 3.times.10.sup.10 phage in 10 mls of PBSM at
the ratios of pAb D1.3 to pAb NQ11 shown in table 2 were passed
over a 1 ml lysozyme Sepharose column. Washing, elution and other
methods were as described in example 8 unless otherwise stated.
Eluates from the columns were used to infect TG1 cells which were
then plated out. Colonies were probed with a probe which
distinguishes pAb D1.3 from pAb NQ11. The sequence of this
oligonucleotide (D1.3CDR3A) is:--5'GTA GTC AAG CCT ATA ATC TCT CTC
3' (SEQ ID NO:8). Table 2 presents the data from this experiment.
An enrichment of almost 1000 fold was achieved in one round and an
enrichment of over a million fold in two rounds of purification.
This parallels the result described in example 8.
Example 11
Insertion of a Gene Encoding an Enzyme (Alkaline Phosphatase) into
fd-CAT2
[0344] As an example of the expression of a functional enzyme on
the bacteriophage surface, the applicants have chosen bacterial
alkaline phosphatase, an enzyme that normally functions as a dimer
(McCracken, S. and Meighen, E., J. Biol. Chem. 255, p 2396-2404,
(1980)). The oligonucleotides were designed to generate a PCR
product with an Apa L1 site at the 5' end of phoA gene and a Not 1
site at its 3' end, thus facilitating cloning into fd-CAT 2 to
create a gene III fusion protein. The oligonucleotides synthesised
were: phoA1:5'TAT TCT CAC AGT GCA CAA ACT GTT GAA CGG ACA CCA GAA
ATG CCT GTT CTG 3' (SEQ ID NO:9) and, phoA2:5' ACA TGT ACA TGC GGC
CGC TTT CAG CCC CAG AGC GGC TTT C3' (SEQ ID NO:10). The sequence of
the phoA gene is presented in Chang C. N. et al., Gene 44, p
121-125 (1986). The plasmid amplified (pEK86) contains an alkaline
phosphate gene which differs from the sequence of Chang et al, by a
mutation which converts arginine to alamine at position 166.
[0345] The PCR reaction was carried out in 100 .mu.l of 10 mM
Tris/HC1 pH 8.3, containing 50 mM KC1, 5 mM dNTP 2.5 mM MgCl.sub.2,
0.01% gelatin, 0.25 units/.mu.l of Taq polymerase (Cetus/Perkin
Elmer) and 0.5 .mu.g/ml template. The template was the pEK86
plasmid (described by Chaidaroglou et al., Biochemistry 27 p
8338-8343, 1988). The PCR was carried out in a Techne (Techne,
Duxford, Cambridge, UK) PHC-2 dri-block using thirty cycles of 1
min at 92.degree. C., 2 min at 50.degree. C., 3 min at 72.degree.
C.
[0346] The resultant product was extracted with phenol:chloroform,
precipitated with ethanol, and the pellet dissolved in 35 .mu.l
water. Digestion with 0.3 units/.mu.l of Apa L1 was carried out in
150 .mu.l volume according to manufacturers instructions for two
hours at 37.degree. C. After heat inactivation of the enzyme at
65.degree. C., NaC1 was added to a final concentration of 150 mM
and 0.4 units/.mu.l Not1 enzyme added. After incubation for 2 hours
at 37.degree. C., the digest was extracted with phenol:chloroform
and precipitated as above, before being dissolved in 30 .mu.l of
water. The vector fd-CAT2 was sequentially digested with Apa L1 and
Not1 according to the manufacturers instructions and treated with
calf intestinal alkaline phosphatase as described in example 2. The
sample was extracted three times with phenol:chloroform,
precipitated with ethanol and dissolved in water. The ligations
were performed with a final DNA concentration of 1-2 ng/.mu.l of
both the cut fd-CAT2 and the digested PCR product. The ligations
were transformed into competent TG1 cells and plated on 2.times.TY
tet plates. Identification of clones containing the desired insert
was by analytical PCR performed using the conditions and primers
above, on boiled samples of the resulting colonies. The correct
clone containing the phoA gene fused in frame to gene III was
called fd-phoAla 166. The sequence at the junction of the cloning
region is given in FIG. 15.
Example 12
Measuring Enzyme Activity of Phage-Enzyme
[0347] Overnight cultures of TG1 or KS272 (E. coli cells lacking
phoA. Strauch K. L., and Beckwith J. PNAS 85 1576-1580, 1988) cells
containing either fd-phoAla 166 or fd-CAT2 were grown at 37.degree.
C. in 2.times.TY with 15 .mu.g/ml tetracycline.
[0348] Concentrated, PEG precipitated phage were prepared as
described earlier. Enzyme assays (Malamy, M. H. and Horecker B. L.,
Biochemistry 3, p 1893-1897, (1964)) were carried out at 24.degree.
C. in a final concentration of 1M Tris/HC1 pH 8.0, 1 mM
4-nitrophenyl phosphate (Sigma), 1 mM MgC12. 100 .mu.l of a two
times concentrate of this reaction mixture was mixed with 100 .mu.l
of the test sample in a 96 well plate.
[0349] Absorbance readings were taken every minute for 30 minutes
at a wavelength of 405 nm in a Titretek Mk 2 plate reader. Initial
reaction rates were calculated from the rate of change of
absorbance using a molar absorbance of 17000 l/mol/cm.
[0350] Standard curves (amount of enzyme vs. rate of change of
absorbance) were prepared using dilutions of purified bacterial
alkaline phosphatase (Sigma type III) in 10 mM Tris/HC1 pH 8.0, 1
mM EDTA. The number of enzyme molecules in the phage samples were
estimated from the actual rates of change of absorbance of the
phage samples and comparison to this standard curve.
[0351] The results in Table 3 show that alkaline phosphatase
activity was detected in PEG precipitated material in the sample
containing fd-phoAla166 but not fd-CAT2. Furthermore, the level of
activity was consistent with the expected number of 1-2 dimer
molecules of enzyme per phage.
[0352] The level of enzyme activity detected was not dependent on
the host used for growth. In particular, fd-phoAla166 grown on phoA
minus hosts showed alkaline phosphatase activity.
[0353] Therefore, the phage expressed active alkaline phosphatase
enzyme, from the phoA-gene III fusion, on the phage surface.
Example 13
Insertion of Binding Molecules into Alternative Sites in the
Phage
[0354] The availability of an alternative site in the phage for the
insertion of binding molecules would open up the possibility of
more easily expressing more than one binding molecule, e.g., an
antibody fragment in a single pAb. This may be used to generate
single or multiple binding specificities. The presence of two
distinct binding activities on a single molecule will greatly
increase the utility and specificity of this molecule. It may be
useful in the binding of viruses with a high mutational rate such
as human immunodeficiency virus. In addition, it may be used to
bring antigens into close proximity (e.g. drug targetting or cell
fusion) or it may act as a "molecular clamp" in chemical,
immunological or enzymatic processes.
[0355] The vector fd-tet and the derivatives described here, have a
single BamHI site in gene 3. This has previously been used for the
expression of peptide fragments on the surface of filamentous
bacteriophage (Smith G P. (1985) Science 228 p 1315-1317 and de la
Cruz et al. (1988) J. Biol. Chem. 263 p 4318-4322). This provides a
potential alternative site for the insertion of antibody
fragments.
[0356] DNA fragments encoding scFv's from D1.3 or NQ11 were
generated by PCR using the primers shown below. These primers were
designed to generate a fragment with BamHI sites near both the
terminii, to enable cloning into the BamH1 site of gene3 (see FIG.
16a). The oligonucleotides used, also ensure that the resulting PCR
product lacks Pst1 and Xhol restriction sites normally used for
manipulating the scFv's (see FIG. 16a). This will facilitate
subsequent manipulation of a second antibody fragment in the usual
way at the N terminus of gene 3. The oligonucleotides used were:--
TABLE-US-00003 G3Bam1 5' TTT AAT GAG GAT CCA CAG (SEQ ID NO:11) GTG
CAG CTG CAA GAG 3' G3Bam2 5' AAC GAA TGG ATC CCG TTT (SEQ ID NO:12)
GAT CTC AAG CTT 3'.
Preparation of Vector and PCR Insert
[0357] The PCR reaction was carried out in an 80 .mu.l reaction as
described in example 11 using 1 ng/.mu.l of template and 0.25
U/.mu.l of Taq polymerase and a cycle regime of 94.degree. C. for 1
minute, 60.degree. C. for 1 minute and 70.degree. C. for 2 minutes
over 30 cycles. The template was either pscFvNQ11 (example 9) or
scFvD1.3 myc (example 2). Reaction products were extracted with
phenol:chloroform, precipitated, dissolved in water and digested
with BamH1 according to manufacturers instructions. The digest was
re-extracted with phenol: chloroform, precipitated and dissolved in
water.
[0358] The vector fdTPs/Xh was cleaved with BamH1 and treated with
calf intestinal phosphatase and purified as described in example 2.
Ligations were set up at a vector concentration of approximately 6
ng/.mu.l and a PCR insert concentration of approximately 3
ng/.mu.l. These were ligated for 2.5 hours at room temperature
before transforming into competent TG1 cells and plating on TY tet
plates. The resultant colonies were probed as described in example
8. DNA was prepared from a number of colonies and the correct
orientation and insert size confirmed by restriction digestion with
Hind III in isolation or in combination with BamH1. (One Hind III
site is contributed by one of the primers and the other by the
vector).
[0359] Two clones containing a D1.3 insert (fdTBam1) and fdTBam2)
and one containing an NQ11 insert (NQ11Bam1) were grown up and
phage prepared as described earlier. ELISAs were carried out as
described in example 6. No specific signal was found for any of
these clones suggesting that the natural BamH1 site is not a
suitable site for insertion of a functional antibody (results not
shown).
[0360] It may be possible to clone into alternative sites to retain
binding activity. The peptide repeats present in gene III may
provide such a site (FIG. 16 blocks A and B). This can be done by
inserting a BamH1 site and using the PCR product described above.
To facilitate this, the natural BamHl site was removed by
mutagenesis with the oligonucleotide G3mut.delta.Bam shown below
(using an in vitro mutagenesis kit (Amersham
International)):-G3mut.delta.Bam 5' CA AAC GAA TGG GTC CTC CTC ATT
A 3' (SEQ ID NO:13). The underlined residue replaces an A residue,
thereby removing the BamHl site. DNA was prepared from a number of
clones and several mutants lacking BamHl sites identified by
restriction digestion.
[0361] The oligonucleotide G3 Bamlink was designed to introduce a
BamHl site at a number of possible sites within the peptide linker
sites A and B, see FIG. 16b. The sequence of the linker is: Bamlink
5'CC (G or A) CC ACC CTC GGA TCC (G or A) CC ACC CTC 3' (SEQ ID
NO:14). Its relationship to the peptide repeats in gene III is
shown in FIG. 16
Example 14
PCR Assembly of Mouse VH and VL Kappa (VLK) Repertoires for Phage
Display
[0362] The principle is illustrated in FIG. 17. Details are
provided in sections A to F below but the broad outline is first
discussed. [0363] 1. cDNA is prepared from spleen RNA from an
appropriate mouse and the VH and VLK repertories individually
amplified. Separately, primers reverse and complementary to
VH1FOR-2 (domain 1) and VLK2BACK (domain 2) are used to amplify an
existing scFv-containing DNA by PCR. (The term FOR refers to, e.g.,
a primer for amplification of sequences on the sense strand
resulting in antisense coding sequences. The term BACK refers to,
e.g., a primer for amplification of sequences on the antisense
strand resulting in sense coding sequences). This generates a
`linker` molecule encoding the linker with the amino acid sequence
(1 letter code) (GGGGS).sub.3 (SEQ ID NO:15) which overlaps the two
primary (VH and VLK) PCR products. [0364] 2. The separate amplified
VH, VLK and linker sequences now have to be assembled into a
continuous DNA molecule by use of an `assembly` PCR. In the
secondary `assembly` PCR, the VH, VLK and linker bands are combined
and assembled by virtue of the above referred to overlaps. This
generates an assembled DNA fragment that will direct the expression
of VH and one VLK domain. The specific VH/VLK combination is
derived randomly from the separate VH and VLK repertoires referred
to above. [0365] The assembly PCR is carried out in two stages.
Firstly, 7 rounds of cycling with just the three bands present in
the PCR, followed by a further 20 rounds in the presence of the
flanking primers VH1BACK (referring to domain 1 of VH) and VLKFOR.
The nucleotide sequences for these oligonucleotide primers are
provided under the section entitled `Primer Sequences` below. This
two stage process, avoids the potential problem of preferential
amplification of the first combinations to be assembled.
[0366] For cloning into the phage system, the assembled repertoires
must be `tagged` with the appropriate restriction sites. In the
example provided below this is illustrated by providing an ApaL1
restriction site at the VH end of the continuous DNA molecule and a
Not 1 site at the VLK end of the molecule. This is carried out by a
third stage PCR using tagged primers. The nucleotide sequences for
these oligonucleotide primers are also provided under the section
entitled `Primer Sequences` below. There are however, 4 possible
kappa light chain sequences (whereas a single consensus heavy chain
sequence can be used). Therefore 4 oligonucleotide primer sequences
are provided for VLK.
[0367] For this third stage PCR, sets of primers which create the
new restriction site and have a further 10 nucleotides on the 5'
side of the restriction site have been used. However, long tags may
give better cutting, in which case 15-20 nucleotide overhangs could
be used.
[0368] Scrupulously clean procedures must be used at all times to
avoid contamination during PCR. Negative controls containing no DNA
must always be included to monitor for contamination. Gel boxes
must be depurinated. A dedicated GENECLEAN kit (B10 101, GENECLEAN,
La Jolla, San Diego, Calif., USA) can be used according to
manufacturers instructions to extract DNA from an agarose gel. The
beads, NaI and the NEW wash should be aliquoted.
[0369] All enzymes were obtained from CP Laboratories, P.O. Box 22,
Bishop's Stortford, Herts CM20 3DH and the manufacturers
recommended and supplied buffers were used unless otherwise
stated.
A. RNA Preparation
[0370] RNA can be prepared using many procedures well known to
those skilled in the art. As an example, the following protocol
(Triton X-100 lysis, phenol/SDS RNase inactivation) gives excellent
results with spleen and hybridoma cells (the addition of VRC
(veronal ribosyl complex) as an RNase inhibitor is necessary for
spleen cells). Guanidinium isothiocyanate/CsCl procedures (yielding
total cellular RNA) also give good results but are more
time-consuming. [0371] 1. Harvest 1 to 5.times.10.sup.7 cells by
centrifugation in a bench tope centrifuge at 800.times.g for 10
minutes at 4.degree. C. Resuspend gently in 50 ml of cold PBS
buffer. Centrifuge the cells again at 800.times.g for 10 minutes at
4.degree. C., and discard supernatant. [0372] 2. On ice, add 1 ml
ice-cold lysis buffer to the pellet and resuspend it with a 1 ml
Gilson pepette by gently pipetting up and down. Leave on ice for 5
minutes. [0373] 3. After lysis, remove cell debris by centrifuging
at 1300 rpm for 5 minutes in a microfuge at 4.degree. C., in
precooled tubes. [0374] 4. Transfer 0.5 ml of the supernatant to
each of two eppendorfs containing 60 .mu.l 10% (w/v) SDS and 250
.mu.l phenol (previously equilibrated with 100 mM Tris-HC1 pH 8.0).
Vortex hard for 2 minutes, then microfuge (13000 rpm) for five
minutes at room temperature. Transfer the upper, aqueous, phase to
a fresh tube. [0375] 5. Re-extract the aqueous upper phase five
times with 0.5 ml of phenol. [0376] 6. Precipitate with 1/10 volume
3M sodium acetate and 2.5 volumes ethanol at 20.degree. C.
overnight or dry ice-isopropanol for 30 minutes. [0377] 7. Wash the
RNA pellet and resuspended in 50 .mu.l to check concentration by
OD260 and check 2 .mu.g on a 1% agarose gel. 40 .mu.g of RNA was
obtained from spleen cells derived from mice. [0378] Lysis buffer
is [10 mM Tris-HC1 pH 7.4, 1 mM MgC12, 150 mM NaCl, 10 mM VRC (New
England Biolabs), 0.5% (w/v) Triton X-100], prepared fresh. [0379]
Lysis buffer is [10 mM Tris-HC1 pH 7.4, 1 mM MgC12, 150 mM NaCl, 10
mM VRC (New England Biolabs), 0.5% (w/v) Triton X-100], prepared
fresh. B. cDNA Preparation
[0380] cDNA can be prepared using many procedures well known to
those skilled in the art. As an example, the following protocol can
be used:
[0381] 1. Set up the following reverse transcription mix:
TABLE-US-00004 .mu.l H.sub.2O (DEPC-treated) 20 5 mM dNTP 10 10
.times. first strand buffer 10 0.1 M DTT 10 FOR primer(s) (10
pmol/.mu.l) 2 (each) (see below) RNasin (Promega; 40 U/.mu.l) 4
NB [0382] i) DEPC is diethylpyrocarbonate, the function of which is
to inactivate any enzymes that could degrade DNA or RNA [0383] ii)
dNTP is deoxynucleotide triphosphate [0384] iii) DTT is
dithiothreitol the function of which is as an antioxidant to create
the reducing environment necessary for enzyme function. [0385] iv)
RNasin is a ribonuclease inhibitor obtained from Promega
Corporation, 2800 Woods Hollow Road, Madison, Wis., USA. [0386] 2.
Dilute 10 .mu.g RNA to 40 .mu.l final volume with DEPC-treated
water. Heat at 65.degree. C. for 3 minutes and hold on ice for one
minute (to remove secondary structure). [0387] 3. Add to the RNA
the reverse transcription mix (58 .mu.l) and 4 .mu.l of the cloned
reverse transcriptase `Super RT` (Anglian Biotech Ltd., Whitehall
House, Whitehall Road, Colchester, Essex) and incubate at
42.degree. C. for one hour. [0388] 4. Boil the reaction mix for
three minutes, cool on ice for one minute and then spin in a
microfuge to pellet debris. Transfer the supernatant to a new tube.
[0389] 10.times. first strand buffer is [1,4M KC1, 0.5M Tris-HC1 pH
8.1 at 42.degree. C. 80MM MgCl.sub.2].
[0390] The primers anneal to the 3' end. Examples of kappa light
chain primers are MJK1FONX, MJK2FONX, MJK4FONX and MJK5FONX
(provided under `Primer Sequences` below) and examples of heavy
chain primers are MIGG1, 2 (CTG GAC AGG GAT CCA GAG TTC CA) (SEQ ID
NO:16) and MIGG3 (CTG GAC AGG GCT CCA TAG TTC CA) (SEQ ID NO:17)
which anneal to CH1.
[0391] Alternatively, any primer that binds to the 3' end of the
variable regions VH, VLK, VL, or to the constant regions CH1, CK or
CL can be used.
C. Primary PCRs
[0392] For each PCR and negative control, the following reactions
are set up (e.g. one reaction for each of the four VLKs and four VH
PCRs). In the following, the Vent DNA polymerase sold by (C.P.
Laboratories Ltd (New England Biolabs) address given above) was
used. The buffers are as provided by C.P. Laboratories.
TABLE-US-00005 .mu.l H.sub.2O 32.5 10 .times. Vent buffer 5 20
.times. Vent BSA 2.5 5 mM dNTPs 1.5 FOR primer 10 pmol/.mu.l) 2.5
BACK primer 10 pmol/.mu.l 2.5
The FOR and BACK primers are given in the section below entitled
`Primer Sequences`. For VH, the FOR primer is VH1FOR-2 and the BACK
primer is VH1BACK. For VLK the FOR primers are MJK1FONX, MJK2FONX,
MJK4FONX and MJK5FONX (for the four respective kappa light chains)
and the BACK primer is VK2BACK. Only one kappa light chain BACK
primer is necessary, because binding is to a nucleotide sequence
common to the four kappa light chains.
[0393] UV this mix 5 minutes. Add 2.5 .mu.l cDNA preparation (from
B above), 2 drops paraffin oil (Sigma Chemicals, Poole, Dorset,
UK). Place on a cycling heating block, e.g., PHC-2 manufactured by
Techne Ltd. Duxford UK, pre-set at 94.degree. C. Add 1 .mu.l Vent
DNA polymerase under the paraffin. Amplify using 25 cycles of
94.degree. C. 1 min, 72.degree. C. 2 min. Post-treat at 60.degree.
C. for 5 min.
[0394] Purify on a 2% imp (low melting point agarose/TAE
(tris-acetate EDTA)gel and extract the DNA to 20 .mu.l H.sub.2O per
original PCR using a GENECLEAN kit (see earlier; Bio101, La Jolla
Calif., USA) in accordance with the manufacturers instructions.
D. Preparation of Linker
[0395] Set Up in Bulk (e.g. 10 Times) TABLE-US-00006 .mu.l H.sub.2O
34.3 10 .times. Vent buffer 5 20 .times. Vent BSA 2.5 5 mM dNTPs 2
LINKFOR primer 10 pmol/.mu.l) 2.5 LINKBACK primer 10 pmol/.mu.l 2.5
DNA from fcFv D1.3 (example 2) 1 Vent enzyme 0.2
The FOR and BACK primers are given in the section below entitled
`Primer Sequences`. The FOR primer is LINKFOR and the BACK primer
is LINKBACK. Cover with paraffin and place on the cycling heating
block (see above) at 94.degree. C. Amplify using 25 cycles of
94.degree. C. 1 min, 65.degree. C. 1 min, 72.degree. C. 2 min.
Post-treat at 60.degree. C. for 5 min.
[0396] Purify on 2% 1 mp/TAE gel (using a loading dye without
bromophenol blue as a 93 bp fragment is desired) and elute with
SPIN-X column (Costar Limited, 205 Broadway, Cambridge, Ma. USA.,)
and precipitation. Take up in 5 .mu.l H.sub.2O per PCR
reaction.
E. Assembly PCRs
[0397] A quarter of each PCR reaction product (5 .mu.l) is used for
each assembly. The total volume is 25 .mu.l.
[0398] For each of the four VLK primers, the following are set up:
TABLE-US-00007 H.sub.2O 4.95 10 .times. Vent buffer 2.5 20 .times.
Vent BSA 1.25 5 mM dNTPs 0.8
UV irradiate this mix for 5 min. Add 5 .mu.l each of Vh and VK band
from the primary PCRs and 1.5 .mu.l of linker as isolated from the
preparative gels and extracted using the GENECLEAN kit as described
in C and D above. Cover with paraffin. Place on the cycling heating
block preset at 94.degree. C. Add 1 .mu.l Vent under the paraffin.
Amplify using 7 cycles of 94.degree. C. 2 min, 72.degree. C. 4 min.
Then return the temperature to 94.degree. C.
[0399] Add 1.5 .mu.l each of VH1BACK and the appropriate VKFOR
primers MJK1FONX, MJK2FONX, MJK4FONX or MJK5FONX (10 pmol/.mu.l) at
94.degree. C. The primers should have been UV-treated as above.
Amplify using 20 cycles of 94.degree. C. 1.5 min, 72.degree. C. 2.5
min. Post-treat at 60.degree. C. for 5 min. Purify on 2% 1 mp/TAE
gel and extract the DNA to 20 .mu.l H.sub.2O per assembly PCR using
a GENECLEAN kit (see earlier) in accordance with the manufacturers
instructions.
F. Adding Restriction Sites
[0400] For Each Assembly and Control Set Up: TABLE-US-00008 .mu.l
H.sub.2O 36.5 10 .times. Taq buffer 5 5 mM dNTPs 2 FOR primer (10
pmol/.mu.l) 2.5 BACK primer (10 pmol/.mu.l) 2.5 Assembly product
1
The FOR and BACK primers are given in the section below entitled
`Primer Sequences`. The FOR primer is any of JK1NOT10, JK2NOT10,
JK4NOT10 or JK5NOT10 (for the four respective kappa light chains)
for putting a Not1 restriction site at the VLK end. The BACK primer
is HBKAPA10 for putting an ApaL1 restriction site at the VH
end.
[0401] Cover with paraffin and place on the cycling heating block
preset at 94.degree. C. Add 0.5 .mu.l Cetus Taq DNA polymerase
(Cetus/perkin-Elmer, Beaconsfield, Bucks, UK) under the paraffin.
Amplification is carried out using 11 to 15 rounds of cycling
(depends on efficiency) at 94.degree. C. 1 min, 55.degree. C. 1
min, 72.degree. C. 2 min. Post-treat at 60.degree. C. for 5
min.
[0402] 10.times.Taq buffer is [0.1M Tris-HC1 pH 8.3 at 25.degree.
C., 0.5M KC1, 15 mM MgCl.sub.2, 1 mg/ml gelatin].
G. Work-Up
[0403] Purify once with CHC1.sub.3/IAA (isoamylalcohol), once with
phenol, once with CHC1.sub.3/IAA and back-extract everything to
ensure minimal losses. Precipitate and wash twice in 70% EtOH.
Dissolve in 70 .mu.l H.sub.2O. TABLE-US-00009 Digest overnight at
37.degree. C. with NotI: .mu.l DNA (joined seq) 70 NEB NotI buffer
.times. 10 10 NEB BSA .times. 10 10 Notl (10 U/.mu.l) 10
The DNA (joined sequence) above refers to the assembled DNA
sequence comprising in the 5' to 3' direction
[0404] ApaL1 restriction site
[0405] VH sequence
[0406] Linker sequence
[0407] VLK sequence
[0408] Not 1 restriction site.
[0409] The VLK sequence may be any one of four possible kappa chain
sequences.
[0410] The enzymes Not 1 above, ApaL1 below and the buffers NEB Not
1, NEB BSA above and the NEB buffer 4 (below) are obtainable from
CP Laboratories, New England Biolabs mentioned above.
[0411] Re-precipitate, take up in 80 .mu.l H.sub.2O. Add to this 10
.mu.l NEB buffer 4 and 10 .mu.l Apal 1.
[0412] Add the enzyme ApaL1 in aliquots throughout the day, as it
has a short half-life at 37.degree. C.
[0413] Purify on 2% 1 mp/TAE gel and extract the DNA using a
GENECLEAN kit, in accordance with the manufacturers instructions.
Redigest if desired.
H. Final DNA Product
[0414] The final DNA product is an approximate 700 bp fragment with
Apa L1 and Not1 compatible ends consisting of randomly associated
heavy and light chain sequences linked by a linker. A typical
molecule of this type is the scFvD1.3 molecule incorporated into
fdscFvD1.3 described in example 3. These molecules can then be
ligated into suitable fd derived vectors, e.g., fdCAT2 (example 5),
using standard techniques.
Primer Sequences
[0415] Primary PCR Oligos (Restrictions Sites Underlined):
TABLE-US-00010 VH1FOR-2 TGA GGA GAC GGT GAC CGT GGT (SEQ ID NO:18)
CCC TTG GCC CC VH1BACK AGG TSM ARC TGC AGS AGT CWG (SEQ ID NO:19) G
MJK1FONX CCG TTT GAT TTC CAG CTT GGT (SEQ ID NO:20) GCC MJK2FONX
CCG TTT TAT TTC CAG CTT GGT (SEQ ID NO:21) CCC MJK4FONX CCG TTT TAT
TTC CAA CTT TGT (SEQ ID NO:22) CCC MJK5FONX CCG TTT CAG CTC CAG CTT
GGT (SEQ ID NO:23) CCC VK2BACK GAC ATT GAG CTC ACC CAG TCT (SEQ ID
NO:24) CCA
Ambiguity codes M=A or C, R=A or G, S=G or C, W=A or T PCR Oligos
to Make Linker: LINKFOR TGG AGA CTC GGT GAG CTC AAT GTC (SEQ ID
NO:25) LINKBACK GGG ACC ACG GTC ACC GTC TCC TCA (SEQ ID NO:26)
[0416] For Adding Restriction Sites: TABLE-US-00011 HBKAPA10 CAT
GAC CAC AGT GCA CAG GTS (SEQ ID NO:27) MAR CTG CAG SAG TCW GG
JKINOT10 GAG TCA TTC TGC GGC CGC CCG (SEQ ID NO:28) TTT GAT TTC CAG
CTT GGT GCC JK2NOT10 GAG TCA TTC TGC GGC CGC CCG (SEQ ID NO:29) TTT
TAT TTC CAG CTT GGT CCC JK4NOT10 GAG TCA TTC TGC GGC CGC CCG (SEQ
ID NO:30) TTT TAT TTC CAA CTT TGT CCC JK5NOT10 GAG TCA TTC TGC GGC
CGC CCG (SEQ ID NO:31) TTT CAG CTC CAG CTT GGT CCC.
Example 15
Insertion of the Extracellular Domain of a Human Receptor for
Platelet Derived Growth Factor (PDGF) Soform BB into fd CAT2
[0417] A gene fragment encoding the extracellular domain of the
human receptor for platelet derived growth factor isoform BB
(h-PDGFB-R) was isolated by amplification, using the polymerase
chain reaction, of plasmid RP41, (from the American Type Culture
collection, Cat. No. 50735), a cDNA clone encoding amino-acids 43
to 925 of the PDGF-B receptor (Gronwald, R. G. K. et al PNAS 85 p
3435-3439 (1988)). Amino acids 1 to 32 of h-PDGFB-R constitute the
signal peptide. The oligonucleotide primers were designed to
amplify the region of the h-PDGFB-R gene corresponding to amino
acids 43 to 531 of the encoded protein. The primer RPDGF3 for the
N-terminal region also included bases encoding amino acids 33 to 42
of the h-PDGFB-R protein (corresponding to the first ten amino
acids from the N-terminus of the mature protein) to enable
expression of the complete extracellular domain. The primers also
incorporate a unique ApaL1 site at the N-terminal end of the
fragment and a unique Xhol site at the C terminal end to facilitate
cloning into the vector fdCAT2. The sequence of the primers is:
TABLE-US-00012 RPDGF3 5' CAC AGT GCA CTG GTC GTC (SEQ ID NO:32) ACA
CCC CCG GGG CCA GAG CTT GTC CTC AAT GTC TCC AGC ACC TTC GTT CTG 3'
RPDGF2 5' GAT CTC GAG CTT AAA GGG (SEQ ID NO:33) CAA GGA GTG TGG
CAC 3'
[0418] PCR amplification was performed using high fidelity
conditions (Eckert, K. A. and Kunkel, T. A. 1990 Nucl Acids
Research 18 3739-3744). The PCR mixture contained: 20 mM Tris HC1
(pH 7.3 at 70.degree. C., 50 mM KC1, 4 mM magnesium chloride, 0.01%
gelatin, 1 mM each of dATP, dCTP, dGTP and dTTP, 500 ng/ml RP41
DNA, 1 .mu.M each primer and 50 units/ml Taq polymerase
(Cetus/Perkin Elmer, Beaconsfield, Bucks, U.K.). Thirty cycles of
PCR were performed with denaturation at 92.degree. C. for 1 min,
annealing at 60.degree. C. for 1 min and extension at 72.degree. C.
for 1.5 min. This reaction resulted in amplification of a fragment
of ca. 1500 bp as expected.
[0419] fdCAT2 vector DNA (see example 5) was digested with ApaL1
and Xhol (New England Biolabs) according to manufacturers
recommendations, extracted with phenol/chloroform and ethanol
precipitated (Sambrook et al, supra). Cloning of amplified RP41 DNA
into this vector and identification of the desired clones was
performed essentially as in example 7 except that digestion of the
PCR product was with ApaL1 and Xho 1. Colonies containing h-PDGFB-R
DNA were identified by probing with 32P labelled RPDGF2 and the
presence of an insert in hybridising colonies was confirmed by
analytical PCR using RPDGF3 and RPDGF2 using the conditions
described in example 7.
Example 16
Binding of 125I-PDGF-BB to the Extracellular Domain of the Human
Receptor for Platelet Derived Growth Factor Isoform BB Displayed on
the Surface of fd Phage. Measured Using an Immunoprecipitation
Assay.
[0420] Phage particles, expressing the extracellular domain of the
human platelet derived growth factor isoform BB receptor (fd
h-PDGFB-R), were prepared by growing E. coli MC1061 cells
transformed with fd h-PDGFB-R in 50 ml of 2.times.TY medium with 15
ug/ml tetracycline for 16 to 20 hours. Phage particles were
concentrated using polyethylene glycol as described in example 6
and resuspended in PDGF binding buffer (25 mM HEPES, pH7.4, 0.15 mM
NaC1, 1 mM magnesium chloride, 0.25% BSA) to 1/33rd of the original
volume. Residual bacteria and undissolved material were removed by
spinning for 2 min in a microcentrifuge. Immunoblots using an
antiserum raised against gene III protein (Prof. I. Rashed,
Konstanz, Germany) show the presence in such phage preparations of
a geneIII-h-PDGFB-R protein of molecular mass 125000 corresponding
to a fusion between h-PDGFB-R external domain (55000 daltons) and
geneIII (apparent molecular mass 70000 on SDS-polyacrylamide
gel).
[0421] Duplicate samples of 35 .mu.l concentrated phage were
incubated with .sup.125I-PDGF-BB (78.7fmol, 70nCi, 882 Ci/mmol;
Amersham International plc, Amersham, Bucks) for 1 hour at
37.degree. C. Controls were included in which fdTPs/Bs vector phage
(FIG. 4) or no phage replaced fd h-BDGFB-R phage. After this
incubation, 10 ul of sheep anti-M13 polyclonal antiserum (a gift
from M. Hobart) was added and incubation continued for 30 min at
200C. To each sample, 40 ul (20 ul packed volume) of protein G
Sepharose Fast Flow (Pharmacia, Milton Keynes) equilibrated in PDGF
binding buffer was added. Incubation was continued for 30 min at
20.degree. C. with mixing by end over end inversion on a rotating
mixer. The affinity matrix was spun down in a microcentrifuge for 2
min and the supernatant removed by aspiration. Non-specifically
bound .sup.125I-PDGF-BB was removed by resuspension of the pellet
in 0.5 ml PDGF binding buffer, mixing by rotation for 5 min,
centrifugation and aspiration of the supernatant, followed by two
further washes with 0.5 ml 0.1% BSA, 0.2% Triton-X-100. The pellet
finally obtained was resuspended in 100 ul PDGF binding buffer and
counted in a Packard gamma counter. For displacement studies,
unlabelled PDGF-BB (Amersham International) was added to the stated
concentration for the incubation of .sup.125I-PDGF-BB with
phage.
[0422] .sup.125I-PDGF-BB bound to the fd h-PDGFB-R phage and was
immunoprecipitated in this assay. Specific binding to receptor
phage was 3.5 to 4 times higher than the non-specific binding with
vector phage fdTPs/Bs or no phage (FIG. 19). This binding of
.sup.125I-PDGF-BB could be displaced by the inclusion of unlabelled
PDGF-BB in the incubation with phage at 37.degree. C. (FIG. 20). At
50 nM, unlabelled PDGF-BB the binding of .sup.125I-PDGF-BB was
reduced to the same level as the fdTPs/Bs and no phage control.
FIG. 21 shows the same data, but with the non-specific binding to
vector deducted.
[0423] These results indicate that a specific saturable site for
.sup.125I-PDGF-BB is expressed on fd phage containing cloned
h-PDGFB-R DNA. Thus, the phage can display the functional
extracellular domain of a cell surface receptor.
Example 17
Construction of Phagemid Containing GeneIII Fused with the Coding
Sequence for a Binding Molecule
[0424] It would be useful to improve the transfection efficiency of
the phage-binding molecule system and also to have the possibility
of displaying different numbers and specificities of binding
molecules on the surface of the same bacteriophage. The applicants
have devised a method that achieves both aims.
[0425] The approach is derived from the phagemid system based on
pUC119 [Vieira, J and Messing, J. (1987) Methods Enzymol. 153:3].
In brief, gene III from fd-CAT2 (example 5) and gene III scFv
fusion from fd-CAT2 scFv D1.3 (example 2) were cloned downstream of
the lac promoter in separate samples of pUC119, in order that the
inserted gene III and gene III fusion could be `rescued` by M13M07
helper phage [Vieira, J and Messing, J. et supra.] prepared
according to Sambrootz et al. 1989 supra. The majority of rescued
phage would be expected to contain a genome derived from the pUC119
plasmid that contains the binding molecule-gene III fusion and
should express varying numbers of the binding molecule on the
surface up to the normal maximum of 3-5 molecules of gene III of
the surface of wild type phage. The system has been exemplified
below using an antibody as the binding molecule.
[0426] An fdCAT2 containing the single chain Fv form of the D1.3
antilysozyme antibody was formed by digesting fdTscFvD1.3 (example
2) with Pstl and Xhol, purifying the fragment containing the scFv
fragment and ligating this into Pstl and Xhol digested fdCAT2. The
appropriate clone, called fdCAT2 scFvD1.3 was selected after
plating onto 2.times.TY tetracycline (15 .mu.g/ml) and confirmed by
restriction enzyme and sequence analysis.
[0427] Gene III from fd-CAT2 (example 5) and the gene III scFv
fusion from fd-CAT2 scFvD1.3 was PCR-amplified using the primers A
and B shown below: TABLE-US-00013 Primer A: TGC GAA GCT TTG GAG CCT
(SEQ ID NO:34) TTT TTT TTG GAG ATT TTC AAC G Primer B: CAG TGA ATT
CCT ATT AAG (SEQ ID NO:35) ACT CCT TAT TAC GCA GTA TGT TAG C.
[0428] Primer A anneals to the 5' end of gene III including the
ribosome binding site is located and incorporates a Hind III site.
Primer B anneals to the 3' end of gene III at the C-terminus and
incorporates two UAA stop codons and an EcoR1 site. 100 ng of
fd-CAT2 and fd-CAT2 scFv D1.3 DNA was used as templates for
PCR-amplification in a total reaction volume of 50 .mu.l as
described in example 7, except that 20 cycles of amplification were
performed: 94.degree. C. 1 minute, 50.degree. C. 1 minute,
72.degree. C. 3 minutes. This resulted in amplification of the
expected 1.2 Kb fragment from fd-CAT2 and a 1.8 Kb fragment from
fd-CAT2 scFv D1.3.
[0429] The PCR fragments were digested with EcoR1 and Hind III,
gel-purified and ligated into Eco-R1- and Hind III-cut and
dephosphorylated pUC119 DNA and transformed into E. coli TG1 using
standard techniques (Sambrook et al., et supra). Transformed cells
were plated on SOB agar (Sambrook et al. 1989 supra) containing 100
.mu.g/ml ampicillin and 2% glucose. The resulting clones were
called pCAT-3 (derived from fd-CAT2) and pCAT-3 scFv D1.3 (derived
from fd-CAT2 scFv D1.3).
Example 18
Rescue of Anti-Lysozyme Antibody Specificity from pCAT-3 scFv D1.3
by M13KO7
[0430] Single pCAT-3 and pCAT-3 scFv D1.3 colonies were picked into
1.5 ml 2TY containing 100 .mu.g/ml ampicillin and 2% glucose, and
grown 6 hrs at 30.degree. C. 30 .mu.l of these stationary cells
were added to 6 mls 2YT containing 100 .mu.g/ml ampicillin and 2%
glucose in 50 ml polypropylene tubes (Falcon, Becton Dickinson
Labware, 1950 Williams Drive, Oxnard, Calif. USA) and grown for 1.5
hrs at 30.degree. C. at 380 rpm in a New Brunswick Orbital Shaker
(New Brunswick Scientific Ltd., Edison House 163 Dixons Hill road,
North Mimms, Hatfield, UK). Cells were pelleted by centrifugation
at 5,000 g for 25 minutes and the tubes drained on tissue paper.
The cell pellets were then suspended in 6 mls 2TY containing
1.25.times.10.sup.9 p.f.u. ml-.sup.1 M13KO7 bacteriophage added.
The mixture was left on ice for 5 minutes followed by growth at
35.degree. C. for 45 minutes at 450 rpm. A cocktail was then added
containing 4 .mu.l 100 .mu.g/ml ampicillin, 0.5 .mu.l 0.1M IPTG and
50 .mu.l 10 mg/ml kanamycin, and the cultures grown overnight at
35.degree. C., 450 rpm.
[0431] The following day the cultures were centrifuged and phage
particles PEG precipitated as described in example 6.
[0432] Phage pellets were resuspended in 100 .mu.l TE (tris-EDTA
see example 6) and phage titred on E. coli TG1. Aliquots of
infected cells were plated on 2TY containing either 100 .mu.g/ml
ampicillin to select for pUC119 phage particles, or 50 .mu.g/ml
kanamycin to select for the M13 KO7 helper phage. Plates were
incubated overnight at 37.degree. C. and antibiotic-resistant
colonies counted: TABLE-US-00014 DNA amp.sup.R kan.sup.R pCAT-3 1.8
.times. 10.sup.11 colonies 1.2 .times. 10.sup.9 colonies pCAT-3scFv
D1.3 2.4 .times. 10.sup.11 colonies 2.0 .times. 10.sup.9
colonies
[0433] This shows that the amp.sup.R phagemid particles are
infective and present in the rescued phage population at a 100-fold
excess over kan.sup.R M13KO7 helper phage.
[0434] Phage were assayed for anti-lysozyme activity by ELISA as
described in example 6, with the following modifications:
1) ELISA plates were blocked for 3 hrs with 21 Marvel/PBS.
2) 50 .mu.l phage, 400 .mu.l 1.times.PBS and 50 .mu.l 20% Marvel
were mixed end over end for 20 minutes at room temperature before
adding 150 .mu.l per well.
3) Phage were left to bind for 2 hours at room temperature.
4) All washes post phage binding were:
[0435] 2 quick rinses PBS/0.5% Tween 20
[0436] 3.times.2 minute washes PBS/0.5% Tween 20
[0437] 2 quick rinses PBS no detergent
[0438] 3.times.2 minute washes PBS no detergent
[0439] The result of this ELISA is shown in FIG. 22, which shows
that the antibody specificity can indeed be rescued
efficiently.
[0440] It is considered a truism of bacterial genetics that when
mutant and wild-type proteins are co-expressed in the same cell,
the wild-type proteins are co-expressed in same cell, the wild-type
protein is used preferentially. This is analogous to the above
situation wherein mutant (i.e. antibody fusion) and wild-type gene
III proteins (from M13K07) are competing for assembly as part of
the pUC119 phagemid particle. It is therefore envisaged that the
majority of the resulting pUC 119 phage particles will have fewer
gene III-antibody fusion molecules on their surface than is the
case for purely phage system described for instance in example 2.
Such phagemid antibodies are therefore likely to bind antigen with
a lower avidity than fd phage antibodies with three or more copies
of the antibody fusion on their surfaces (there is no wild-type
gene III, in the system described, for instance, in example 2), and
provide a route to production of phage particles with different
numbers of the same binding molecule (and hence different acidities
for the ligand/antigen) or multiple different binding specificities
on their surface, by using helper phage such as M13K07 to rescue
cells expressing two or more gene III-antibody fusions.
[0441] It is also possible to derive helper phage that do not
encode a functional gene III in their genomes (by for example
deleting the gene III sequence or a portion of it or by
incorporating an amber mutation within the gene). These defective
phages will only grow on appropriate cells (for example that
provide functional gene III in trans, or contain an amber supressor
gene), but when used to rescue phage antibodies, will only
incorporate the gene III antibody fusion encoded by the phagemid
into the released phage particle.
Example 19
Transformation Efficiency of pAT-3 and pCAT-3 scFv D1.3
Phagemids
[0442] pUC 19, pCAT-3 and pCAT-3 scFv D1.3 plasmid DNAs, and
fdCAT-2 phage DNA was prepared, and used to transform E. coli TG1,
pCAT-3 and pCAT-3 scFv D1.3 transformations were plated on SOB agar
containing 100 .mu.g/ml ampicillin and 2% glucose, and incubated
overnight at 30.degree. C. fdCAT-2 transformations were plated on
TY agar containing 15 .mu.g/ml tetracycline and incubated overnight
at 37.degree. C. Transformation efficiencies are expressed as
colonies per .mu.g of input DNA. TABLE-US-00015 DNA Transformation
efficiency pUC 19 1 10.sup.9 pCAT-3 1 10.sup.8 pCAT-3scFv D1.3 1
10.sup.8 fd CAT-2 8 10.sup.5
[0443] As expected, transformation of the phagemid vector is
approximately 100-fold more efficient that the parental fdCAT-2
vector. Furthermore, the presence of a scFv antibody fragment does
not compromise efficiency. This improvement in transformation
efficiency is practically useful in the generation of phage
antibodies libraries that have large repertoires of different
binding specificities.
Example 20
PCR Assembly of a Single Chain Fv Library from an Immunised
Mouse
[0444] To demonstrate the utility of phage for the selection of
antibodies from repertoires, the first requirement is to be able to
prepare a diverse, representative library of the antibody
repertoire of an animal and display this repertoire on the surface
of bacteriophage fd.
[0445] Cytoplasmic RNA was isolated according to example 14 from
the pooled spleens of five male Balb/c mice boosted 8 weeks after
primary immunisation with 2-phenyl-5-oxazolone (ph OX) coupled to
chicken serum albumin. cDNA preparation and PCR assembly of the
mouse VH and VL kappa repertoires for phage display was as
described in example 14. The molecules thus obtained were ligated
into fdCAT2.
[0446] Vector fdCAT2 was extensively digested with Not1 and ApaL1.,
purified by electroelution (Sambrook et al. 1989 supra) and 1 .mu.g
ligated to 0.5 .mu.g (5 .mu.g for the hierarchial libraries: see
example 22) of the assembled scFv genes in 1 ml with 8000 units T4
DNA ligase (New England Biolabs). The ligation was carried out
overnight at 16.degree. C. Purified ligation mix was electroporated
in six aliquots into MC1061 cells (w. J. Dower, J. F. Miller &
C. W. Ragsdale Nucleic Acids Res. 16 6127-6145 1988) and plated on
NZY medium (Sambrook et al. 1989 supra) with 15 .mu.g/ml
tetracycline, in 243.times.243 mm dishes (Nunc): 90-95% of clones
contained scFv genes by PCR screening. Recombinant colonies were
screened by PCR (conditions as in example 7 using primers VH1BACK
and MJK1FONX, MJK2FONX, MJK4FONX and MJK5FONX (see example 14)
followed by digestion with the frequent cutting enzyme BstN1 (New
England Biolabs, used according to the manufacturers instructions).
The library of 2.times.10.sup.5 clones appeared diverse as judged
by the variety of digestion patterns seen in FIG. 23a and FIG. 23b,
and sequencing revealed the presence of most VH groups (R. Dildrop,
Immunol. Today 5 85-86. 1984) and VK subgroups (Kabat. E. A. et al.
1987 supra) (data not shown). None of the 568 clones tested bound
to phOx as detected by ELISA as in example 9.
[0447] Thus the ability to select antibody provided by the use of
phage antibodies (as in example 21) is essential to readily isolate
antibodies with antigen binding activity from randomly combined VH
and VL domains. Very extensive screening would be required to
isolate antigen-binding fragments if the random combinatorial
approach of Huse et al. 1989 (supra) were used.
Example 21
Selection of Antibodies Specific for 2-phenyl-5-oxazolone from a
Repertoire Derived from an Immunised Mouse
[0448] The library prepared in example 20 was used to demonstrate
that ability of the phage system to select antibodies on the basis
of their antibody specificity.
[0449] None of the 568 clones tested from the unselected library
bound to phOx as detected by ELISA.
[0450] Screening for binding of the phage to hapten was carried out
by ELISA: 96-well plates were coated with 10 .mu.g/ml phOx-BSA or
10 .mu.g/ml BSA in phosphate-buffered saline (PBS) overnight at
room temperature. Colonies of phage-transduced bacteria were
inoculated into 200 .mu.l 2.times.TY with 12.5 .mu.g/ml
tetracycline in 96-well plates (`cell wells`, Nuclon) and grown
with shaking (300 rpm) for 24 hours at 37.degree. C. At this stage
cultures were saturated and phage titres were reproducible
(10.sup.10 TU/ml). 50 .mu.l phage supernatant, mixed with 50 .mu.l
PBS containing 4% skimmed milk powder, was then added to the coated
plates. Further details as in example 9.
[0451] The library of phages was passed down a phOx affinity column
(Table 4A), and eluted with hapten. Colonies from the library
prepared in example 22 were scraped into 50 ml 2.times.TY medium
and shaken at 37.degree. C. for 30 min. Liberated phage were
precipitated twice with polyethylene glycol and resuspended to
10.sup.12 TU (transducing units)/ml in water (titred as in example
8). For affinity selection, a 1 ml column of phOx-BSA-Sepharose (O.
Makela, M. Kaartinen, J. L. T. Pelonen and K. Karjalainen J. Exp.
Med. 148 1644-1660, 1978) was washed with 300 ml phosphate-buffered
saline (PBS), and 20 ml PBS containing 2% skimmed milk powder
(MPBS). 10.sup.12 TU phage were loaded in 10 ml MPBS, washed with
10 ml MPBS and finally 200 ml PBS. The bound phage were eluted with
5 ml 1 mM 4-.epsilon.-amino-caproic acid methylene
2-phenyl-oxazol-5-one (phOx-CAP; O. Makela et al. 1978, supra).
About 10.sup.6 TU eluted phage were amplified by infecting 1 ml log
phase E. coli TG1 and plating as above. For a further round of
selection, colonies were scraped into 10 ml 2.times.TY medium and
then processed as above. Of the eluted clones, 13% were found to
bind to phOx after the first round selection, and ranged from poor
to strong binding in ELISA.
[0452] To sequence clones, template DNA was prepared from the
supernatants of 10 ml cultures grown for 24 hours, and sequenced
using the dideoxy method and a Sequenase kit (USB), with primer
LINKFOR (see example 14) for the VH genes and primer fdSEQ1 (5'-GAA
TTT TCT GTA TGA GG-3') (SEQ ID NO:36) for the Vk genes.
Twenty-three of these hapten-binding clones were sequenced and
eight different VH genes (A to H) were found in a variety of
pairings with seven different Vk genes (a to g) (FIG. 24). Most of
the domains, such as VH-B and vk-d were `promiscuous`, able to bind
hapten with any of several partners.
[0453] The sequences of the V-genes were related to those seen in
the secondary response to phOx, but with differences (FIG. 24).
Thus phOx hybridomas from the secondary response employ somatically
mutated derivatives of three types of Vk genes--Vkoxl. `Vkox-like`
and Vk45.1 genes (C. Berek, G. M. Griffiths & C. Milstein,
Nature 316 412-418 (1985). These can pair with VH genes from
several groups, from Vkoxl more commonly pairs with the VHoxl gene
(VH group 2. R.Dildrop uupra). Vkoxl genes are always, and
Vkox-like genes often, found in association with heavy chains
(including VHoxl) and contain a short five residue CDR3, with the
sequence motif Asp-X-Gly-X-X (SEQ ID NO:37) in which the central
glycine is needed to create a cavity for phOx. In the random
combinatorial library however, nearly all of the VH genes belonged
to group 1, and most of the Vk genes were .alpha.-like and
associated with VH domains with a five residue CDR3, motif
Asp/Asn-X-Gly-X-X (SEQ ID NO:38) (FIG. 24). Vkoxl and VHoxl were
found only once (Vk-f and VH-E), and not in combination with each
other. Indeed Vk-f lacks the Trp91 involved in phOx binding and was
paired with a VH (VH-C) with a six residue CDR3.
[0454] A matrix combination of VH and VK genes was identified in
phOx-binding clones selected from this random combinational
library. The number of clones found with each combination are shown
in FIG. 25. The binding to phOx-BSA, as judged by the ELISA signal,
appeared to vary (marked by shading in FIG. 25). No binding was
seen to BSA alone.
[0455] A second round of selection of the original, random
combinational library from immune mice resulted in 93% of eluted
clones binding phOx (Table 4). Most of these clones were Vk-d
combinations, and bound strongly to phOx in ELISA (data not shown).
Few weak binders were seen. This suggested that affinity
chromatography had not only enriched for binders, but also for the
best.
[0456] Florescence quench titrations determined the Kd of VH-B/Vk-d
for phOx-GABA as 10.sup.-8 M (example 23), indicating that
antibodies with affinities representative of the secondary response
can be selected from secondary response, only two (out of eleven
characterised) secrete antibodies of a higher affinity than
VH-B/Vk-d (C. Berek et al. 1985 supra). The Kd of VH-B/Vk-b for
phOx-GABA was determined as 10.sup.-5 M (example 23). Thus phage
bearing scFv fragments with weak affinities can be selected with
antigen, probably due to the avidity of the multiple antibody heads
on the phage.
[0457] This example shows that antigen specificities can be
isolated from libraries derived from immunised mice. It will often
be desired to express these antibodies in a soluble form for
further study and for use in therapeutic and diagnostic
applications. Example 23 demonstrates determination of the affinity
of soluble scFv fragments selected using phage antibodies. Example
27 demonstrates that soluble fragments have similar properties to
those displayed on phage. For many purposes it will be desired to
construct and express an antibody molecule which contains the Fc
portions of the heavy chain, and perhaps vary the immunoglobulin
isotype. To accomplish this, it is necessary to subclone the
antigen binding sites identified using the phage selection system
into a vector for expression in mammalian cells, using methodology
similar to that described by Orlandi, R. et al. (1989, supra). For
instance, the VH and VL genes could be amplified separately by PCR
with primers containing appropriate restriction sites and inserted
into vectors such as pSV-gpt HuIgG1 (L. Riechmann, et al, Nature
332, 323-327), 1988) which allows expression of the VH domain as
part of a heavy chain IgG1 isotype and pSV-hyg HuCK which allows
expression of the VL domain attached to the K light chain constant
region. Furthermore, fusions of VH and VL domains can be made with
genes encoding non-immunoglobulin proteins, for example,
enzymes.
Example 22
Generation of Further Antibody Specificities by the Assembly of
Hierarchical Libraries
[0458] Further antibody specificities were derived from the library
prepared and screened in examples 20 and 21 using a hierarchical
approach.
[0459] The promiscuity of the VH-B and Vk-d domains prompted the
applicants to force further pairings, by assembling these genes
with the entire repertoires if either Vk or VH genes from the same
immunised mice. The resulting `hierarchical` libraries,
(VH-B.times.Vk-rep and VH-rep.times.Vk-d), each with
4.times.10.sup.7 members, were subjected to a round of selection
and hapten-binding clones isolated (Table 4). As shown by ELISA,
most were strong binders. By sequencing twenty-four clones from
each library, the applicants identified fourteen new partners for
VH-B and thirteen for Vk-d (FIG. 24). Apart from VH-B and Vk-c,
none of the previous partners (or indeed other clones) from the
random combinatorial library was isolated again. Again the Vk genes
were mainly ox-like and the VH genes mainly group 1 (as defined in
Dildrop, R. 1984 supra), but the only examples of Vkoxl (vk-h, -p,
-q and -r) have Trp91, and the VH-CDR3 motif Asp-X-Gly-X-X (SEQ ID
NO:37) now predominates. Thus some features of the phOx hybridomas
seemed to emerge more strongly in the hierarchial library. The new
partners differed from each other mainly by small alterations in
the CDRs, indicating that much of the subtle diversity had remained
untapped by the random combinatorial approach. More generally it
has been shown that a spectrum of related antibodies can be made by
keeping one of the partners fixed and varying the other, and this
could prove invaluable for fine tuning of antibody affinity and
specificity.
[0460] Therefore, again, phage antibodies allow a greater range of
antibody molecules to be analysed for desired properties.
[0461] This example, and example 21, demonstrate the isolation of
individual antibody specificities through display on the surface of
phage. However, for some purposes it may be more desirable to have
a mixture of antibodies, equivalent to a polyclonal antiserum (for
instance, for immunoprecipitation). To prepare a mixture of
antibodies, one could mix clones and express soluble antibodies or
antibody fragments or alternatively select clones from a library to
give a highly enriched pool of genes encoding antibodies or
antibody fragments directed against a ligand of interest and
express antibodies from these clones.
Example 23
Selection of Antibodies Displayed on Bacteriophage with Different
Affinities for 2-phenyl-5-oxazolone Using Affinity
Chromatography
[0462] The ELISA data shown in example 21 suggested that affinity
chromatography had not only enriched for binders, but also for the
best. To confirm this, the binding affinities of a strong binding
and a weak binding phage were determined and then demonstrated that
they could be separated from each other using affinity
chromatography.
[0463] Clones VH-B/Vk-b and VH-B/Vk-d were reamplified with
MJK1FONX, MJK2FONX, MJK4FONX and MJK5FONX (see example 14) and
VH1BACK-Sfil (5'-TCG CGG CCC AGC CGG CCA TGG CC(G/C) AGG
T(C/G)(A/C) A(A/G)C TGC AG(C/G) AGT C(A/T)G G-3') (SEQ ID NO:39), a
primer that introduces an SfiI site (underlined) at the 5' end of
the VH gene. VH-B/Vk-d was cloned into a phagemid, e.g., pJM1 (a
gift from A. Griffiths and J. Marks) as an SfiI-NotI cassette,
downstream of the pelB leader for periplasmic secretion (M. Better
at al. supra), with a C-terminal peptide tag for detection (see
example 24 and figure), and under the control of a P.sub.L promoter
(H. Shimatake & M. Rosenberg, Nature, 292, 128-132, 1981). The
phagemid should have the following features: a) unique SfiI and
Not1 restriction sites downstream of a pelB leader; b) a sequence
encoding a C-terminal peptide tag for detection; and c) a
.lamda.P.sub.L promoter controlling expression. 10 litre cultures
of E. coli N4830-1 (M. E. Gottesman, S. Adhya & A. Das, J. Mol.
Biol., 140, 57-75, 1980) harbouring each phagemid were induced as
in K. Nagai & H. C. Thogerson (Methods Enzymol 153 461-481
1987) and supernatants precipitated with 50% ammonium sulphate. The
resuspended precipitate was dialysed into PBS+0.2 mM EDTA (PBSE),
loaded onto a 1.5 ml column of phOx:Sepharose and the column washed
sequentially with 100 ml PBS: 100 ml 0.1 M Tris-HC1, 0.5 M NaC1, pH
8.0: 10 ml 50 mM citrate, pH 5.0: 10 ml 50 mM citrate, pH4.0, and
20 ml 50 mM glycine, pH 3.0. scFv fragments were eluted with 50 mM
glycine, pH 2.0, neutralised with Tris base and dialysed against
PBSE. VH-B/Vk-b was cloned into a phagemid vector based on pUC119
encoding identical signal and tag sequences to pJM1, and expression
induced at 30.degree. C. in a 10 litre culture of E. coli TG1
harbouring the phagemid as in D. de Bellis & I. Schwartz (1980
Nucleic Acids Res 18 1311). The low affinity of clone VH-B/Vk-b
made its purification on phOx-Sepharose impossible. Therefore,
after concentration by ultrafiltration (Filtron, Flowgen), the
supernatant (100 ml of 600 ml) was loaded onto a 1 ml column of
protein A-Sepharose coupled (E. Harlow & D. Lane, 1988, supra)
to the monoclonal antibody 9E10 (Evan, G. I. et al., Mol. Cell
Biol., 5, 3610-3616, 1985) that recognises the peptide tag. The
column was washed with 200 ml PBS and 50 ml PBS made 0.5 M in NaC1.
scFv fragments were eluted with 100 ml 0.2M glycine, pH 3.0, with
neutralisation and dialysis as before.
[0464] The Kd (1.0.+-.0.2.times.10.sup.8 M) for clone VH-B/Vk-d was
determined by fluorescence quench titration with 4-E-amino-butyric
acid methylene 2-phenyl-oxazol-5-one (phOx-GABA Co. Makela et al,
1978 supra). Excitation was at 280 nm, emission was monitored at
340 nm and the K.sub.d calculated. The K.sub.d of the low affinity
clone VH-B/Vk-b was determined as 1.8.+-.0.3.times.10-.sup.5 M (not
shown). To minimise light adsorption by the higher concentrations
of phOx-GABA required, excitation was at 260 nm and emission was
monitored at 304 nm. In addition the fluorescence values were
divided by those from a parallel titration of the lysozyme binding
Fv fragment D1.3. The value was calculated as in H. N. Eisen, Meth.
Med. Res., 10, 115-121, 1964. A mixture of clones VH-B/Vk-b and
VH-B/Vk-d, 7.times.10.sup.10 TU phage in the ratio 20 VH-B/Vk-b:1
VH-B/Vk-d were loaded onto a phOx-BSA-Sepharose column in 10 ml
MPBS and eluted as above. Eluted phage were used to reinfect E.
coli TG1, and phage produced and harvested as before. Approximately
10.sup.11 TU phage were loaded onto a second affinity column and
the process repeated to give a total of three column passes.
Dilutions of eluted phage at each stage were plated in duplicate
and probed separately with oligonucleotides specific for Vk-b
(5'-GAG CGG GTA ACC ACT GTA CT-3') (SEQ ID NO:40) or Vk-d (5'-GAA
TGG TAT AGT ACT ACC CT-3') (SEQ ID NO:41). After these two rounds,
essentially all the eluted phage were VH-B/Vk-d (table 4).
[0465] Therefore, phage antibodies can be selected on the basis of
the antigen affinity of the antibody displayed.
Example 24
Construction of Phagemid pHEN1 for the Expression of Antibody
Fragments Expressed on the Surface of Bacteriophage Following
Superinfection
[0466] The phagemid pHEN1 (FIG. 26A) is a derivative of pUC119
(Vieira, J. & Messing, J. Methods Enzymol, 153, pp 3-11, 1987).
The coding region of g3p from fdCAT2, including signal peptide and
cloning sites, was amplified by PCR, using primers G3FUFO and
G3FUBA (given below) (which contain EcoRI and HindIII sites
respectively), and cloned as a HindIII-EcoRI fragment into pUC119.
The HindIII-NotI fragment encoding the g3p signal sequence was then
replaced by a pelB signal peptide (Better, M. et al., Science, 240,
1041-1043, 1988) with an internal SfiI site, allowing antibody
genes to be cloned as fiI-NotI fragments. A peptide tag, c-myc,
(Munro, S. & Pelham, H. Cell 46 291-300, 1986) was introduced
directly after the NotI site by cloning an oligonucleotide
cassette, and followed by an amber codon introduced by
site-directed mutagenesis using an in vitro mutagenesis kit
(Amersham International) (FIG. 26B). TABLE-US-00016 G3FUFO, 5'-CAG
TGA ATT CTT ATT AAG (SEQ ID NO:42) ACT CCT TAT TAC GCA GTA TGT TAG
C-3'; G3FUBA, 5'-TGC GAA GCT TTG GAG CCT (SEQ ID NO:43) TTT TTT TTG
GAG ATT TTC AAC G-3';
Example 25
Display of Single Chain Fv and Fab Fragments Derived from the
Anti-Oxazolone Antibody NQ10.12.5 on Bacteriophage fd Using pHEN1
and fdCAT2
[0467] A range of constructs (see FIG. 27) were made from a clone
(essentially construct II in pUC19) designed for expression in
bacteria of a soluble Fab fragment (Better et al., 1988, see above)
from the mouse anti-phOx (2-phenyl-5-oxazolone) antibody NQ10.12.5
(Griffiths, G. M., et al., Nature, 312, 271-275, 1984). In
construct II, the V-regions are derived from NQ10.12.5 and attached
to human Ck and CH1 (.gamma.1 isotype) constant domains. The
C-terminal cysteine residues, which normally form a covalent link
between light and heavy antibody chains, have been deleted from
both the constant domains. To clone heavy and light chain genes
together as Fab fragments (construct II) or as separate chains
(constructs III and IV) for phage display, DNA was amplified from
construct II by PCR to introduce a NotI restriction site at the 3'
end, and at the 51 end either an ApaLI site (for cloning into
fd-CAT2) or SfiI sie (for cloning into pHEN1). The primers
FABNOTFOK with VH1BACKAPA (or VH1BACKSFI15) were used for PCR
amplification of genes encoding Fab fragments (construct II), the
primers FABNOTFOH with VH1BACKAPA (or VH1BACKSFI15) for heavy
chains (construct III), and the primers FABNOTFOK and MVKBAAPA (or
MVKBASFI) for light chains (construct IV).
[0468] The single-chain Fv version of NQ10.12.5 (construct I) has
the heavy (VH) and light chain (Vk) variable domains joined by a
flexible linker (Gly.sub.4Ser).sub.3 (Huston, J. S. et al. Proc.
Natl. Acad. Sci., USA, 85, 5879-5883, 1988) and was constructed
from construct II by `splicing by overlap extension` as in example
14. The assembled genes were reamplified with primers VK3F2NOT and
VH1BACKAPA (or VH1BACKSFI15) to append restriction sites for
cloning into fd-CAT2 (ApaLI-NotI) or pHEN1 (SfiI-NotI).
TABLE-US-00017 VH1BACKAPA, 5'-CAT GAC CAC AGT GCA (SEQ ID NO:44)
CAG GT(C/G) (A/C)A (A/G) CTG CAG (C/G)AG TC(A/T) GG-3';
VH1BACKSFI15, 5'-CAT GCC ATG ACT CGC (SEQ ID NO:45) GGC CCA GCC GGC
CAT GGC C(C/G)A GGT (C/G) (A/C)A (A/G)CT GCA G (C/G)A GTC
(A/T)GG-3'; FABNOTFOH, 5'-CCA CGA TTC TGC GGC (SEQ ID NO:46) CGC
TGA AGA TTT GGG CTC AAC TTT CTT GTC GAC-3'; FABNOTFOK, 5'-CCA CGA
TTC TGC GGC (SEQ ID NO:47) CGC TGA CTC TCC GCG GTT GAA GCT CTT TGT
GAC-3'; MVKBAAPA, 5'-CAC AGT GCA CTC GAC (SEQ ID NO:48) ATT GAG CTC
ACC CAG TCT CCA-3'; MVKBASFI, 5'-CAT GAC CAC GCG GCC (SEQ ID NO:49)
CAG CCG GCC ATG GCC GAC ATT GAG CTC ACC CAG TCT CCA-3'; VK3F2NOT,
5'-TTC TGC GGC CGC CCG (SEQ ID NO:50) TTT CAG CTC GAG CTT GGT
CCC-3'.
Restriction Sites are Underlined. Rescue of Phage and Phagemid
Particles
[0469] Constructs I-IV (FIG. 27) were introduced into both fd-CAT2
and pHEN1. Phage fd-CAT2 (and fd-CAT2-I, II, III or IV) was taken
from the supernatant of infected E. coli TG1 after shaking at
37.degree. C. overnight in 2.times.TY medium with 12.5 .mu.g/ml
tetracycline, and used directly in ELISA. Phagemid pHEN1 (and
pHEN1-I and II) in E. coli TG1 (supE) were grown overnight in 2 ml
2.times.TY medium, 100 .mu.g/ml ampicillin, and 1% glucose (without
glucose, expression of g3p prevents later superinfection by helper
phage). 10 .mu.l of the overnight culture was used to innoculate 2
ml of 2.times.TY medium, 100 .mu.g/ml ampicillin, 1% glucose, and
shaken at 37.degree. C. for 1 hour. The cells were washed and
resuspended in 2.times.TY, 100 .mu.g/ml ampicillin, and phagemid
particles rescued by adding 2 .mu.l (10.sup.8 pfu) VCSM13 helper
phage (Stratagene). After growth for one hour, 4 .mu.l kanamycin
(25 mg/ml) was added, and the culture grown overnight. The phagemid
particles were concentrated 10-fold for ELISA by precipitation with
polyethylene glycol.
ELISA
[0470] Detection of phage binding to 2-phenyl-5-oxazolone (phOx)
was performed as in example 9. 96-well plates were coated with 10
.mu.g/ml phOx-BSA or 10 .mu.g/ml BSA in PBS overnight at room
temperature, and blocked with PBSS containing 2% skimmed milk
powder. Phage (mid) supernatant (50 .mu.l) mixed with 50 .mu.l PBS
containing 4% skimmed milk powder was added to the wells and
assayed. To detect binding of soluble scFv or Fab fragments
secreted from pHEN1, the c-myc peptide tag described by Munro and
Pelham 1986 supra, was detected using the anti-myc monoclonal 9E10
(Evan, G. I., et al. Mol Cell Biol, 5, 3610-3616, 1985) followed by
detection with peroxidase-conjugated goat anti-mouse
immonoglobulin. Other details are as in example 9.
[0471] The constructs in fdCAT2 and pHEN1 display antibody
fragments of the surface of filamentous phage. The phage vector,
fd-CAT2 (FIG. 8) is based on the vector fd-tet (Zacher, A. N., et
al., Gene 9 127-140, 1980) and has restriction sites (ApaLI and
NotI) for cloning antibody genes (or other protein) genes for
expression as fusions to the N-terminus of the phage coat protein
g3p. Transcription of the antibody-g3p fusions in fd-CAT2 is driven
from the gene III promoter and the fusion protein targetted to the
periplasm by means of the g3p leader. Fab and scFv fragments of
NQ10.12.5 cloned into fd-CAT2 for display were shown to bind to
phOx-BSA (but not BSA) by ELISA (table 5). Phage were considered to
be binding if A.sub.405 of the sample was at least 10-fold greater
than the background in ELISA.
[0472] The phagemid vector, pHEN1 (FIG. 26A), is based upon pUC119
and contains restriction sites (SfiI and NotI) for cloning the
fusion proteins. Here the transcription of antibody-g3p fusions is
driven from the inducible lacZ promoter and the fusion protein
targetted to the periplasm by means of the pelB leader. Phagemid
was rescued with VCSM13 helper phage in 2.times.TY medium
containing no glucose or IPTG: under these conditions there is
sufficient expression of antibody-g3p. Fab and scFv fragments of
NQ10.12.5 cloned into pHEN1 for display were shown to bind to
phOx-BSA (but not BSA) by ELISA (Table 5) using the same criterion
as above.
[0473] An alternative methodology for preparing libraries of Fab
fragments expressed on the surface of phage would be to:
1. Prepare a library of phage expressing heavy chain (VHCH) genes
from inserts in the phage genome.
2. Prepare a library of light chain genes in a plasmid expression
vector in E. coli, preferably a phagemid, and isolate the soluble
protein light chains expressed from this library.
3. Bind the soluble protein light chains from the library to the
heavy chain library displayed on phage.
4. Select phage with the desired properties of affinity and
specificity. These will encode the heavy chain (VHCH) genes.
[0474] 5. Isolate the light chain genes encoding light chains which
form suitable antigen binding sites in combination with the
selected heavy chains, preferably by using superinfection of
bacteria, containing phagemid expressing the light chain, with
phage expressing the selected heavy chain (as described in example
20) and then assaying for antigen binding.
Example 26
Rescue of Phagemid Encoding a Gene III Protein Fusion with Antibody
Heavy or Light Chains by Phage Encoding the Complementary Antibody
Chain Displayed on Phage and the Use of this Technique to Make Dual
Combinatorial Libraries
[0475] With random combinatorial libraries there is a limitation on
the potential diversity of displayed Fab fragments due to the
transformation efficiency of bacterial cells. Described here is a
strategy (dual combinatorial libraries) to overcome this problem,
potentially increasing the number of phage surveyed by a factor of
10.sup.7.
[0476] For assembly of heavy and light chains expresses from
different vectors, phagemid (pHEN1-III or IV) was grown in E. coli
HB2151 (a non-supressor strain) to allow production of soluble
chains, and rescued as above (example 27) except that helper phage
were used expressing partner chains as fusions to g3p (10.sup.9 TU
fd-CAT2-IV or III respectively) and 2 .mu.l tetracycline (12.5
mg/ml) in place of kanamycin. Separate Vectors to Encode Fab Heavy
and Light Chains
[0477] The heavy and light chains of Fab fragments can be encoded
together in the same vector (example 25) or in different vectors.
To demonstrate this the heavy chain (construct III) was cloned into
pHEN1 (to provide soluble fragments) and the light chain (construct
IV) into fd-CAT2 (to make the fusion with g3p). The phagemid
pHEN1-III, grown in E. coli HB2151 (non-supressor) was rescued with
fd-CAT2-IV phage, and phage(mid) shown to bind to phOx:BSA, but not
to BSA (Table 5). This demonstrates that soluble light chain is
correctly associating with the heavy chain anchored to the g3p,
since neither heavy chain nor light chain alone bind antigen (Table
5).
[0478] Similar results were obtained in the reverse experiment
(with phagemid pHEN-1-IV and fd-CAT2-III phage) in which the heavy
chain was produced as a soluble molecule and the light chain
anchored to g3p (Table 5). Hence a Fab fragment is assembled on the
surface of phage by fusion of either heavy or light chain to g3p,
provided the other chain is secreted using the same or another
vector (FIG. 28).
[0479] The resulting phage population is a mixture of phage and
rescued phagemid. The ratio of the two types of particles was
assessed by infecting log phase E. coli TG1 and plating on TYE
plates with either 15 .mu.g/ml tetracycline (to select for fd-CAT2)
or 100 .mu.g/ml ampicillin (to select for pHEN1). The titre of
fd-CAT2 phage was 5.times.10.sup.11 TU/ml and the titre of pHEN1
2.times.10.sup.10 TU/ml, indicating a packaging ratio of 25 phage
per phagemid.
[0480] Demonstrated here is an alternative strategy involving
display of the heterodimeric antibody Fab fragments on the surface
of phage. One of the chains is fused to g3p and the other is
secreted in soluble form into the periplasmic space of the E. coli
where it associates non-covalently with the g3p fusion, and binds
specifically to antigen. Either the light or heavy chain can be
fused to the g3p: they are displayed on the phage as Fab fragments
and bind antigen (FIG. 28). Described are both phage and phagemid
vectors for surface display. Phagemids are probably superior to
phage vectors for creation of large phage display libraries.
Particularly in view of their higher transfection efficiencies (Two
to three orders of magnitude higher), allowing larger libraries to
be constructed. The phagemid vector, pHEN1 also allows the
expression of soluble Fab fragments in non-suppressor E. coli.
[0481] Also demonstrated here is that heavy and light chains
encoded on the same vector (construct II), or on different vectors
(constructs III and IV) can be displayed as Fab fragments. This
offers two distinct ways of making random combinatorial libraries
for display. Libraries of heavy and light chain genes, amplified by
PCR, could be randomly linked by a `PCR assembly` process (example
14) based on `splicing by overlap extension`, cloned into
phage(mid) display vectors and expressed from the same promoter as
part of the same transcript (construct II) as above, or indeed from
different promoters as separate transcripts. Here the phage(mid)
vector encodes and displays both chains. For a combinatorial
library of 10.sup.7 heavy chains and 10.sup.7 light chains, the
potential diversity of displayed Fab fragments (10.sup.14) is
limited by the transfection efficiency of bacterial cells by the
vector (about 10.sup.9 clones per .mu.g cut and ligated plasmid at
best) (W. J. Dower, et al, Nucl. Acids. Res., 16, 6127-6145, 1988).
Libraries thus prepared are analogous to the random combinatorial
library method described by Huse, W. D. et al, Science, 246,
1275-1281 (1989), but have the important additional feature that
display on the surface of phage gives a powerful method of
selecting antibody specificities from the large number of clones
generated.
[0482] Alternatively, libraries of heavy and light chains could be
cloned into different vectors for expression in the same cell, with
a phage vector encoding the g3p fusion and a phagemid encoding the
soluble chain. The phage acts as a helper, and the infected
bacteria produced both packaged phage and phagemid. Each phage or
phagemid displays both chains but encodes only one chain and thus
only the genetic information for half of the antigen-binding site.
However, the genes for both antibody chains can be recovered
separately by plating on the selective medium, suggesting a means
by which mutually complementary pairs of antigen binding heavy and
light chain combinations could be selected from random
combinatorial libraries. For example, a light chain repertoire on
fd phage could be used to infect cells harbouring a library of
soluble heavy chains on the phagemid. The affinity purified
phagemid library could then be used to infect E. coli, rescued with
the affinity purified phage library, and the new combinatorial
library subjected to a further round of selection. Thus, antibody
heavy and light chain genes are reshuffled after each round of
purification. Finally, after several rounds, infected bacteria
could be plated and screened individually for antigen-binding
phage. Such `dual` combinatorial libraries are potentially more
diverse than those encoded on a single vector. By combining
separate libraries of 10.sup.7 light chain phage(mid)s, the
diversity of displayed Fab fragments (potentially 10.sup.14) is
limited only by the number of bacteria (10.sup.12 per litre). More
simply, the use of two vectors should also facilitate the
construction of `hierarchical` libraries, in which a fixed heavy or
light chain is paired with a library or partners (example 22),
offering a means of `fine-tuning` antibody affinity and
specificity.
Example 27
Induction of Soluble scFv and Fab Fragments Using Phagemid
pHEN1
[0483] Further study of antibodies which have been expressed on the
surface of phage would be greatly facilitated if it is simple to
switch to expression in solution.
[0484] E. coli HB2151 was infected with pHEN phagemid (pHEN1-I or
II), and plated on YTE, 100 .mu.g/ml ampicillin plates. Colonies
were shaken at 37.degree. C. in 2.times.TY medium, 100 .mu.g/ml
ampicillin, 1% glucose to OD.sub.550=0.5 to 1.0. Cells were
pelleted, washed once in 2.times.TY medium, resuspended in medium
with 100 .mu.g/ml ampicillin, 1 mM isopropyl
.beta.-D-thiogalactoside (IPTG), and grown for a further 16 hours.
Cells were pelleted and the supernatant, containing the secreted
chains, used directly in ELISA.
[0485] The phagemid pHEN1 has the advantage over phage fd-CAT2, in
that antibody can be produced either for phage display (by growth
in supE strains of E. coli) or as a tagged soluble fragment (by
growth in non-suppressor strains), as a peptide tag (example 24)
and amber codon were introduced between the antibody and g3p.
Secretion of soluble Fab fragments from pHEN1-II or scFv fragments
from pHEN1-I was demonstrated after growth in E. coli HB2151 and
induction with IPTG using Western blots (FIG. 29). For detection of
secreted proteins, 10 .mu.l supernatant of induced cultures were
subjected to SDS-PAGE and proteins transferred by electroblotting
to Immobilon-P (Millipore). Soluble heavy and light chain were
detected with goat polyclonal anti-human Fab antiserum (Sigma) and
peroxidase conjugated rabbit anti-goat immunoglobulin (Sigma), each
at a dilution of 1:1000. The tagged VK domain was detected with
9E10 antibody (1:1000) and peroxidase conjugated goat anti-mouse
immunoglobulin (Fc specific) (1:1000) (Sigma) or with a peroxidase
labelled anti-human CK antiserum (Dako). 3,3'-diaminobenzidine
(DAB; Sigma) was used as peroxidase substrate (Harlow E., et al.
1988 Supr). With the scFv, the fragments were detected using the
9E10 anti-myc tag antibody (data not shown). With the Fab, only the
light chain was detected by 9E10 (or anti-human CK) antibody, as
expected, while the anti-human Fab antiserum detected both heavy
and light chains. Binding of the soluble scFv and Fab fragments to
phOx-BSA (but not to BSA) was also demonstrated by ELISA (Table
5B). Thus scFv and Fab fragments can be displayed on phage or
secreted as soluble fragments from the same phagemid vector.
Example 28
Increased Sensitivity in ELISA Assay of Lysozyme Using FDTscFvD1.3
as Primary Antibody Compared to Soluble scFvD1.3
[0486] In principle the use of phage antibodies should allow more
sensitive immunoassays to be performed than with soluble
antibodies. Phage antibodies combine the ability to bind a specific
antigen with the potential for amplification through the presence
of multiple (ca.2800) copies of the majorcoat protein (g8p) on each
virion. This would allow the attachment of several antibody
molecules directed against M13 to each virion followed by the
attachment of several molecules of peroxidase-conjugated
anti-species antibody (anti-sheep) IgG in the case below). Thus for
every phage antibody bound to antigen there is the potential for
attaching several peroxidase molecules whereas when a soluble
antibody is used as the primary antibody this amplification will
not occur.
[0487] ELISA plates were coated overnight at room temperature using
200 .mu.l of 10 fold dilutions of hen egg lysozyme (1000, 100, 10,
1, 0.1 and 0.01 .mu.g/ml) in 50 mM NaHCO.sub.3, pH9.6. ELISA was
performed as described in example 4 except that (i) incubation with
anti-lysozyme antibody was with either FDTscFvD1.3 (pAb; 10.sup.11
phage per well; 1.6 mol) or soluble affinity purified scFvD1.3 (18
.mu.g per well; 0.7 nmol) (ii) incubation with second antibody was
with 1/100 dilution of sheep anti-M13 serum for FDTscFvD1.3 samples
or with or 1/100 dilution of rabbit anti-scFvD1.3 serum (from S.
Ward) for soluble scFvD1.3 samples (iii) peroxidase-conjugated
rabbit anti-goat immunoglobulin (Sigma; 1/5000) was used for
FDTscFvD1.3 samples and peroxidase-conjugated goat anti-rabbit
immunoglobulin (Sigma; 1/5000) was used for soluble scFvD1.3
samples. Absorbance at 405 nm was measured after 15h. The results
are shown in FIGS. 30 and 31. In these figures lysozyme
concentrations for coating are shown on a log scale of dilutions
relative to 1 .mu.g/ml. (i.e., log =-3=1 mg/ml; log=2=0.01
.mu.g/ml)
[0488] Higher signals were obtained with FDTscFvD1.3 at all
concentrations of lysozyme (FIG. 31) but the difference was very
marked at the greatest dilutions, where antigen quantities are most
limiting (FIGS. 30 and 31). This suggests that phage antibodies may
be particularly valuable for sandwich type assays where the capture
of small amounts of antigen by the primary antibody will generate
an amplified signal when phage antibodies directed against a
different epitope are used as the second antigen binding
antibody.
Example 29
Direct Rescue and Expression of Mouse Monoclonal Antibodies as
Single Chain Fv Fragments on the Surface of Bacteriophage fd.
[0489] The principle is very similar to that described in example
14. It consists of the PCR assembly of single chain antibodies from
cDNA prepared from mouse monoclonals. As an example, the rescue and
expression of two such antibodies from monoclonals expressing
antibodies against the steroid hormone oestriol is described.
A. RNA Preparation
[0490] RNA can be prepared using many procedures well known to
those skilled in the art. In this example, the use of Triton X-100
lysis, phenol/SDS RNase inactivation gave excellent results.
[0491] 1. The mouse monoclonal cells that were used here had been
harvested by centrifugation and resuspended in serum free medium.
They were then centrifuged and resuspended in saline and after a
final centrifugation step, resuspended in sterile water at
1.times.10.sup.7 cells per ml. (Normally cells would be washed in
PBS buffer and finally resuspended in PBS buffer, but these
particular cells were supplied to us as described frozen in
water.).
2. To 750 .mu.l of cells was added 250 ul of ice cold 4.times.
lysis buffer (40 mM Tris HC1 pH 7.4/4 mM MgCl.sub.2/600 mM NaC1/40
mM VRC (Veronyl ribosyl complex)/2% Triton X-100). The suspension
was mixed well and left on ice for 5 minutes.
3. Centrifugation was carried out at 4.degree. C. in a microfuge at
13000 rpm for 5 min.
The supernatant is then phenol extracted three times, phenol
chloroform extracted three times and finally, ethanol precipitated
as described in the materials and methods. The precipitate was
resuspended in 50 ul water.
4. The optical density of the RNA at 260 nm with a 2.5 ul sample in
1 ml water was measured. The RNA was checked by electrophoresis of
a 2 ug sample on a 1% agarose gel. RNA in the range of 32 ug to 42
ug was obtained by this method.
B. cDNA Preparation
[0492] The method used is the same as that described in example 14.
Two cDNA preparations were made. These were from RNA extracted from
the monoclonals known as cell lines 013 and 014 which both express
antibodies against the steroid hormone, oestriol.
C. Primary PCRs
[0493] The method used is essentially the same as that described in
example 14. The VH region was amplified with the primers VH1BACK
and VH1FOR-2. For the Vkappa region, four separate reactions were
carried out using the primer VK2BACK and either MJK1FONX, MJK2FONX,
MJK4FONX or MJK5FONX. Samples (5 ul) were checked on a 1.5% agarose
gel. From this it was observed that for cDNA prepared from the two
oestriol monoclonals the primers VK2BACK and MJK1FONX gave the best
amplification of the Vkappa region.
[0494] The VH bands and the Vkappa bands amplified with
VK2BACK/MJK1FONX were purified on 2% low melting point agarose gels
for each monoclonals. The DNA bands were excised from the gel and
purified using a dedicated GENECLEAN kit as described in example
14.
D. Preparation of Linker
[0495] The method used is essentially the same as that described in
example 14. In this case, the amplified linker DNA was purified on
a 2% agarose gel and recovered from the gel with a dedicated
"Mermaid" kit (BIO 101, GENECLEAN, La Jolla, San Diego, Calif.,
USA) using the manufacturers instructions.
E. Assembly PCRs
[0496] The method used is essentially the same as that described in
example 14. In this case, the assembled PCR product was purified on
a 2% agarose gel and recovered from the gel with a dedicated
"Mermaid" kit.
F. Adding Restriction Sites and Work-Up
[0497] The assembled product was "tagged" with Apa LI and Not I
restriction sites. The DNA was then digested with Apa LI and Not I
to give the appropriate sticky ends for cloning and then purified
on a 2% low melting point agarose gel and extracted using a
GENECLEAN kit. The method used is the same as that described in
example 14.
G. Cloning into Vector fd-CAT2
[0498] A total of 15 ug of CsC1 purified fd-CAT2 DNA was digested
with 100 units of the restriction enzyme Not I (New England
Biolabs) in a total volume of 200 ul 1.times.NEB Not I buffer with
1.times.NEB acetylated BSA for a total of 3 hours at 37.degree. C.
The vector DNA was the treated twice with 15 ul Strataclean (a
commercially available resin for the removal of protein), following
the manufacturers instructions (Stratagene, 11099 North Torrey
Pines Road, La Jolla, Calif., USA). The DNA was then ethanol
precipitated and redissolved in TE buffer (Sambrook et al., 1989
supra). The DNA was then digested with 100 units of the restriction
enzyme Apa LI (New England Biolabs) in a total volume of 200 ul
1.times.NEB Buffer 4 overnight at 37.degree. C. The vector was then
purified with a Chroma Spin 1000 column following the manufacturers
instructions (Clontech Laboratories Inc, 4030 Fabian Way, Palo
Alto, Calif., USA). This step removes the Apa LI/Not I fragment to
give cut vector DNA for maximum ligation efficiency.
[0499] Ligation reactions were carried out with 2.5-long of the DNA
insert and long of vector in a total volume of 10 ul of 1.times.NEB
ligase buffer with 1 ul of NEB ligase (New England Biolabs) at
16.degree. C. overnight (approx 16 hours).
H. Transformation and Growth
[0500] E. coli strain TG1 was made competent and transformed with
the fdCAT2 recombinant DNA as described by Sambrook et al., 1989
Supra. The cells were plated out on LBtet plates (10 g tryptone, 5
g yeast extract, 10 g NaC1, 15 g bacto-agar per litre with 15 ug/ul
of tetracycline added just before pouring the plates) and grown
overnight.
[0501] Single well isolated colonies were then inoculated into 10
ml of LBtet broth (LB medium with 15 ug/ul of tetracycline) in 50
ml tubes. After overnight growth at 35.degree. C./350 rpm in a
bench top centrifuge. The supernatants were transferred to 15 ml
centrifuge tubes and 2 ml 20% PEG 8000/2.5M NaC1 added to each.
After incubating at room temperature for 20-30 minutes, the
recombinant phage was pelleted by centrifugation at 9000 rpm in a
Sorval SM24 rotor for 30 minutes. The PEG supernatant was
discarded. Any remaining PEG was removed with a pasteur pepette
after a brief (2 minutes) centrifugation step. This last step was
repeated to make sure that no PEG remained. The phage pellet was
then resuspended in 500 ul PBS buffer. This was transferred to a
microcentrifuge tube and spun at 13000 rpm to remove any remaining
cells. The phage supernatant was transferred to a fresh tube.
I. Assay for Antibody Expression
[0502] Bacteriophage fd recombinants were screened for the
expression of antibody against oestriol by ELISA. This method is
described in example 6. In this case the following alterations are
relevant.
1. Microtitre plates were coated overnight with 40 ug/ml oestriol-6
carboxymethyloxime-BSA (Steraloids, 31 Radcliffe Road, Croydon, CRO
5QJ, England).
2. 1st antibody was the putative phage anti oestriol antibody. 50
ul of phage in a final volume of 200 ul of sterile PBS combining
0.25% gelatin was added to each well.
3. 2nd antibody was sheep anti M13 at 1:1000 dilution.
4. 3rd antibody was peroxidase conjugated rabbit anti goat
immunoglobulin.
[0503] Recombinants expressing functional antibody were detected by
incubation with the chromogenic substrate 2'2' axinobis (3-ethyl
benzthiazoline sulphonic acid). The results are shown in FIGS. 32
and 33.
Example 30
Kinetic Properties of Alkaline Phosphatase Displayed on the Surface
of Bacteriophage fd
[0504] This example demonstrates that kinetic properties of an
enzyme expressed on phage are qualitatively similar to those in
solution. Bacteriophage fd displaying alkaline phosphatase fusions
of gene 3 with either the native arginine (see example 31) or the
mutant residue alanine at position 166 (see example 11) were
prepared by PEG precipitation as described in the materials and
methods.
[0505] The kinetic parameters of alkaline phosphatase expressed on
the surface of fd phage were investigated in 1M Tris/HC1, pH8.0 at
20.degree. C. with 1 ml 4-nitrophenyl phosphate as substrate. The
reactions were initiated by the addition of 100 .mu.l of a
phage-alkaline phosphatase fusion preparation, 50 fold concentrated
with respect to the original culture supernatant. The rate of
change of absorbance was monitored at 410 nm using a Philips 8730
spectrophotometer and the initial reaction rate calculated using a
molar absorbance of 16200 1/mol/cm. For the fdphoAla 166 enzyme but
not fdphoArg166 a lag phage was seen following this addition, the
reaction rate accelerating until a steady state was obtained after
approximately 60 to 90 secs. This steady state rate was used for
determination of kinetic parameters. No deviation form Michaelis
Menten kinetics was apparent for either phage enzyme. Values of
K.sub.m and k.sub.cat were derived from plots of s/v against s and
are shown in Table 6.
[0506] Because of the difficulty in establishing the relationship
between the number of phage particles an the number of active
enzyme dimers formed on the phage k.sub.cat values are expressed
not as absolute values, but as relative values between the two
enzyme forms. Western blots (carried out as in example 31 using
antig3p antiserum) of the phage enzyme preparations used in this
experiment showed approximately equal intensities for the full
length fusion band with the Arg166 and Ala166 enzymes when detected
using antibody directed against gene3. In these preparations the
intact fusion represents approximately 30% of the detected
material. The two preparations were therefore assumed to be
expressing approximately the same concentrations of intact
fusions.
[0507] Table 6 summarises the kinetic data from this experiment and
compares it with data from Chaidaroglou, A. et al (Biochemistry 27,
8338-8343 (1988)) obtained with soluble preparations of the wild
type and mutant enzyme forms. The same substrate and assay
conditions were used in both experiments. Soluble alkaline
phosphatase was also tested in parallel in our experiments
(K.sub.m=8.5 .mu.M; kcat=3480 mol substrate converted mol
enzyme.sup.-1 min.sup.-1).
[0508] The effect of mutating arginine at position 166 to alanine
is qualitatively similar for the phage enzyme as for the soluble
enzyme. K.sub.m is increased about 15 fold and the relative
k.sub.cat is decreased to 36% of that for wild type.
[0509] This increased K.sub.m would reflect a reduction in
substrate affinity in the phage enzyme on mutation of Arg166, as
was proposed for the soluble enzyme (Chaidaroglou et al, 1988
supra), assuming the same kinetic mechanism applies. There are,
however, some quantitative differences in the behaviour of K.sub.m
of the phage enzyme. The K.sub.m of 73 .mu.M observed for
fdphoArg166 compares with a K.sub.m of 12.7 .mu.M for the free
enzyme; the K.sub.m for fdphoAla166 is 1070 .mu.M whereas the free
mutant enzyme has a K.sub.m of 1620 .mu.M. One can speculate that
the higher K.sub.m for fdphoArg 166 and the lower K.sub.m for
fdphoAla166, compared to the soluble enzymes result from the
`anchored` alkaline phosphatase fusion molecules interacting to
form dimers in a different manner to the enzyme in free
solution.
[0510] The relative values of k.sub.cat for the Arg166 and Alal66
forms are however very similar for both the phage enzymes and the
soluble enzymes, a reduction occurring on mutation to 35 to 40% of
the value for the native enzyme. The rate limiting step,
determining k.sub.cat, for soluble phoArg166 is thought to be
dissociation of non-covalently bound phosphate from the enzyme
(Hull W. E. et al., Biochemistry, 15, 1547-1561 1976). Chaidaroglou
et al, (1988) supra suggest that, for the soluble enzyme, mutation
of Arg166 to alanine alters additional steps, one of which may be
hydrolysis of the phosphoenzyme intermediate. The similarity in the
reduction in k.sub.cat on mutation of Arg166 to alanine for the
phage enzymes suggests that the same steps may be altered in a
quantitatively similar manner in the mutant phage enzyme as in the
mutant soluble enzyme.
[0511] Thus, enzymes displayed on phage show qualitatively similar
characteristics to soluble enzymes.
Example 31
Demonstration Using Ultrafiltration that Cloned Alkaline
Phosphatase Behaves as Part of the Virus Particle
[0512] The construct fdphoAla166 (derived in example 11) was
converted back to the wild type residue (arginine) at position 166
by in vitro mutagenesis (Amersham International) using the printer
TABLE-US-00018 APARG166: 5' TAGCATTTGCGCGAGGTCACA 3'. (SEQ ID
NO:51)
This construct with the wild type insert was called
fdphoArg166.
[0513] E. coli TG1 or KS272 cells (cells with a deletion in the
endogenous phoA gene, Strauch and Beckwith, 1988 Supra) containing
either fd-phoAla166, fdphoArg166 or fd-CAT2 were grown for 16 hours
at 37.degree. C. in 2.times.TY with 15 .mu.g/ml tetracycline.
Concentrated phage were prepared as follows.
[0514] Phage-enzyme cultures are clarified by centrifugation (15
min at 10,000 rpm, 8.times.50 ml rotor, sorval RC-5B centrifuge).
Phage are precipitated by adding 1/5 volume 20% polyethylene
glycol, 2.5 M Nacl, leaving for 1 hr at 4.degree. C., and
centrifuging (as above). Phage pellets are resuspended in 10 mM
Tris-HC1, pH 8.0 to 1/100th of the original volume, and residual
bacteria and aggregated phage removed by centrifugation for 10 to
15 minutes in a bench microcentrifuge at 13000 rpm at 4.degree.
C.
[0515] SDS/Polyacrylamide gel electrophoresis and western blotting
were basically as described previously (example 2). Denatured
samples consisting of 16 .mu.l of a 50 fold concentrate of phage
were separated using a 10% SDS/polyacrylamide gel and detected with
polyclonal antiserum raised against either E. coli alkaline
phosphatase (Northumbria Biologicals, South Nelson Industrial
Estate, Cramlington, Northumberland, NE23 9HL) or against the minor
coat protein encoded by gene 3 (from Prof. I. Rasched, Universitat
Konstanz, see Stengele et al, 1990) at 1 in 1000 dilution. This was
followed by incubation with peroxidase-conjugated goat-anti-rabbit
immunoglobulin (Sigma 1 in 5000) and detection with the ECL Western
blotting system (Amersham International).
[0516] The presence of fusion proteins was confirmed by western
blotting of proteins from phage particles derived from fd-phoAla166
(phage-enzyme) or fd-CAT2 (vector phage). Detection with antiserum
raised against the gene 3 protein reveals a product of apparent
relative molecular mass (Mr) of 63,000 in vector phage (FIG. 34E).
Although this is different from the predicted molecular weight
based on the amino acid sequence (42,000), the natural product of
gene 3 has previously been reported to exhibit reduced mobility
during electrophoresis (Stengele et al, 1990).
[0517] In the fd-phoAla166 sample the largest band has an apparent
Mr of 115,000, (FIG. 34). Taking into account the aberrant mobility
of the gene 3 portion of the fusion, this is approximately the size
expected from fusing with an alkaline phosphatase domain of 47 kD.
This analysis also reveals that a proportion of the Gene3 reactive
material in this phage-enzyme preparation is present at the size of
the native gene3 product, suggesting that degradation is occurring.
In the preparation shown in FIG. 34, approximately 5-10% of the
gene 3 fusions are intact. In more recent preparations and in all
the preparations used in this example and example 32, approximately
30-60% of fusions are full length.
[0518] The protein of Mr 115,000 is the major protein observed in
Western blots of phage-enzyme derived from TG1 cells when probed
with antiserum raised against E. coli alkaline phosphatase
(anti-BAP), confirming the assignment of this band to intact
fusion. Further, when phage enzyme is prepared using KS272 cells,
which have a deletion in the endogenous phoA gene (Strauch &
Beckwith, 1988, supra.) it is also the major band. There are
additional bands at Mr 95000 and 60000 reactive with anti-BAP
antiserum which may indicate degradation of the fusion product.
[0519] The anti-BAP antiserum also reacts wit material running with
the dye front and with a molecule of Mr 45,000 but evidence
suggests that this material is not alkaline phosphatase. This
pattern is detected in PEG precipitated vector phage samples (FIG.
34C) and is not therefore contributed by protein expressed from the
cloned phoA gene. These bands are detected in culture supernatants
of cells carrying fd-CAT2 but is not detected in the supernatant of
uninfected cells (not shown) and so either represents
cross-reactivity with phage encoded material or with a PEG
precipitable cellular component leaked from infected cells (Boeke
et al, Mol. Gen. Genet. 186, 185-192 1982). Although the fragment
of Mr, 45,000 is close to the size of free alkaline phosphatase
(47,000), it is present in phage preparations from KS272 cells
which have a deletion in the phoA locus. Furthermore its mobility
is different from purified alkaline phosphatase and they can be
distinguished by electrophoresis (FIG. 34).
[0520] Ultrafiltration was used to confirm that the fusion protein
behaved as though it were part of a larger structure, as would be
expected for an enzyme bound to a phage particle. Phage samples
(100 .mu.l of a 50 fold concentrate) were passed through
ultrafiltration filters with a nominal molecular weight limit of
300000 daltons (Ultrafree-MC filters, Millipore) by centrifugation
for 5 to 15 minutes at 13,000 r.p.m. in an MSE microcentaur
microfuge. Retained material was recovered by resuspending in 100
.mu.l of 10 mM Tris, pH 8.0.
[0521] Phage-enzyme or free alkaline phosphatase (83 ng) mixed with
vector phage were passed through filters with a nominal molecular
weight limit of 300,000 daltons (Ultrafree-MC filters, Millipore).
FIG. 35A again shows that the band of Mr, 115,000 is the major
product reactive with anti-BAP antiserum. This and the other minor
products reactive with anti-BAP are present in material retained by
the ultrafiltration membrane. Analysis of retained and flow through
fractions of phage preparations derived from KS272 demonstrates
that different molecular species are being separated by the
ultrafiltration membranes. FIG. 35B shows the protein of Mr 115,000
is retained by the filter whereas the putative degradation products
of Mr 95,000 and 60,000 found in phage preparations derived from
KS272 cells, are not retained.
[0522] In mixture of alkaline phosphatase and vector phage FIG.
35B(c-f), free alkaline phosphatase (dimer size of 94,000 daltons)
is detected in the flow through as a monomer band with Mr 47,000 on
denaturing polyacrylamide gels (FIG. 35B), while the cross reactive
molecule found in vector phage preparations (Mr 45,000) is in
retained on the filter (FIG. 35B). This suggests that the cross
reactive molecule is part of the phage particle and underlines the
fact that the ultrafiltration membranes are effecting a separation.
Thus the expected fusion band in this phage-enzyme is present in
material retained on ultrafiltration membranes demonstrating that
it is part of a larger structure as would be expected for viral
bound enzyme.
[0523] Catalytic activity has been demonstrated on phage particles
expressing alkaline phosphatase. Table 7 shows that the wild type
alkaline phosphatase gene expressed on phage (fd-phoArg166) has a
specific activity (moles of substrate converted per mole of viral
particles) of 3,700/min. This is close to the turnover value of
4540/min found for purified alkaline phosphatase by Malamy and
Horecker, Biochemistry 3, 1893-1897 1964).
[0524] Chaidaroglou et al, 1988 supra have shown that substituting
alanine for arginine at the active site (residue 166) leads to a
reduction in the rate of catalysis. Preparations of phage
displaying alkaline phosphatase with this mutation derived from TG1
and KS272 show reduced specific activities of 380 and 1400 mol
substrate converted/mol phage/min respectively. Enzyme activity was
measured in the retained and flow-through fractions prepared by
ultrafiltration, shown in FIG. 35(A) and FIG. 35(B). The bulk of
activity from phage-enzyme was retained on the filters whereas the
majority of activity from free enzyme passes through. Therefore,
the enzyme activity in these fusions behaved as would be expected
for virally associated enzyme (not shown). Little or no catalytic
activity is measured in preparations of vector phage from either
TG1 or KS272 cells (Table 7), indication that the catalytic
activities above are due to phage enzyme and not contamination with
bacterial phosphatase. Addition of phage particles to soluble
enzyme does not have a significant effect on activity (Table
7).
[0525] Therefore, both the catalytic and immunochemical activity of
alkaline phosphatase have been demonstrated to be due to enzyme
which is part of the phage particle.
Example 32
Affinity Chromatography of Phage Alkaline Phosphatase
[0526] Affinity chromatography, using the specific binding
properties of enzymes has proved to be a very powerful method for
their purification. The purification of phage-enzymes by this
approach would enable the genetic material encoding the enzyme to
be isolated with the enzyme itself. Thus, mutagenesis of cloned
enzymes expressed on the surface of filamentous bacteriophage will
lead to a whole population of enzyme variants, from which variants
with desired binding properties could be isolated.
[0527] Soluble alkaline phosphatase (from calf intestine) has been
purified by binding to immobilised arsenate (a competitive
inhibitor), and eluting with inorganic phosphate, which is a
product (and competitive inhibitor) of the enzyme reaction (Brenna,
O. et al, Biochem. J. 151 291-296 1975). The applicants have
determined that soluble alkaline phosphatase from E. coli is also
retained by this matrix (not shown). In this example it is
demonstrated that phage displaying E. coli alkaline phosphatase
binds to arsenate-Sepharose and can be specifically eluted.
[0528] Arsenate-Sepharose was prepared by coupling
4-(p-aminophenylazo)phenyl arsonic acid to tyraminyl-Sepharose
according to the method of Breena et al, (1975; supra). Affinity
chromatography of phage enzyme fdphoArg166 (example 31) was carried
out in a disposable chromatography column with a 0.5 ml column
volume. Columns were prewashed with 110 volumes of column buffer
(100 mM Tris pH 8.4, 1 mM MgCl.sub.2, 0.1 mM ZnCl.sub.2, 0.1% Tween
20, Brenna et al, 1975, supra.) 1 ml of a 40 fold concentrate of
phage-enzyme (in column buffer; prepared as in example 31) was
loaded and washed through with 100 volumes of column buffer. Bound
phage-enzyme was eluted with 5 mls of column buffer containing 20
mM NaHPO.sub.4. The eluate and wash fractions were quantitated by
dot blotting onto nitrocellulose and comparing with known amounts
of phage-enzyme. The blots were detected using sheep anti-M13
antiserum (gift from M. Hobart), anti-sheep peroxidase (Sigma) and
enhanced chemiluminescent substrate (Amersham). A range of
exposures were taken.
[0529] Table 8 shows the results of affinity chromatography of
phage displaying alkaline phosphatase on arsenate-Sepharose. In
separate experiments phage particles expressing either mutant
(fdphoAla 166; example 11) and or wild type (fdphoArg 166) forms
are retained on arsenate-Sepharose and eluted with inorganic
phosphate. Approximately 0.5 to 3% of added phage enzyme particles
loaded (`input phage`) were specifically eluted with phosphate
(`output phage`) compared to only 0.05% of vector particles.
Arsenate is a competitive inhibitor with K.sub.i of 20 .mu.M with
respect to 4-nitrophenyl phosphate. Phage particles antibodies have
previously been isolated on the basis of interactions with similar
affinities (example 23).
[0530] This association is in within the range of a large number of
enzyme-ligand interactions suggesting wide applicability for this
approach.
[0531] Table 8 also shows that the infectivity of phage particles
expressing enzyme is reduced with compared with vector phage
particles. This makes titration of infectious particles an
inappropriate means of quantitating the number of phage enzyme
particles. For this reason the number of phage were measured by dot
blotting and phage were detected with anti-M13 antiserum as
above.
[0532] Whereas, overall recovery of catalytic activity may be an
important consideration in enzyme purification, this is not
critical with phage-enzymes. Even if only low levels of
phage-enzyme bind to and are specifically eluted from affinity
columns, this will generate clones which can subsequently be grown
up in bulk as phage-enzymes or can be transferred to expression
vectors yielding soluble products.
Example 33
PCR Assembly of DNA Encoding Fab Fragments of an Antibody Directed
Against Oxazolone
[0533] Example 25 showed that genes encoding Fab fragments could be
subcloned into vectors fdCAT2 and pHEN1 and the protein domains
displayed on the surface of phage with retention of binding
function. This example shows that the VHCH and VKCK domains can be
amplified separately and then joined by a linker allowing the
expression of the light chain as a geneIII protein fusion and the
VHCH fragment as a soluble molecule. A functional Fab fragment is
then displayed on phage by association of these domains. The
assembly process, described in this example, is required for
display of a library of Fab fragments derived from the immune
repertoire if both heavy and light chain domains are to be encoded
within a single vector.
[0534] The VHCH1 and VKCK domains of a construct (example 25;
construct II in pUC19) derived from antibody NQ10 12.5 directed
against 2-phenyl-5-oxazolone were amplified using PCR. For cloning
into the vector fdCAT2 the oligonucleotides VH1BACKAPA (example 25)
and HuIgG1-4 CH1FOR (example 40) were used to amplify the VHCH1
domains. For cloning into pHEN1 VH1BACKSFH5 (example 25) replaced
VH1BACKAPA for this amplification. For cloning into both vectors
the VKCK domains were amplified using VK2BACK (example 25) and
CKNOTFOR (example 40). A linker oligonucleotide fragment containing
the bacteriophage fd gene 8 terminator and the fd gene 3 promoter
was prepared by amplifying the region containing them from the
vector fdCAT2 by PCR using the oligonucleotides. TABLE-US-00019
VK-TERM-FOR 5' TGG AGA CTG GGT GAG CTC AAT GTC (SEQ ID NO:52) GGA
GTG AGA ATA GAA AGG 3' (overlapping with VK2BACK and CH1-TERM-BACK
5' AAG CCC AGC AAC ACC AAG GTG GAC (SEQ ID NO:53) AAG AAA GTT GAG
CCC AAA TCT AGC TGA TAA ACC GAT ACA ATT AAA GGC 3'
(Overlapping with HuIgG1-4 CH1-FOR)
[0535] Assembly of the Fab fragment from the amplified VHCH1 and
VKCK domains and the linker prepared as above was as described in
example 14E except that the primers VH1BACKAPA (when cloning into
fdCAT2) or VH1BACKSFH5 (when cloning into pHEN1) and CKNOTFOR were
used for the final reamplification, thereby introducing restriction
sites for cloning into fdCAT2 (Apa1I-NotI) or pHEN1 (SfiI-NotI) the
assembled Fab fragment is shown in FIG. 34. No assembled product
was seen in the absence of linker. An assembled scFv prepared
according to example 14 is shown for comparison.
[0536] Phage antibodies were prepared as in example 25 and ELISA
was performed with oxazolone as antigen according to example 6.
Results were as expected for Fab fragments cloned in both fdCAT2
and pHEN1 samples, phage particles bound to oxazolone as detected
by a positive ELISA signal.
Example 34
Construction of a Gene III Deficient Helper Phage
[0537] To fully realise the potential of the phagemid cloning
system, a helper phage lacking gene III is desirable. Rescue of
gene III fusions with such a helper phage would result in all the
progeny phagemids having a gene III fusion on their capsid, since
there would be no competition with the wild type molecule.
[0538] Control over the number of fusion molecules contained on
each phage will provide particularly useful. For example, a gene
III deficient helper phage can be used to rescue low affinity
antibodies from a naive repertoire, in which high avidity will be
necessary to isolate those phage bearing the correct antibody
specificity. The unmutated helper phage can then be used when
higher affinity versions are constructed, thereby reducing the
avidity component, and permitting selection purely on the basis of
affinity. This will prove a surprisingly successful strategy for
isolation and affinity maturation of antibodies from naive
libraries.
[0539] The strategy chosen to construct the helper phage was to
partially delete gene III of M13K07 using exonuclease Bal 31.
However, phage lacking gene III protein are non-infective so an E.
coli strain expressing gene III was constructed. Wild type M13 gene
III was PCR-amplified with primers gIIIFUFO and gIIIFUBA, exactly
as described in example 24. The PCR product was digested with Eco
R1 and Hind III and inserted into Eco R1 and Hind III-cut pUC19
(not a phagemid as it lacks the filamentous phage origin of SS DNA
replication) under control of the lac promoter. The plasmid was
transformed into E. coli TG1, and the resulting strain called
TG1/pUC19gIII. This strain provides gIII protein in trans to the
helper phage.
[0540] There is a single unique Bam HI site in M13KO7, which is
approximately in the centre of gIII. Double-stranded M13K07 DNA was
prepared by alkaline lysis and caesium chloride centrifugation
(Sambrook et al, et supra. 1989); twenty pg of DNA was cut with Bam
H1, phenol extracted and ethanol precipitated then resuspended in
50 .mu.l of Bal 31 buffer (600 mM NaC1, 20 mM Tris-HC1 pH 8.0, 12
mM CaCl.sub.2, 12 mM MgC1.sub.2 and 1 mM EDTA) and digested for 4
minutes with 1 unit of Bal 31 (New England BioLabs). This treatment
removed approximately 1 Kb of DNA. EGTA was added to 20 mM and the
reaction phenol extracted and ethanol precipitated prior to
purification of the truncated genome on an agarose gel. The DNA was
repaired with klenow enzyme and self-ligated with T4 DNA ligase
(New England BioLabs).
[0541] Aliquots of the ligation reaction were transformed into
competent TG1/pUC19gIII and plated on SOB medium containing
ampicillin at 100 .mu.g/ml and kanamycin at 50 .mu.g/ml. Colonies
were screened for the presence of a deletion by PCR with primers
gIIIFUBA and KSJ12 (CGGAATACCCAAAAGAACTGG) (SEQ ID NO:54).
[0542] KSJ 12 anneals to gene VI which is immediately downstream of
gIII in the phage genome, so distinguishing gIII on the helper
phage from that resident on the plasmid. Three clones gave
truncated PCR products corresponding to deletions of ca. 200, 400
and 800 bp. These clones were called M13K07 gIII .DELTA. Nos 1, 2
and 3 respectively. No clones were isolated from the earlier Bal 31
time points, suggesting that these are in some way lethal to the
host cell. Several clones were isolated from later time points, but
none of these gave a PCR product, indicating that the deletion
reaction had gone too far.
[0543] M13K07 gIII .DELTA. Nos. 1, 2 and 3 were cultured and the
resulting helper phage tested for their ability to rescue an
antibody gIII fusion (scFv D1.3) by ELISA, exactly as described in
example 18. As shown in FIG. 37, only one clone, M13K07 gIII
.DELTA. No3 was found to rescue the antibody well; in fact the
signal using this helper was greater than that observed with the
parent M13 KO7. M13KO7 gIII.DELTA. No3 rescued phagemids should
have a much higher density of antibody fusions on their surfaces.
That this was indeed the case was demonstrated when the phage used
in this ELISA were analysed by Western blotting with anti gIII
protein antiserum (FIG. 38). This analysis enables estimation of
the amount of gIII fusion protein versus free gIII protein present
on the phage(mid) particles.
[0544] Only a minute fraction of the gIII protein on the
M13K07-rescued material is present as an intact fusion (FIGS.
38A-38B). The fusion protein band is induced by IPTG, so is
indisputably that synthesised by the phagemid. As expected, even
when the lac promoter driving gIII fusion protein synthesis is
fully induced (100 .mu.M IPTG), wild type gIII protein, at a lower
copy number and driven from a far weaker promoter, predominates.
This is in contrast to the pattern generated by the same clone
rescued with M13K07 gIII.DELTA.No3, and the pattern generated by fd
CAT2-scFv D1.3. In both of these latter cases, there is no
competition with wild-type gIII and the fusion protein band is
correspondingly stronger.
[0545] It is worthy of note that construction of M13K07 gIII
.DELTA. No3 was immensely inefficient: one clone from 20 .mu.g of
starting DNA. Moreover, the yield of gIII helper phage from
overnight cultures is extremely low ca.10.sup.6 cfu/ml compared
with ca. 10.sup.6 cfu/ml for the parental phage. Despite this,
M13K07 gIII No3 rescues the phagemid as well as the parental phage,
as judged by the number of phagemid particles produced after
overnight growth. This indicates that trans replication and
packaging functions of the helper are intact and suggest that its
own replication is defective. Hence it may be that inactivation of
gIII is normally toxic to the host cell, and that M13K07 gIII
.DELTA. No3 was isolated because of a compensating mutation
affecting, for example, replication. Phage fd-tet is unusual in
that it tolerates mutations in structural genes that are normally
lethal to the host cell, since it has a replication defect that
slows down accumulation of toxic phage products; M13K07 gIII.DELTA.
No3 may also have such a defect.
[0546] M13K07g III.DELTA. No 3 has been deposited at the National
Collection of Type Cultures, 61 Colindale Avenue, London, NW9 6HT,
UK (Accession No. NCTC 12478). On 28 Jun. 1991, in accordance with
the regulations of the Budapest Treaty. It contains a deletion of
the M13 genome from bases 1979 to 2768 inclusive (see Van
Wezenbeek, P. G. M. F. et al., Gene II p 129-148, 1980 for the DNA
sequence of the M13 genome).
Example 35
Selection of Bacteriophage Expressing scFv Fragments Directed
Against Lysozyme from Mixtures According to Affinity Using a
Panning Procedure
[0547] For isolation of an antibody with a desired high affinity,
it is necessary to be able to select an antibody with only a few
fold higher affinity than the remainder of the population. This
will be particularly important when an antibody with insufficient
affinity has been isolated, for example, from a repertoire derived
from an immunised animal, and random mutagenesis is used to prepare
derivatives with potentially increased affinity. In this example,
mixtures of phage expressing antibodies of different affinities
directed against hen egg lysozyme were subjected to a panning
procedure. It is demonstrated that phage antibodies give the
ability to select for an antibody with a K.sub.d of 2 nM against
one with a K.sub.d of 13 nM.
[0548] The oligonucleotides used in this example are shown in the
list below:
[0549] Oligonucleotides TABLE-US-00020 VHBHD13APA: 5'-CAC AGT GCA
CAG GTC (SEQ ID NO:55) CAA CTG CAG GAG AGC GGT- 3' VHFHD13: 5'-CGG
TGA CGA GGC TGC (SEQ ID NO:56) CTT GAC CCC-3' HD13BLIN: 5'-GGG GTC
AGG GCA GCC (SEQ ID NO:57) TCG TCA CCG-3' HD13FLIN3: 5'-TGG GCT CTG
GGT CAT (SEQ ID NO:58) CTG GAT GTC CGA T-3' T VKBHD13: 5'-GAC ATC
CAG ATG ACC (SEQ ID NO:59) CAG AGC CCA-3' VKFHD13NOT: 5'-GAG TCA
TTC TGC GGC (SEQ ID NO:60) CGC ACG TTT GAT TTC CAC CTT GGT CCC-3'
MURD13SEQ: 5'-GAG GAG ATT TTC CCT (SEQ ID NO:61) GT-3' HUMD13SEQ:
5'-TTG GAG CCT TAC CTG (SEQ ID NO:62) GC-3' FDPCRFOR: 5'-TAG CCC
CCT TAT TAG (SEQ ID NO:63) CGT TTG CCA-3' FDPCRBAK: 5'-GCG ATG GGT
GTT GTC (SEQ ID NO:64) ATT GTC GGC-3'
Phage displaying scFv fragments directed against lysozyme were
derived from cloned Fab fragments in plasmids.
[0550] Heavy and light chain variable regions were amplified by the
polymerase chain reaction (PCR) from plasmids containing humanized
VH-CH1 or VK-CK inserts suitable for production of Fab fragments
(gift of J. Foote). The dissociation constant, Kd for different
combinations of the two plasmids combined as Fabs, are shown below:
TABLE-US-00021 Heavy Chain Plasmid Light Chain Plasmid Kd HuH-1
HuK-3 52 nM HuH-1 HuK-4 180 nM HuH-2 HuK-3 13 nM HuH-2 HuK-4 (not
determined)
Primary PCR
[0551] The primary PCR of the variable regions was performed by
combining the following:
36.5 .mu.l Water
5 .mu.l PCR buffer (10.times.)
2 .mu.l dNTP (5 mM)
2.5 .mu.l Back oligo (10 pmoles/.mu.l) (VHBHD13APA or VKBHD13)
2.5 .mu.l Forward oligo (10 pmoles/.mu.l) (VHFHD13 or
VKFHD13NOT)
[0552] The reaction is decontaminated by UV irradiation to destroy
foreign DNA for 5 minutes, and 1 .mu.l of plasmid DNA added (0.1
.mu.g/.mu.l). The pcr mixture was covered with 2 drops of paraffin
oil, and placed on the pcr block at 94.degree. C. for 5 minutes
before the addition of 0.5 .mu.l of Taq DNA polymerase under the
paraffin. The cycling conditions used were 94.degree. C. 1 min,
40.degree. C. 1 min, 72.degree. C. 1.5 min 17 cycles.
[0553] The linker (Gly.sub.4-Ser).sub.3, was amplified from the
anti-phOx (2-phenyloxazol-5-one) clone fd-CAT2-scFv NQ11, using the
oligos HD13BLIN and HD13FLIN3, with 0.1 .mu.g of plasmid DNA. The
PCR cycling used was 94.degree. C. 1 min, 25.degree. C. 1.5 min,
for 17 cycles.
[0554] Amplified DNA was purified by running the samples on a 2%
low melting point agarose gel at 90 mA, excising the appropriate
bands and extracting the DNA using the GENECLEAN II Kit (BIO 101
Inc.) for the VH and VK, or by using Spin-X filter units (Costar)
for the linker. A final volume of 10 .mu.l was used to resuspend
the extracted DNA.
PCR Assembly
[0555] Assembly of the four single chain Fv Humanized D1.3 (scFv
HuD1.3) constructs was by the process of `assembly by overlap
extension` example 14.
The following were combined:
34.5 .mu.l Water
5 .mu.l PCR Buffer (10.times.)
2 .mu.l dNTP (5 nM)
2.5 .mu.l Back oligo (10 pmoles/.mu.l) (VHBHD13APA)
2.5 .mu.l Forward oligo (10 pmoles/.mu.l) (VKFHD13NOT)
[0556] Once again, the reaction is decontaminate by UV treatment
for 5 minutes before the addition of 1 .mu.l of the primary PCR
products; VH-1 or VH-2, VK-3 or VK-4, plus the linker DNA. The
reaction was covered with 2 drops of paraffin, and heated at
94.degree. C. for 5 minutes before the addition of 0.5 .mu.l of Taq
Polymerase. The PCR cycling conditions used were 94.degree. C. 1
min, 60.degree. C. 1.5 min, 72.degree. C. 2.5 min for 20
cycles.
[0557] The aqueous layer under the paraffin was extracted once with
phenol, once with phenol: chloroform, once with ether, ethanol
precipitated, and resuspended in 36 .mu.l of water. To this was
added, 5 .mu.l of 10.times. Buffer for NotI, 5 .mu.l 1 mg/ml BSA,
and 4 .mu.l (40 U) of NotI (New England Biolabs). The restriction
was incubated at 37.degree. C. overnight.
[0558] The DNA was ethanol precipitated and resuspended in 36 .mu.l
of water, and 5 .mu.l 10.times.NEB Buffer 4, 5 .mu.l 1 mg/ml BSA,
and 2 .mu.l (40 U) of ApaLI (New England Biolabs). This was
incubated at 37.degree. C. for 5 hours; a further 2 .mu.l of ApaLI
was added and the reaction incubated at 37.degree. C.
overnight.
[0559] The cut DNA was extracted by gel purification on a 1.3% low
melting point agarose gel followed by treatment with GENECLEAN, to
yield the insert DNA for cloning.
[0560] Vector fd CAT2 (prepared and digested with ApaLI and NotI as
in example 20) and the scFv DNA were ligated as in example 20.
Analysis of Clones
[0561] Colonies from the ligations were first screened for inserts
by PCR screening. The PCR mixture was prepared in bulk by combining
14.8 .mu.L 1.times.PCR Buffer, 1 .mu.l dNTP (5 mM), 1 .mu.l Back
oligo (FDPCRBAK), 1 .mu.l Forward oligo (FDPCRFOR), and 0.2 .mu.l
Taq polymerase per colony screened. 20 .mu.l of this PCR mixture
was aliquoted into a 96 well Techne plate. The top of a colony was
touched with a toothpick and twirled quickly into the PCR mixture
and the colony rescued by placing the toothpick in a Cellwell plate
(Nunc) containing 250 .mu.l of 2.times.TY medium. The PCR mixture
is covered with 1 drop of paraffin and the plate placed on the
block at 94.degree. C. for 10 minutes before cycling at 94.degree.
C. 1 minute, 60.degree. C. 1 minute, 72.degree. C. 2.5 minutes.
[0562] The clones thus derived were named as below. The affinity of
scFv fragments derived the Fab fragments was not determined but
previous results suggests that these are closely related although
not necessarily identical (R.E. Bird & B.W. Walker TIBTECH 9
132-137, 1991). TABLE-US-00022 Construct Affinity Name Composition
of Fab (Kd) TPB1 VH-HuH2-(Gly.sub.4- 13 nM (SEQ ID NO:269)
Ser).sub.3-VK-HuK3 TPB2 VH-HuH1-(Gly.sub.4- 180 nM (SEQ ID NO:270)
Ser).sub.3-VK-HuK4 TPB3 VH-HuH2-(Gly.sub.4- (Unknown) (SEQ ID
NO:271) Ser).sub.3-VK-HuK4 TPB4 VH-HuH1-(Gly.sub.4- 52 nM (SEQ ID
NO:272) Ser).sub.3-VK-HuK3
[0563] Preparation of phage and ELISA was as described in example
6. The clones generated in fd CAT2 were shown to bind lysozyme as
expected.
Affinity Selection
Selection of Highest Affinity Binding Phage
[0564] Mixing experiments were performed in which fd-CAT2 scFvD1.3
phage (example 19) were mixed with either fd-CAT2 TPB1, fd-CAT2
TPB2, or fd-CAT2 TKPB4, and used in one round of panning.
[0565] The general method used for affinity selection by panning is
that detailed below. Any deviation from this protocol is described
at the relevant point. Panning plates were placed on a rocking
platform between manipulations.
[0566] Falcon 35 mm Tissue Culture dishes were coated overnight
with 1 ml of Lysozyme (various concentrations) dissolved in 50 mM
Sodium Hydrogen Carbonate, pH 9.6, and blocked with 2 ml 2% MPBS at
room temperature for 2 hours. Phage were prepared in 1 ml 2% MPBS
and rocked at room temperature for 2 hours. Plates were washed for
5 minutes with 2 ml of the following solutions; 5 times with PBS,
PBS-Tween, 50 mM Tris-HC1, pH 7.5; 500 mM Sodium Chloride, 50 mM
Tris-HCl, pH 8.5; 500 mM Sodium Chloride, 50 mM Tris-HC1, pH 9.5;
500 mM Sodium Chloride, 50 mM Sodium Hydrogen Carbonated, pH 9.6;
500 mM Sodium Chloride. Phage were then eluted by adding 1 ml 100
mM Triethylamine and rocking for 5 minutes before removing the
eluate which was neutralised with 100 .mu.l 1.0 M Tris-HC1, pH
7.4.
[0567] Plates were coated overnight with Lysozyme at the
concentration listed below.
[0568] Colonies from the single round of panning were probed with
either MURDSEQ (for fdCAT2 scFvD1.3) or HUMD13SEQ (for fdCAT2 TPB
constructs).
[0569] Circles of nitrocellulose (Schleicher & Schuell, BA 85,
0.45 .mu.m) were labelled in pencil and lowered gently onto the
colonies derived from the panning experiments and left for one
minute. The filters were then pulled off quickly from one edge and
placed colony side up on a piece of 3 MM paper (Whatman) soaked in
Denaturing solution (500 mM Sodium Hydroxide; 1.5 M Sodium
Chloride) for 5 minutes. They were then transferred to 3 MM soaked
in Neutralizing Solution (3.0 M Sodium Chloride; 500 mM Tris-HC1,
pH 7.5) for 1 minute, and then to 3 MM soaked in 5.times.SSC; 250
mM Ammonium Acetate for 1 minute. The filters were then air dried
before baking in an 80.degree. C. vacuum oven for 30 minutes.
[0570] The oligonucleotide probe was prepared by combining the
following:
2 .mu.l oligonucleotide (1 pmoles/.mu.l)
2 .mu.l .gamma.-32P ATP (3000 Ci/mmole) (Amersham International
plc)
2 .mu.l 10.times. Kinase buffer (0.5 M Tris-HC1, pH 7.5; 100 mM
Magnesium Chloride; 10 mM DTT)
12 .mu.l Water
2 .mu.l Polynucleotide Kinase (20 Units)
This was incubated at 37.degree. C. for 1 hour.
[0571] Hybridization was performed in the Techne HB-1 Hybridiser.
The baked filters were pre-hybridized at 37.degree. C. in 40 ml of
Hybridization Buffer (10 ml 100 mM Sodium pyrophosphate; 180 ml 5.0
M Sodium chloride; 20 ml 50.times. Denharts Solution; 90 ml 1.0 M
Tris-HC1, pH 7.5; 24 ml 250 mM EDTA; 50 ml 10% NP40; made to 1
litre with water; 60.3 mg rATP; 200 mg yeast RNA (Sigma)), for 15
minutes before the addition of the 20 .mu.l of the kinased oligo.
The filters were incubated at 37.degree. C. for at least one hour,
and then washed 3 times with 50 ml of 6.times.SSC at 37.degree. C.
for 10 minutes (low stringency wash). Filters were air dried,
covered with Saran wrap and exposed overnight with Kodak X-AR
film.
Selection of fd-CAT2 scFv D1.3 from fd-CAT2 TPB4
[0572] FIG. 39, summarizes the results from panning experiments
using a mixture of the high affinity fd-CAT2 scFv D1.3 phage (Kd-2
nM) and the fd-CAT2 TPB4 construct (Kd-52 nM).
[0573] At a coating concentration of 3000 .mu.g/ml Lysozyme, little
or no enrichment could be obtained. It was however, possible to get
enrichment for the scFv D1.3 phage when a lower concentration of
Lysozyme was used for coating the plates. The best enrichment value
obtained was from 1.5% fd-CAT2 scFv D1.3 in the starting mixture,
to 33% fd-CAT2 scFv D1.3 in the eluted faction, on a plate coated
overnight with 30 .mu.g/ml Lysozyme.
Selection of fd-CAT2 scFv D1.3 from fd-CAT2 TPB1
[0574] Enrichment for the high affinity scFv D1.3 phage over the
fd-CAT2 TPB1 phage (Kd-13) nM, could only be shown from experiments
where the plates had been coated overnight with low concentrations
of Lysozyme, as shown in FIG. 40.
[0575] In summary, single chain Fv versions of a series of
humanized D1.3 antibodies have been constructed in phage fd-CAT2.
By affinity selection of fd-CAT2 phage mixtures, by panning in
small petri dishes, it was shown that the high affinity scFv D1.3
phage, could be preferentially selected for against a background of
lower affinity scFv HuD1.3 phage.
Example 36
Expression of Catalytically Active Staphylococcal Nuclease on the
Surface of Bacteriophage fd
[0576] Examples 11 and 12 showed that alkaline phosphatase from E.
coli can be expressed as a catalytically active enzyme on the
surface of bacteriophage fd. Here we show that Staphylococcal
nuclease can also be expressed in a catalytically active form
suggesting that this methodology may be general.
[0577] The gene for the enzyme Staphylococcal nuclease (SNase) was
amplified from M13 mp18-SNase (Neuberger, M. S. et al, Nature, 312,
604-608, 1984) by PCR using primers with internal ApaLI
(5'-GGAATTCGTGCACAGAGTGCAACTTCAACTAAAAAATTAC-3') (SEQ ID NO:65) and
NotI (5'-GGGATCCGCGGCCGCTTGACCTGAATCAGCGTTGTCTTCG-3') (SEQ ID
NO:66) restriction sites, cloned into phage vector fd-CAT2 after
digestion with ApaLI-NotI restriction enzymes and the nucleotide
sequence of the SNase gene and junctions with gene III checked by
DNA sequencing. The fd-tet-SNase phage was prepared from the
supernatant of infected E. coli TG1 cultures by three rounds of PEG
precipitation, and the fusion protein demonstrated by SDS-gel
electrophoresis and Western blotting using rabbit anti-g3p
antiserum (Prof. I. Rasched, Konstanz) and peroxidase-labelled goat
anti-rabbit antibodies (Sigma) (FIG. 41) as described in example
27. As well as the fusion protein band (calculated Mr 59749, but
runs at a higher position due to the aberrant g3p behaviour), a
smaller proteolytic product is seen.
[0578] The fusion protein was shown to be catalytically active by
incubation of the fd-tet-SNase phage (4.times.10.sup.9 tetracycline
resistant colonies [TU]) with single stranded DNA (1 .mu.g) for 1
hr at 37.degree. C. in the presence of Ca.sup.2, and analysis of
the digest by agarose gel electrophoresis (FIG. 42). Nuclease
activity was not detected with the parent fd-CAT2
(2.times.10.sup.10 TU) phage alone or after three rounds of PEG
precipitation of mixtures of fd-CAT2 (2.times.10.sup.10 TU) with
SNase (0.7 .mu.g). Thus the nuclease activity results from the
display of the enzyme on the surface of the phage and not from
co-precipitated or soluble SNase set free by degradation of the
fusion protein. The nuclease activity of fd-tet-SNase (FIG. 42)
lies in the same order of magnitude, (2.times.10.sup.8 TU and
assuming three copies of SNase per TU) as an equimolar amount of
SNase (0.03 ng or 10.sup.9 particles), and like the authentic SNase
was dependent on Ca.sup.2+, since incubation with 40 mM MgCl.sub.2
and 25 mM EGTA blocked activity (not shown).
Example 37
Display of the Two Aminoterminal Domains of Human CD4 on the
Surface of fd Phage
[0579] The protein CD4, a member of the immunoglobulin superfamily,
is a cell surface receptor involved in MHC class II restricted
immune recognition. It is also recognised by the protein gp120
derived from the human immunodeficiency virus (AIDS virus). The
first two domains (named V1 and V2, residues 1-178) of the surface
antigen CD4 were amplified from pUC13-T4 (gift from T. Simon)
containing the human cDNA of CD4, by PCR using primers with
internal ApaLI (5'-GGA ATT CGT GCA CAG AAG AAA GTG GTG CTG GGC AAA
AAA GGG G-3') (SEQ ID NO:67) and NotI (5'-GGG ATC CGC GGC CGC AGC
TAG CAC CAC GAT GTC TAT TTT GAA CTC-3') (SEQ ID NO:68) restriction
sites. After digestion with these two enzymes, the PCR-product was
cloned into fdCAT2, and the complete nucleotide sequence of the
CD4-V1V2 DNA and junctions with gene III checked by dideoxy
sequencing using oligonucleotides fd-seq1 (5'-GAA TTT TCT GTA TGA
GG) (SEQ ID NO:69), CD4-seq1 (5'-GAA GTT TCC TTG GTC CC-3') (SEQ ID
NO:70) and CD4-seq2 (5'-ACT ACC AGG GGG GCT CT-3') (SEQ ID NO:71).
In the same way, a fd-CD4-V1 version was made, linking residues
1-107 to the N-terminus of gene III, using previously mentioned
primers and oligonucleotide 5'-GGG ATC CGC GGC CGC GGT GTC AGA GTT
GGC AGT CAA TCC GAA CAC-3' (SEQ ID NO:72) for amplification, PCR
conditions and cloning were essentially as described in example 15
except that digestion was with ApaLI and NotI (used according to
the manufacturers instructions).
[0580] Both fd-CD4-V1 and fd-CD4-V1V2 phages were prepared from the
supernatant of infected E. coli TG1 cultures by three rounds of PEG
precipitation, thereby concentrating the sample 100-fold for ELISA
analysis. The fusion protein was detected in a Western blot
(results not shown) with a rabbit anti-gene III antiserum, and
revealed bands of the expected size.
[0581] Binding of the CD4 moiety to soluble gp120 (recombinant
HIV-IIIB gp120 from CHO cells, ADP604, obtained from the Aids
Directed Programme, National Institute for Biological Standards and
Controls, South Mimms, Potters Bar, UK) was analysed in an ELISA,
using 5 .mu.g/ml gp120 for coating (overnight, in PBS). Anti-M13
antiserum was used to detect bound phage; all other conditions were
as in Example 9. FIG. 43 shows the ELISA signals of wild-type phage
(fd-tet) and both CD4-phages. Both CD4-phages can bind gp120, but
fd-CD4-V1V2 binds much stronger to gp120 than fd-CD4-V1. The
binding competitors, soluble CD4 (recombinant soluble CD4 from
Baculovirus, ADP 608; from the AIDS Directed Programme) (25
.mu.g/ml) or soluble gp120 (20 .mu.g/ml), added together with the
50 .mu.l phage stock sample during the ELISA, decreased the signal
to background level. These results indicate that phage binding to
gp120 is mediated by the CD4 molecule displayed at its surface, and
that binding is stronger when the two aminoterminal domains of CD4
are presented.
[0582] Thus, CD4 is a cell surface receptor molecule which is
active when displayed on bacteriophage fd. Like the PDGF-BB
receptor, the functional display of which is described in examples
15 and 16, CD4 is a member of the immunoglobulin superfamily and
this result suggests that this class of molecule may be generally
suitable for display on the surface of phage.
Example 38
Generation and Selection of Mutants of an
Anti-4-hydroxy-3-nitrophenylacetic Acid (NP) Antibody Expressed on
Phage Using Mutator Strains
[0583] It will sometimes be desirable to increase the diversity of
a pool of genes cloned in phage, for example a pool of antibody
genes, or to produce a large number of variants of a single cloned
gene. There are many suitable in vitro mutagenesis methods.
However, an attractive method, particularly for making a more
diverse population of a library of antibody genes, is to use
mutator strains. This has the advantage of generating very large
numbers of mutants, essentially limited only by the number of phage
that can be handled. The phage display system allows full advantage
to be taken of this number to isolate improved or altered
clones.
[0584] Nucleotide sequences encoding an antibody scFv fragment
directed against 4-hydroxy-3-nitrophenylacetic acid (NP), scFvB18,
derived as in example 14 from a monoclonal antibody against NP were
cloned into fdCAT2 using ApaLI and NotI restriction sites as in
example 11 to create fdCAT2scFvB18 or into fdDOGKan (fdCAT2 with
its tetracycline resistance gene removed and replaced by a
kanamycin resistance gene) using PstI and NotI restriction sites to
create fdDOGKanscFvB18 or into the phagemid vector pHEN1 using the
restriction sites SfiI and NotI as a fusion protein with gene III
to create pHEN1scFvB18.
[0585] The following mutator strains (R. M. Schaaper & R. L.
Dunn, J. Mol. Biol., 262, 1627-16270, 1987; R. M. Schaaper, Proc.
Natl. Acad., Sci., U.S.A., 85, 8126-8130, 1988) were used:
NR9232: ara, thi, mutD5-zaf13::Tn10, prolac, F'prolac
NR9670: ara, thi, azi, mutT1, leu::Tn10, prolac
NR9292: ara, thi, mutH101, prolac, F'prolac
NR9084: ara, thi, mutT1, azi, prolac, F'prolacI.sup.- Z.sup.-
.DELTA.M15 M15
NR9046: ara, thi, supE, rif, nalA, metB, argE(am), prolac,
F'prolac
were kind gifts of Dr. R. M. Schaaper (Department of Health &
Human Services, N1H, PO Box 12233, Research Triangle Park, N.C.
27709)
NR9046mutD5: NR9046 mutD5::Tn10
NR9046mutT1: NR9046 mutT1::Tn10
[0586] were constructed by P1 transduction according to standard
procedures. Mutator strains were transfected with fdCAT2scFvB18 of
fdDOGKanscFvB18 and transfectants selected for antibiotic
resistance. Transfectants were grown for 24 h at 37.degree. C.
before mutant phage was harvested by PEG precipitation. The mutant
phage were selected on a 1 ml NIP
(4-hydroxy-3-iodo-5nitrophenylacetic acid)-BSA-Sepharose affinity
column (prepared according to the manufacturers instructions)
prewashed with 200 ml of PBS and blocked by 20 ml MPBS. Phage were
loaded on the column in 10 ml MPBS and unbound material reapplied
to ensure complete binding. The column was subsequently washed with
10 ml of MPBS and 500 ml of PBS. Phage bound to the affinity matrix
was eluted with 5 column volumes of 0.33 mM NIP-Cap (example
48).
[0587] Phage eluate was incubated for 30 min to 1 h with log phase
(2.times.10.sup.8 cells/ml) E. coli mutator strains without
antibiotic selection. The infected cells were then diluted 1:100 in
2.times.TY and grown for 24h with antibiotic selection (15 .mu.g/ml
tetracycline or 30 .mu.g/ml kanamycin for fdCAT2scFvB18 or
fdDOGKanscFvB18 respectively). Phage from this culture was used for
another round of affinity selection and mutation.
[0588] Binding of phage antibodies was assayed by ELISA as in
example 9 except that ELISA plates were coated with NIP-BSA
(4-hydroxy-3-iodo-5-nitrophenylacetyl-BSA; 0.4 mg/ml). Culture
supernatants were prepared following growth in Cellwells as
described in example 21 and 20 .mu.l of culture supernatant was
added to each well diluted to 200 .mu.l with MPBS.
[0589] Phage samples giving signals in ELISA of more than twice the
background were tested ELISA as above for non-specific binding
against lysozyme, BSA or Ox-BSA (example 9). Specificity for NIP
was further confirmed by an ELISA in which serial dilutions of
NIP-CAP were added together with phage antibodies. Addition of
increasing concentrations of NIP-CAP reduced the ELISA signal to
the background level.
[0590] Phage giving positive signals in ELISA were sequenced and 2
different mutants were subcloned into pHEN1 phagemid and
transformed into HB2151 for soluble expression and TG1 for phage
display (example 27).
[0591] For expression of soluble scFv fragments, transformants in
E. coli HB2151 were grown at 37.degree. C. in 1 litre 2.times.TY,
0.2% glucose, 0.1 mg/ml ampicillin to an OD600 of 1 and expression
of soluble scFv fragments induced by adding IPTG to 1 mM. Cultures
were shaken at 30.degree. C. for 16 h.
[0592] Soluble scFvB18 was concentrated from crude bacterial
supernatant in a FLOWGEN ultrafiltration unit to a volume of 200
ml.
[0593] The concentrate was passed two times over a 2 ml column of
NIP-BSA-Sepharose prewashed with 200 ml of PBS. The column was
washed with 500 ml of PBS and 200 ml of 0.1M Tris pH7.5, 0.5M NaC1
and phage antibodies eluted with 50 mM Citrate buffer pH2.3. The
eluate was immediately neutralised with 1 MTris pH8. The eluate was
dialysed against two changes of 1 litre PBS, 0.2 mM EDTA,
Precipitated protein was removed by centrifugation at 10000 g and
protein yield was determined by measuring the absorbance at 280 nm
of the supernatant.
[0594] After 4 rounds of mutation and selection, isolated clones
were screened and in one or two rare examples strongly positive
ELISA signals were obtained from phage antibodies derived from the
mutation of each of fdCAT2scFvB18 and fdDOGKanscFvB18 in the ELISA.
The ELISA conditions were such that the parent phage fdCAT2scFvB18
only generated weak signals. These phage antibodies giving strongly
positive ELISA signals were enriched in further rounds by a factor
of roughly 2.5 per round. Forty phage antibodies giving strongly
positive signals were sequenced and they each displayed single
mutations in six different positions in the scFvB18 nucleotide
sequences, five of which reside in the light chain. More than 70%
of the mutations occurred at positions 724 and 725 changing the
first glycine in the J segment of the light chain (framework 4) to
serine (in 21 cases) or aspartate (in 3 cases). The mutations found
are shown in Table 9. The sequence of scFvB18 is shown in FIG. 44A
through 44B.
[0595] The nucleotide sequences encoding the scFv fragments of a
framework mutant with the above glycine to serine mutation, as well
as a mutant where Tyr in the CDR3 of the light chain had been
mutated to aspartate, were amplified by PCR from the phage antibody
clones and subcloned into pHEN1 phagemid (essentially as in example
25). This avoids possible problems with geneIII mutations caused by
the mutator strains. The same pattern of ELISA signals was seen
when the mutants were displayed on phage following rescue of the
phagemid with helper phage (as described in example 25) as when the
mutants were assayed when expressed from the phage genome as
above.
[0596] The scFv fragments from scFvB18 and the scFv fragments
containing the glycine to serine and tyrosine to aspartate
mutations respectively were expressed in solution (following
transformation into E. coli HB2151 as in example 27) at 30.degree.
C. They showed no differences in the ELISA signals between
wild-type B18 and the framework mutant. The signal obtained from
the phage antibody with the Tyr mutated to aspartate in CDR3 of
scFvB18 was about 10.times. stronger. Expression yields were found
to be comparable as judged by Western blotting using an antiserum
raised against g3p (as described above). Affinity measurements were
performed using fluorescence quenching as described in example 23.
Affinity measurement of affinity purified scFv fragments however
showed scFvB18, and the scFvB18 (Gly->Ser) and
scFvB18(Tyr->Asp) mutants all to have a comparable affinity of
20 nM for NIP-CAP.
[0597] A Western blot using an anti-geneIII antibody showed the
framework mutant had suffered significantly less proteolytic
cleavage than scFvB18.
[0598] Hence, the use of mutator strains generates a diverse range
of mutants in phage antibodies when they are used as hosts for
clones for gene III fusions. in this case some of the clones
exhibit higher ELISA signals probably due to increased stability to
proteolyic attack. The mutator strains can therefore be used to
introduce diversity into a clone or population of clones. This
diversity should generate clones with desirable characteristics
such as a higher affinity or specificity. Such clones may then be
selected following display of the proteins on phage.
Example 39
Expression of a Fv Fragment on the Surface of Bacteriophage by
Non-Covalent Association of VH and VL Domains
[0599] This example shows that functional Fv fragments can be
expressed on the surface of bacteriophage by non-covalent
association of VH and VL domains. One chain is expressed as a gene
III fusion and the other as a soluble polypeptide. Thus Fv
fragments can be used for all the strategies discussed for Fab
fragments including dual combinatorial libraries (example 26).
[0600] A useful genetic selection system for stably associated Fv
fragments could be established if the expression of Fv fragments as
fusion proteins on the phage surface would be possible such that
one V domain is fused to the gene III protein and the other V
domain is expressed separately in secreted form, allowing it to
associate with the V domain on the fusion protein provided the
interaction strength is sufficiently high. This idea was tested in
a model experiment using the V domains from the anti-hen egg
lysozyme antibody D1.3 by fusing the D1.3 VK gene to gene III and
separately expressing the D1.3 VH domain.
[0601] Experimentally this was achieved as follows: The vector
fd-DOG1 was digested with the restriction enzymes PstI and Xho1.
From the Fv expression plasmid pSW1-VHD1.3-VKD1.3myc version
3/pUC119 (Ward, et al., 1989 supra) a Pst 1/Xho I-digested
restriction fragment was isolated that carries the VH domain coding
sequence (terminated by 2 stop codons), a spacer region between VH
and VK genes including a ribosome-binding site for expression of
the VK gene, a pelB leader sequence, and, following in frame, the
VK gene. This fragment was cloned into the digested fd-DOG vector
to generate the construct fd-tet Fv D1.3. As shown on the map in
FIG. 45, the dicistronic VH/VK-gene III operon is transcribed from
the gene III promoter; secretion of the VH domain is achieved by
the gene III protein leader, secretion of the VK-geneIII fusion
protein by the pelB leader sequence. For control purposes a second
construct with the name fd-tet Fv D1.3 (.DELTA.S-Stuffer) was made
by a similar route as described above: the VH used in this
construct carries an insertion of a 200 bp fragment in the Sty I
restriction site at the junction of VH CDR 3/FR4, thus interrupting
the VH with several in frame stop codons. It is known from previous
work that this insertion sufficiently disrupts the VH structure to
abolish binding to the antigen lysozyme when expressed either as a
soluble Fv or single-chain Fv fragment or as a single-chain Fv
fragment on phage surface. This construct was used as a control.
TG1 bacteria carrying either the fd-tet Fv D1.3, fd-tet Fv D1.3
(.DELTA.S-Stuffer) or as single-chain wild-type control fd-tet scFv
D1.3 plasmids were grown in liquid culture (medium 2.times.TY
containing 15 .mu.g/ml tetracycline) for 24 h to produce phage
particles in the supernatant. After removal of bacterial cells by
centrifugation the phage titer in the supernatants was determined
by re-infecting exponentially growing TG1 cells with dilutions of
the supernatants and scoring tetracycline-resistants colonies after
plating on tetracycline-plates. The infectious phage titers
achieved were 1.times.10.sup.11 tetR transducing units/ml for the
single-chain wild-type control fd-tet scFv D1.3 and
2.times.10.sup.10 tetR transducing units/ml for Fv phage constructs
fd-tet Fv D1.3 and fd-tet Fv D1.3 (.DELTA.S-Stuffer).
ELISA of Hen Egg Lysozyme was Performed as in Example 2
[0602] The results are shown in FIG. 46. Phage derived from
bacteria carrying and expressing the Fv construct fd-tet Fv D1.3
bind to the immobilised hen egg lysozyme, and when taking the phage
titer into account, indeed apparently better than the single-chain
Fv bearing phages produced by fd-tet scFv D1.3 carrying bacteria.
The specificity of the reaction and the requirement for a
functional VH domain is demonstrated by the fd-tet Fv D1.3
(.DELTA.S-Stuffer) control in which disruption of the VH domain and
consequently of the Fv fragment association eliminates binding to
lysozyme.
[0603] As a final control of the expected structure of the
VK/geneIII fusion protein a Western Blot was carried out. 20 .mu.l
of phage suspensions concentrated 100 fold by two sequential
precipitations with PEG were applied to a 10% SDS-PAGE gel,
electrophoretically separated and then transferred to a PVDF
membrane (Immobilon, Millipore) in a semi-dry Western transfer
apparatus (Hoefer). Remaining binding sites on the filter were
blocked by 1 h incubation with 3% BSA in PBS, and detection of the
gene III protein accomplished by incubation with a 1:1000 diluted
rabbit anti-gene III antiserum for 2h, several washes in PBS/0.1%
Tween 20, incubation with peroxidase-conjugated goat anti-rat
immunoglobulin antibodies, washes and development with the
chromogenic substrate diaminobenzidine/COCl.sub.2/0.03%
H.sub.2O.sub.2. The Fv phage fd-tet Fv D1.3 yields a band for the
gene III fusion protein (data not shown), that is intermediate in
size between the bands obtained for a wild-type gene III protein
from fd-DOG1 and the scFv-gene III fusion protein from fd-tet scFv
D1.3, thus proving the presence of a single immunoglobulin domain
covalently fused to the gene III product in the Fv phage.
[0604] In summary, Fv-gene III fusions in which one V domain is
fused to the gene III protein and the other V domain associates
non-covalently can be presented in functionally active form on the
surface of filamentous phage. This opens the possibility to
genetically select for stably associated Fv fragments with defined
binding specificities from V gene libraries expressed in
phages.
Example 40
A PCR Based Technique for One Step Cloning of Human V-Genes as Fab
Constructs
[0605] This example describes a PCR based technique to "assemble"
human Fabs by splicing together the heavy and light chain DNA with
a separate piece of `linker` DNA. A mixture of universal primers is
used which should make the technique applicable to all human
V-genes.
[0606] The general technique for PCR assembly of human V-genes to
create a Fab construct is described. The efficiency of this
technique was assessed by "assembling", cloning and expressing a
human anti rhesus-D (Rh-D) Fab from a IgG-K monoclonal hybridoma.
We also demonstrate the potential to rescue human monoclonal
antibodies from polyclonal cell populations by assembling, cloning,
expressing and isolating an IgG-lambda monoclonal anti-Rh-D Fab
from a polyclonal lymphoblastic cell line (LCL).
[0607] The overall strategy for the PCR assembly is shown in FIG.
47 and is described in more detail below. For Fab assembly, the
VH-CH1 and VK-CK or V lambda-C lambda light chains are amplified
from first strand cDNA and gel purified. Heavy and light chain DNA
are then combined together with linker DNA and flanking
oligonucleotides in a new PCR reaction. This results in a full
length Fab construct since the 5' end of the linker DNA is
complementary to the 31 end of the CH1 domain and the 3' end of the
linker is complementary to the 5' end of the light chain domain.
The linker DNA contains terminal residues of the human CH1 domain,
the bacterial leader sequence (pelB) for the light chain and the
initial residues of the VK or V lambda light chain. Finally, after
gel purification, the Fab construct is reamplified with flanking
oligonucleotides containing restriction sites for cloning.
Oligonucleotide Primers:
[0608] In order to develop the PCR cloning of human V genes it was
necessary to design a new range of human specific oligonucleotide
primers.
[0609] The PCR primers at the 51 end of the VH and VK and Vlambda
gene exon (BACK primers) are based on sequence data extracted from
the Kabat database, (Kabat, E. A. et al, Sequences of Proteins of
Immunological Interest. 4th Edition. US Department of Health and
Human Services. 1987) the EMBL database, the literature (Chuchana,
P., et al, Eur J. Immunol., 1990. 20:1317) and unpublished data.
The sequence of the VH, VK and Vlambda primers are given in table
1. In addition, extended VH primers with SfiI sites at the 5' end
were also designed (Table 10) for adding a restriction site after
assembly.
[0610] Table 10 also shows the 3' primers (FORWARD primers)
designed for the PCR based cloning of human V genes. There are two
sets of these depending on whether a Fab or scFv is to be produced.
For Fab assembly, the forward primer was based at the 3' end of the
CH1 domain, CK domain and Clambda domain. In addition, the CK and
C2 FORWARD primers were also synthesized as extended versions with
Not1 sites at their 5' ends.
[0611] Primers complementary to the CH1 forward primers and the VkK
and V lambda back primers were synthesized to permit generation of
linker DNA by PCR amplification of a plasmid template containing
the Fab linker (Table 10). To ensure adequate amplification, the
primers were extended into the actual linker sequence.
A RNA Preparation
[0612] This is essentially the same as described in Example 14, but
using material of human origin. In the results given in this
example human hybridoma and human polyclonal lymphoblastic cell
lines were used.
B cDNA Preparation
[0613] Approximately 4 .mu.g of total RNA in 20 ul water was heated
at 65.degree. C. for 3 minutes, quenched on ice and added to a 30
ul reaction mixture resulting in a 50 ul reaction mixture
containing 140 mM KC1, 50 mM Tris, HC1 (pH8.1 @ 42.degree. C.), 8
mM MgCl2, 10 mM DTT, 500 uM deoxythymidine triphosphate 500 uM
deoxycytosine triphosphate, 500 uM deoxyadenosine triphosphate and
500 uM deoxyguanosine triphosphate, 80 units of human placental
RNAse inhibitor and 10 pmol of the appropriate Forward primer
(HulgG1-4CH1FOR, HuIgMFOR, HuCKFOR, HuCLFOR). Two ul (50 units) of
avian myeloblastosis virus (AMV) reverse transcriptase was added,
the reaction incubated at 42.degree. C. for 1 hour, heated to
100.degree. C. for 3 minutes, quenched on ice and centrifuged for 5
minutes.
C Primary PCRs
[0614] For the primary PCR amplifications, an equimolar mixture of
the appropriate family based BACK and FORWARD primers was used.
(See specific examples 40A and 40B given later in this example). A
50 ul reaction mixture was prepared containing 5 ul of the
supernatant from the cDNA synthesis, 20 pmol total concentration of
the FORWARD primers, 250 uM dNTPs, 50 mM KC1, 100 mM Tris. HC1 (pH
8.3), 1.5 mM MgCl.sub.2, 175 ug/ml BSA and 1 ul (5 units) Thermus
aquaticus (Taq) DNA polymerase (Cetus, Emeryville, Calif.). The
reaction mixture was overlaid with paraffin oil and subjected to 30
cycles of amplification using a Techne thermal cycler. The cycle
was 94.degree. C. for 1 minute (denaturation), 57.degree. C. for 1
minute (annealing) and 72.degree. C. for 1 minute (extension). The
product was analyzed by running 5 ul on a 2% agarose gel. The
remainder was extracted twice with ether, twice with
phenol/chloroform, ethanol precipitated and resuspended in 50 ul of
H.sub.2O.
D Preparation of Linker
[0615] To make the Fab linker DNA, 13 separate PCR reactions were
performed using HulgG1-4CH1FOR and each of the reverse VK or V
lambda oligonucleotides. The template was approximately 1 ng of
pJM-1Fab D1.3 (FIG. 48) The PCR reaction reagents were as described
above and the cycle was 94.degree. C.:1 min, 45.degree. C.:1 min
and 72.degree. C.:1 min. The linkers were analyzed on a 4% agarose
gel, purified on a 2% agarose gel, eluted from the gel on a Spin-X
column and ethanol precipitated.
E Assembly PCRs
[0616] For PCR assembly of a human Fab approximately 1 ug of a
primary heavy chain amplification and 1 ug of a primary light chain
amplification were mixed with approximately 250 ng of the
appropriate linker DNA in a PCR reaction mixture without primers
and cycled 7 times (94.degree. C.: 2 min, 72.degree. C., 2.5 min)
to join the fragments. The reaction mixture was then amplified for
25 cycles (94.degree. C.:1 ml, 68.degree. C.-72.degree. C.:1 min,
72.degree. C., 2.5 min) after the addition of 20 pmol of the
appropriate flanking BACK and FORWARD primers.
F Adding Restriction Sites
[0617] The assembled products were gel purified and reamplified for
25 cycles (94.degree. C.:1 min, 550C:1 min, 72.degree. C.:25 min)
with the flanking oligonucleotides containing the appended
restriction sites. PCR buffers and NTPs were as described
previously.
Specific Examples of PCR Assembly of Human Immunoglobulin Genes
[0618] a. PCR assembly of a Fab from a human hybridoma: the human
monoclonal anti Rh-D cell lines Fog-1 (IgG-k) was derived from EBV
transformation of the PBLs of a Rh-D negative blood donor immunized
with Rh-D positive blood and has been previously described
(Melamed, M. D., et al., J. Immunological Methods 1987. 104:245)
(Hughes-Jones N. C., et al., Biochem. J. 1990. 268:135) (Gorick, B.
D. et al., Vox. Sang. 1988. 55:165) Total RNA was prepared from
approximately 10.sup.7 hybridoma cells. First strand cDNA synthesis
was performed as described above using the primers HulgG1-4CH1FOR
and HuCKFOR. Primary PCRs were performed for the VH-CH1 using a
mixture of the 6 HuVHBACK primers and HuIgG1-4CG1FOR and for the
VK-CK using a mixture of the 6 HuVKBACK primers and HuCKFOR. A Fab
construct was assembled as described above, restricted with SfiI
and NotI, gel purified and ligated into pJM-1Fab D1.3 restricted
with SfiI and NotI. The ligation mixture was used to transform
competent E. coli E.M.G. cells. Ninety-six clones were toothpicked
into media in microtitre plate wells, grown to mid-log phase at
30.degree. C. and then expression of the Fab was induced by heat
shocking at 42.degree. C. for 30 min followed by growing for 4
hours at 37.degree. C. The ninety-six clones were then screened for
anti-Rh-D activity as described below.
[0619] b. assembly of human Fabs from a polyclonal (LOL) A
polyclonal LCL "OG" was derived from EBV transformation of
approximately 10.sup.7 peripheral blood lymphocytes (PBLs) from a
Rh-D negative donor immunized with Rh-D positive red blood cells.
The cells were plated at a concentration of approximately 10.sup.5
cells per well. Positive wells were identified by screening the
cells harvested and then subcloned once. Typing of the well
indicated that an IgG-lambda antibody was being produced. At this
stage, total RNA was prepared from approximately 10.sup.6 cells.
First strand cDNA synthesis was performed as described above using
the primers HulgG1-4CG1FOR and HuCLFOR. Primary PCRs were performed
for the VH-CH1 using a mixture of the 6 HuVHBACK2 primers and
HulgG1-4 CG1FOR and for the V lambda-C lambda using a mixture of
the 7 HuV BACK primers and HuC FOR. Restriction, cloning and
screening proceeded as described. To determine the diversity of the
clones, the VH and V lambda genes of 15 clones were PCR amplified,
restricted with the frequent cutting restriction enzyme BstN1 and
analyzed on a 4% agarose gel (see example 20).
[0620] Assay for anti-Rh-D activity and demonstration of
specificity: A 5% (vol/vol) suspension of either Rh-D positive
(OR2R2) or Rh-D negative (Orr) erythrocytes in phosphate buffered
saline (PBS, pH 7.3) were incubated with a papain solution for 10
min at 37.degree. C. The erythrocytes were washed three times in
PBS and a 1% (vol/vol) suspension of erythrocytes was made up in
PBS supplemented with 1% (vol/vol) of bovine serum albumin (BSA).
Fifty ul of a papain treated erythrocyte suspension and Soul of
phage supernatant were placed in the wells of round bottom
microtitre plates and the plates were placed on a T/Itertek plate
shaker for 2 min. After 15 min incubation at 37.degree. C. 100 ul
of PBS/BSA was added to each well. The plates were centrifuged at
200 g for 1 min and the supernatant was discarded. The erythrocytes
were resuspended in the remaining PBS/BSA and the Fab fragments
were crosslinked by addition of the 9E10 monoclonal antibody (Soul
a 1 ug/ml solution in PBS/BSA) directed against the myc peptide tag
(Ward, E. S., et al., Nature 1989. supra). The plates were placed
at room temperature (RT) until sedimentation had occurred.
Agglutination of erthrocytes caused a diffuse button of
erythrocytes and the results were evaluated macroscopically.
Specificity was confirmed with a standard prepapainized (as above)
panel of 9 erythrocyte suspensions in PBS (all suspensions blood
group O, 4 D positive and 5 D negative) known to have homozygous
expression of all the clinically relevant erythrocyte blood group
alloantigens. The number of copies of the D antigen on the D
positive cells varied between 10,000 and 20,000 per erythrocyte
depending on the Rh genotype. Briefly, 50 ul phage supernatant in
PBS supplemented with 2% (vol/vol) skimmed milk was mixed with 50
ul of a 2% erythrocyte suspension in PBS in glass tubes and
incubated for 15 min at 37.degree. C. After one wash with PBS/BSA
the erythrocytes were pelleted and resuspended in 50 ul donkey
anti-human lambda light chain (Sigma L9527, diluted 1:40 in
PBS/BSA). The tubes were centrifuged for 1 min at 200 g and
agglutination was read macroscopically using "tip and roll"
method.
Results
[0621] a PCR assembly of a Fab from a human hybridoma: A single
band of the correct size was obtained after amplification.
Thirty-eight of 96 clones (40%) screened specifically agglutinated
Rh-D positive but not Rh-D negative red blood cells. The results
demonstrate a high frequency of successful splicing in the assembly
process and the potential of this technique for one step cloning of
human hybridomas.
[0622] b Assembly of human Fabs from a polyclonal lymphoblastic
cell line (LCL): Analysis of the diversity of the clones indicated
that 3 different heavy chain families and 2 different light chains
families were present. Five anti-Rh-D specific clones were
identified out of 96 screened. The VH and V.lamda. chains had
identical nucleotide sequences in each clone and were typical of
anti-Rh-D V-genes (unpublished results). The results demonstrate
the potential of this technique to assemble, clone and isolate
human antibody fragments from polyclonal cell populations (see also
section on isolation of specific binding activities from an
`unimmunized` human library (examples 42 and 43).
Example 41
Selection of Phage Displaying a Human Fab Fragment Directed Against
the Rhesus-D Antigen by Binding to Cells Displaying the Rhesus D
Antigen on their Surface
[0623] A large number of important antigens are integral components
of cell surface membranes, i.e. they are cell surface antigens.
These include tumor specific antigens and red and white blood cell
surface antigens. In many instances, it would be important to
isolate antibodies against these antigens. For example, antibodies
directed against the rhesus-D (Rh-D) antigen on red blood cells are
used both diagnostically and therapeutically. Many of these
antigens are difficult to purify and some, like Rh-D, are not
biologically active when isolated from the membrane. Thus, it would
be useful to be able to affinity purify antibody fragments
displayed on the surface of bacteriophage directly on cell surface
antigens. To test the feasibility of affinity purification on cell
surface antigens, the anti-Rh-D human monoclonal antibody Fog-B was
displayed as a Fab fragment on the surface of bacteriophage fd. The
displayed Fog-B Fab fragment bound antigen as determined by
agglutination assay and could be affinity purified on the basis of
its binding on the surface of Rh-D positive red blood cells but not
Rh-D negative red blood cells.
Materials and Methods
[0624] Construction of a clone encoding an anti-Rh-D Fab fragment
in phagemid pHENI and display of the Fab fragment on the surface of
bacteriophage fd.
[0625] The human hybridoma Fog-B has been previously described
(N.C. Hughes-Jones et al, Biochem, J., 268 135 (1990). It produces
an IgG-1/lambda antibody which binds the Rh-D antigen. RNA was
prepared from 10.sup.7 hybridoma cells using a modified method of
Cathala (as described in example 14) and 1st strand cDNA
synthesized using specific immunoglobulin heavy and light chain
primers (HuVH1FOR and HuC.lamda. FOR (5'-GGA ATT CTT ATG AAG ATT
CTG TAG GGG CCA C-3') (SEQ ID NO:73)) as described in example 14.
The VH gene was subsequently amplified from an aliquot of the 1st
strand cDNA using HuVH4aBACK and HuVH1FOR. The V.lamda. gene was
amplified using a V.lamda. primer specific for Fog-B
(V.lamda.Fog-B: 5'-AAC CAG CCA TGG CC AGT CTG TGT TGA CGC AGC C-3')
(SEQ ID NO:74). The PCR conditions were as described in example 40.
The PCR products were analyzed by running 5 .mu.l on a 2% agarose
gel. The remainder was extracted twice with ether, twice with
phenol/chloroform, ethanol precipitated and resuspended in 50 .mu.l
of H.sub.2O. The amplified VH DNA was digested with Pst1 and
BstEII, and the amplified V.lamda.-C.lamda. DNA with Ncol and
EcoR1. The fragments were purified on a 2% agarose gel, extracted
using GENECLEAN, and sequentially ligated into the soluble
expression vector pJM-1 Fab D1.3 (FIG. 48A). Clones containing the
correct insert were initially identified by restriction analysis
and verified by assay of expressed soluble Fab (see example 23 for
induction conditions). The Fog-B Fab cassette was amplified from
pJM-1 by PCR using HuVH4BACK-Sfi and Hu C.lamda.-Not, digested with
the appropriate restriction enzymes and ligated into pHEN1. Clones
containing the correct insert were identified initially by
restriction analysis and subsequently by assay (see example 25 for
induction conditions).
[0626] Assay for soluble Fog-B Fab fragment and phage displayed
Fog-B Fab fragment for anti-Rh-D activity and documentation of
specificity.
[0627] Assay of the soluble expressed Fab was performed on
unconcentrated E. coli supernatant. Assay of Fog-B displayed on the
phage surface was performed on phage that had been concentrated 10
fold by PEG precipitation and then resuspended in PBS. The assays
for activity and specificity are as described in example.
[0628] Cell Surface Affinity Purification of Phage Displaying Fog-B
Anti-Rh-D Fab Fragment
[0629] Purified Fog-B phage was mixed with purified phage Fd-Tet
CAT-1 displaying the anti-lysozyme scFv D1.3 (pAbD1.3) in a ratio
of approximately 1 Fog-B:50 scFvD1.3. Prepapainized erythrocytes
(OR2R2 [Rhesus positive] or Orr [Rhesus negative]) were suspended
in PBS supplemented with 2% skimmed milk powder in a concentration
of 4.times.10.sup.7/ml. One ml of this suspension was mixed with
10.sup.11 phage suspended in 2 ml of PBS supplemented with 2%
skimmed milk and incubated for 30 min at room temperature under
continuous rotation. The erythrocytes were washed three times with
an excess of ice-cold PBS (10 ml per wash) and subsequently
pelleted. The phage were eluted from the cells by resuspending in
200 .mu.l of 76 mM citric acid pH 2.8 in PBS for 1 min. The cells
were then pelleted by centrifugation for 1 min at 3000 rpm and the
supernatant containing the eluted phage was neutralized by adding
200 .mu.l of 240 mM Tris-base, 22 mM Disodium hydrogen phosphate in
1% w/vol albumin. Serial dilutions of the eluate was used to infect
TG1 cells. Fog-B Fab phage were selected on ampicillin plates and
scFvD1.3 phage on tetracycline plates and the titre of each
determined prior to selection, after selection on rhesus-D negative
cells and after selection on rhesus-D positive cells.
Results
[0630] Fog-B Fab fragment displayed on the surface of the phage
derived from the phagemid PHEN clone specifically agglutinated
rhesus-D positive but not rhesus D-negative red blood cells.
Affinity purification of the Fog-1 Fab phagemid on Rh-D positive
red blood cells resulted in an enrichment from 1:50 to 1500:1
(Fog-B Fab:scFvD1.3), whereas purification on Rh-D negative red
blood cells demonstrated essentially no enrichment (10 fold).
TABLE-US-00023 TITRE RATIO Fog-B Fab scFvD1.3 Fog-B FAb/scFvD1.3
Prior to selection 1.0 .times. 10.sup.8 5.0 .times. 10.sup.9 1:50
Selection on Rh-D 2.0 .times. 10.sup.4 1.0 .times. 10.sup.5 1:5
negative cells Selection on Rh-D 6.0 .times. 10.sup.6 4.0 .times.
10.sup.3 1500:1 positive cells
Example 42
A PCR Based Technique for One Step Cloning of Human scFv
Constructs
[0631] Assembly of human scFv is similar to the assembly of mouse
scFvs described in example 14. To develop the PCR cloning of human
V genes it was necessary to design a new range of human specific
oligonucleotide primers (table 10).
[0632] The use of these primers for the generation of human Fabs is
described in example 40. The assembly of human scFvs is essentially
the same but requires a set of FORWARD primers complementary to the
J segments of the VH, VK and V lambda genes. (For Fabs FORWARD
primers complementary to the constant region are used). The J
segment specific primers were designed based on the published JH,
JK and J lambda sequences (Kabat, E. A. et al, Sequences of
Proteins of Immunological Interest, 4th Edition, US Department of
Health and Human Services. 1987).
[0633] In addition, a different linker is needed for scFvs than for
Fabs so for human scFvs a new set of primers was needed to prepare
the linker. Primers complementary to the JH forward primers and the
VK and V lambda back primers were synthesized to permit generation
of linker DNA by PCR amplification of a plasmid template containing
the scFv linker (Table 10, FIG. 49). To ensure adequate
amplification, the primers were extended into the actual linker
sequence. Using these primers to make the scFv linker DNA, 52
separate PCR reactions were performed using each of the 4 reverse
JH primers in combination with each of the 13 reverse VK and V
lambda oligonucleotides. The template was approximately 1 ng of
pSW2scD1.3 (Ward, E. S. 1989 supra) containing the short peptide
(Gly4Ser)3 (Huston, J. S. et al., Gene 1989. 77:61)
A Specific Example of PCR Assembly of a Human scFv Library
[0634] This example describes the generation of a human library of
scFvs made from an unimmunized human:
[0635] 500 ml of blood, containing approximately 10.sup.8 B-cells,
was obtained from a healthy volunteer blood donor. The white cells
were separated on Ficoll and RNA was prepared as described in
example 14.
[0636] Twenty percent of the RNA, containing the genetic material
from approximately 2.times.10.sup.7 B-cells, was used for cDNA
preparation as described in example 40. Heavy chains originating
from IgG and IgM antibodies were kept separate by priming cDNA
synthesis with either an IgG specific primer (HuIgG1-4CH1FOR) or an
IgM specific primer (HuIgMFOR). Aliquots of the cDNA was used to
generate four separate scFv libraries (IgG-K, IgG-lambda, IgM-K and
IgM-lambda) as described in example 40. The resulting libraries
were purified on 1.5 agarose, electroeluted and ethanol
precipitated. For subsequent cloning, the K and lambda libraries
were combined giving separate IgG and IgM libraries.
[0637] Cloning of the library: The purified scFv fragments (1-4 ug)
were digested with the restriction enzymes NotI and either Sfil or
NcoI. After digestion, the fragments were extracted with
phenol/chloroform, ethanol precipitated. The digested fragments
were ligated into either SfiI-NotI or NcoI-NotI digested, agarose
gel electrophoresis purified pHEN1 DNA (6 ug) (see example 24), in
a 100 .mu.l ligation mix with 2,000 U T4 DNA ligase (New England
Biolabs) overnight at room temperature. The ligation mix was
purified by phenol extraction and ethanol precipitated. The ligated
DNA was resuspended in 10 .mu.l of water, and 2.5 .mu.l samples
were electroporated into E. coli TG1 (50 .mu.l). Cells were grown
in 1 ml SOC for 1 hr and then plated on 2.times.TY medium with 100
.mu.g/ml ampicillin and 1% glucose (AMP-GLU), in 243.times.243 mm
dishes (Nunc). After overnight growth colonies were scraped off the
plates into 10 ml 2.times.TY containing AMP-GLU and 15% glycerol
for storage at -70.degree. C. as a library stock.
[0638] Cloning into SfiI-NotI and NcoI-NotI digested pHEN1 yielded
libraries of 10.sup.7 and 2.times.10.sup.7 clones respectively for
the IgM libraries and approximately 5.times.10.sup.7 clones for
each of the two IgG libraries.
Example 43
Isolation of Binding Activities from a Library of scFvs from an
Unimmunized Human
[0639] The ability to select binding activities from human antibody
libraries displayed on the surface of phage should prove even more
important than isolation of binding activities from murine
libraries. This is because the standard way of generating
antibodies via hybridoma technology has not had the success with
human antibodies that has been achieved with mouse. While in some
instances it will be possible to make libraries from immunized
humans, in many cases, it will not prove possible to immunize due
to toxicity or lack of availability of an appropriate immunogen or
ethical considerations. Alternatively, binding activities could be
isolated from libraries made from individuals with diseases in
which therapeutic antibodies are generated by the immune response.
However, in many cases, the antibody producing cells will be
located in the spleen and not available in the circulating pool of
peripheral blood lymphocytes (the most easily accessible material
for generating the library). In addition, in diseases associated
with immunosuppression, therapeutic antibodies may not be
produced.
[0640] An alternative approach would be to isolate binding
activities from a library made from an unimmunized individual. This
approach is based on estimates that a primary repertoire of 107
different antibodies is likely to recognize over 99% of epitopes
with an affinity constant of 10.sup.5 M.sup.-1 or better.
(Pewrelson, A. S. Immunol. Rev, (1989) 110:5). While this may not
produce high affinity antibodies, affinity could be boosted by
mutation of the V-genes and/or by using the isolated VH domain in a
hierarchical approach with a library of light chains (or vice
versa). In this section, we demonstrate the feasibility of this
approach by isolating specific antigen binding activities against
three different antigens from a library of scFvs from an
unimmunized human.
Materials and Methods
[0641] The generation of the human scFv library used for the
isolation of binding activities described in this example is
detailed in example 42.
Estimation of Diversity of Original and Selected Libraries:
[0642] Recombinant clones were screened before and after selection
by PCR (example 20) with primers LMB3 (which sits 5' of the pelB
leader sequence and is identical to the reverse sequencing primer
(-40 n) of pUC19) and fd-SEQ1 (see example 37) followed by
digestion with the frequent-cutting enzyme BstN1. Analysis of 48
clones from each unselected library indicated that 90% of the
clones had inset, and the libraries appeared to be extremely
diverse as judged by the BstNI restriction pattern.
[0643] Rescue of Phagemid Libraries for Enrichment Experiments: To
rescue phagemid particles from the library, 100 ml 2.times.TY
containing AMP-GLU (see example 42) was inoculated with 10.sup.9
bacteria taken from the library (prepared in example 42) (approx.
10 .mu.l) and grown for 1.5 hr, shaking at 37.degree. C.
[0644] Cells were spun down (IEC-centrifuge, 4 K, 15 min) and
resuspended in 100 ml prewarmed (37.degree. C.) 2.times.TY-AMP (see
example 41) medium, 2.times.10.sup.10 pfu of VCS-M13 (Stratagene)
particles added and incubated 30 min at 37.degree. without shaking.
Cells were then transferred to 900 ml 2.times.TY containing
ampicillin (100 .mu.g/ml) and kanamycin (25 .mu.g/ml) (AMP-KAN),
and grown overnight, while shaking at 37.degree. C. Phage particles
were purified and concentrated by three PEG-precipitations (see
materials and methods) and resuspended in PBS to 10.sup.13 TU/ml
(ampicillin resistant clones).
[0645] Enrichment for phOx:BSA binders by selection on tubes: For
enrichment, a 75.times.12 mm Nunc-immunotube (Maxisorp; Cat. No.
4-44202) was coated with 4 ml phOx:BSA (1 mg/ml; 14 phOx per BSA in
50 mM NaHCO3 pH 9.6 buffer) overnight at room temperature. After
washing three times with PBS, the tube was incubated for 2 hr at
37.degree. C. with PBS containing 2% Marvel (2% MPBS) for blocking.
Following three PBS washes, phagemid particles (1013 TU) in 4 ml of
2% MPBS were added, incubated 30 min at room temperature on a
rotating turntable and left for a further 1.5 hours. Tubes were
then washed with 20 washes of PBS, 0.1% Tween 20 and 20 washes PBS
(each washing step was performed by pouring buffer in and out
immediately). Bound phage particles were eluted from the tube by
adding 1 ml 100 mM triethylamine pH 11.5 and rotating for 15 min.
The eluted material was immediately neutralised by adding 0.5 ml
1.0 M Tris-HC1, pH 7.4 and vortexed. Phage was stored at 4.degree.
C.
[0646] Eluted phage (in 1.5 ml) was used to infect 8 ml logarithmic
growing E. coli TG1 cells in 15-ml 2.times.TY medium, and plated on
AMP-GLU plates as above yielding on average 10.sup.7 phage infected
colonies.
[0647] For selection of phOx:BSA binders, the rescue-tube
enrichment -plating cycle was repeated 4 times, after which
phagemid clones were analysed for binding by ELISA.
[0648] Enrichment for lysozyme binders by panning and on columns: A
petri dish (35.times.10 mm Falcon 3001 Tissue culture dish) was
used for enrichment by panning. During all steps, the plates were
rocked on an A600 rocking plate (Raven Scientific). Plates were
coated overnight with 1 ml turkey egg white lysozyme (3 mg/ml) in
50 mM sodium hydrogen carbonate (pH 9.6), washed three times with 2
ml PBS, and blocked with 2 ml 2% MPBS at room temperature for 2
hours. After three PBS washes approximately 10.sup.12 TU phage
particles in 1 ml 2% MPBS were added per plate, and left rocking
for 2 hr at room temperature. Plates were washed for 5 min with 2
ml of the following solutions: 5 times PBS, PBS-Tween (0.02%
Tween-20), 50 mM Tris-HC1 (pH 7.5)+500 mM NaC1, 50 mM Tris-HC1 (pH
8.5)+500 mM NaC1, 500 mM Tris-HC1 (pH 9.5)+500 mM NaC1 and finally
50 mM sodium hydrogen carbonate pH 9.6. Bound phage particles were
then eluted by adding 1 ml 100 mM triethylamine pH 11.5 and rocking
for 5 min before neutralising with 1 M Tris-HC1 (pH 7.4) (as
above). Alternatively, 1 ml turkey egg white lysozyme-Sepharose
columns were used for affinity purification (McCafferty, J., et
al., Nature, 1990, 348:552). Columns were washed extensively with
PBS, blocked with 15 ml 2% MPBS, and phage (10.sup.12 TU) in 1 ml
2% MPBS loaded. After washing with 50 ml PBS, 10 ml PBS-- Tween
(PBS+0.02% Tween-20), 5 ml of 50 mM Tris-HC1 (pH 7.5)+500 mM NaC1,
5 mM Tris-HC1 9pH 8.5)+500 mM NaC1, 5 ml of 50 mM Tris-HC1 (pH
9.5)+500 mM NaC1 and finally 5 ml of 50 mM sodium hydrogen
carbonate pH 9.6. Bound phage was eluted using 1.5 ml 100 mM
triethylamine and neutralised with 1 M Tris-HC1 (pH 7.4).
[0649] For selection of turkey egg white lysozyme binders, the
rescue-tube enrichment-plating cycle or rescue-column-plating cycle
was repeated 4 times, after which phagemid clones were analysed for
binding by ELISA.
[0650] Rescue of individual phagemid clones for ELISA: Clones
resulting from reinfected and plated phage particles eluted after 4
rounds of enrichment, were inoculated into 150 .mu.l of
2.times.TY-AMP-GLU in 96-well plates (cell wells, Nunclon), grown
with shaking (250 rpm) overnight at 37.degree. C. A 96-well plate
replicator (`plunger`) was used to inoculate approximately 4 .mu.l
of the overnight cultures on the master plate into 200 .mu.l fresh
2.times.TY-AMP-GLU. After 1 hr, 50 .mu.l 2.times.TY-AMP-GLU
containing 10.sup.8 pfu of VCS-M13 was added to each well, and the
plate incubated at 37.degree. C. for 45 min, followed by shaking
the plate at 37.degree. C. for 1 hr. Glucose was then removed by
spinning down the cells (4K, 15 min), and aspirating the
supernatant with a drawn out glass pasteur pipet. Cells were
resuspended in 200 .mu.l 2.times.TY-AMP-KAN (Kanamycin 50 ug/ml)
and grown 20 hr, shaking 37.degree. C. Unconcentrated supernatant
containing phage was taken for analysis by ELISA.
ELISA
[0651] Analysis for binding to phOx:BSA, BSA or lysozyme was
performed by ELISA (see example 9), with 100 .mu.g/ml phOx:BSA or
BSA, or 3 mg/ml turkey egg white lysozyme used for coating.
Determination of cross reactivity to unrelated antigens with the
isolated clones was also determined by ELISA on plates coated with
100 ug/ml of an irrelevant antigen (keyhole limpet haemocyanin
(KLH), ovalbumin, chymotrypsinogen, cytochrome C, thyroglobulin,
GAP-DH (glyceraldehyde-3-phosphate dehydrogenase), or trypsin
inhibitor).
[0652] Characterization of ELISA positive clones: All antigen
specific clones isolated were checked for cross reactivity against
a panel of irrelevant antigens as described above. The diversity of
the clones was determined by PCR screening as described above and
at least two clones from each restriction pattern were sequenced by
the dideoxy chain termination method.
Results
[0653] Isolation and characterization of phOx:BSA binders: After 4
rounds of selection, ELISA-positive clones were isolated for
phOx:BSA. All clones originated from the IgM library. Of 96 clones
analysed, 43 clones were binding to both phOx:BSA and BSA, with ODs
ranging from 0.4 to 1.3 (background 0.125). These clones are
designated as BSA binders. The binding to BSA seemed to be
specific, since none of the 11 clones analysed gave a signal above
background when used in an ELISA with KLH, ovalbumin,
chymotrypsinogen, cytochrome C, lysozyme, thyroglobulin, GAP-DH, or
trypsin inhibitor. All BSA binding clones had the same BstNI
restriction pattern, and 14 clones were completely sequenced.
Thirteen of the fourteen clones had the same sequence, the VH was
derived from a human VH3 family gene and the VL from a human V
lambda 3 family gene (Table 1). The other BSA binder was derived
from a human VH4 family gene and a human Vk1 family gene (data not
shown).
[0654] One clone was isolated which bound to phOx:BSA only (OD
0.3), and bound phage could be completed off completely by adding
0.02 mM 4-.epsilon.-amino-caproic acid methylene
2-phenyl-oxazol-5-one (phOx-CAP) as a competitor. Also no binding
above background could be detected to the panel of irrelevant
proteins described above. The sequence revealed a VH derived from a
human VH1 family gene and a VL derived from a human V lambda 1
family gene (Table 11).
[0655] Isolation and characterisation of lysozyme binders: After 4
rounds of selection, 50 ELISA-positive clones were isolated for
turkey lysozyme. The majority of the clones, greater than 95%, were
from the IgM library. The binding to lysozyme seemed to be
specific, since none of the clones analysed gave a signal above
background when used in an ELISA with KLH, ovalbumin,
chymotrypsinogen, cytochrome C, thyroglobulin, GAP-DH, or trypsin
inhibitor. The lysozyme binding clones gave 3 different BstNI
restriction patterns, and at least 2 clones from each restriction
pattern were completely sequenced. The sequences indicated the
presence of 4 unique human VH-VL combinations. (Table 11).
CONCLUSION
[0656] The results indicate that antigen binding activities can be
isolated from repertoires of scFvs prepared from IgM cDNA from
human volunteers that have not been specifically immunized.
Example 44
Rescue of human IgM Library Using Helper Phage Lacking Gene 3
(.delta.g3)
[0657] This example describes the rescue of gene 3 fusions from a
human library using a helper phage with a gene 3 deletion.
[0658] 100 .mu.l of bacterial stock of the IgM phagemid library
prepared as described (example 42), containing 5.times.10.sup.8
bacteria, was used to inoculate 100 mls of 2.times.TY medium
containing 100 .mu.g/ml ampicillin, 2% glucose (TY/Amp/Glu). This
was grown at 37.degree. C. for 2.5 hours. 10 mls of this culture
was added to 90 mls of prewarmed TY/Amp/Glu and infection carried
out by adding 10 mls of a 200 fold concentrate of K07 helper phage
lacking gene 3 (M13KO7gIII.DELTA. No. 3) (example 34) and
incubating for 1 hour at 37.degree. C. without shaking. Preparation
of M13KO7gIII No. 3 was as described in example 34. After
centrifugation at 4,000 r.p.m. for 10 minutes the bacteria were
resuspended in 100 mls of 2.times.TY medium containing 100 .mu.g/ml
ampicillin (with no glucose). Titration of the culture at this
point revealed that there were 1.9.times.10.sup.8 infected bacteria
as judged by their ability to grow on plates containing both
ampicillin (100 .mu.g/ml) and kanamycin (50 .mu.g/ml). Incubation
was continued for 1 hour with shaking before transferring to 2.5
litres of 2.times.TY medium containing 100 .mu.g/ml ampicillin, 50
.mu.g/ml kanamycin, contained in five 2.5 litre flasks. This
culture was incubated for 16 hours and the supernatant prepared by
centrifugation. (10-15 minutes at 10,000 r.p.m. in a Sorvall RC5B
centrifuge at 40C ). Phage particles were harvested by adding 1/5th
volume of 20% polyethylene glycol, 2.5 M NaC1, standing at 40C for
30 minutes and centrifuging as above. The resulting pellet was
resuspended in 40 mls of 10 mM Tris, 0.1 mM EDTA pH 7.4 and
bacterial debris removed by centrifugation as above. The packaged
phagemid preparation was then re-precipitated, collected as above
and resuspended in 10 mls of 10 mM Tris, 0.1 mM EDTA pH 7.4. The
litre of this preparation was 4.1.times.10.sup.13 transducing
units/ml (ampicillin resistance).
[0659] Tubes coated with OX-BSA were prepared as described in
example 45 for panning the phagemid library from example 42. The
rescued library was also panned against tubes coated with bovine
thyroglobulin (Sigma). These were coated at a concentration of 1
mg/ml thyroglobulin in 50 mM NaHCO3 pH9.6 at 37.degree. C.,
overnight. Tubes were blocked with PBS containing 2% milk powder
(PBS/M) and incubated with 1 ml of the rescued phagemid library
(the equivalent of 250 mls of culture supernatant) mixed with 3 mls
of PBS/M for 3 hours. Washing, elution, neutralisation and
infection were as described in example 45.
Results: Panning Against Oxazalone--BSA
[0660] The first round of panning against OX-BSA yielded
2.8.times.10.sup.6 phage. A large bacterial plate with
1.4.times.10.sup.6 colonies derived from this eluate was scraped
into 10 mls of 2.times..times.TY, 20% glycerol, shaken for 10
minutes, aliquoted and stored. This was also used to inoculate a
fresh culture for rescue with M13KO7gIII No. 3. (Bacteria and
rescued phage derived from first round panning against OX-BSA are
named OXPAN1. Bacteria or rescued phage derived from second and
third round pannings are named OXPAN2 and OXPAN3 respectively)
Rescue of phagemid with M13KO7gIII No. 3 after each round of
panning was essentially as described above but using 5 ml volumes
for the initial cultures in TY/Amp/Glu, using 1 ml of helper phage
and transferring to 100-500 mls of 2.times.TY medium containing 100
.mu.g/ml ampicillin, 50 .mu.g/ml kanamycin. Second and third round
panning steps were as described above for the first round, but
using 0.8-11.0 mls of 100 fold concentrated phage (the equivalent
of 80-100 mls of culture supernatant). The eluate from the second
round panning contained 8.times.10.sup.8 infectious particles and
the eluate from the third round panning contained
3.3.times.10.sup.9 infectious particles.
Panning Against Thyroglobulin
[0661] The first round panning against thyroglobulin yielded
2.52.times.10.sup.5 infectious particles. Half of the eluate was
used to generate 1.26.times.10.sup.5 bacterial colonies on a large
plate. These colonies were scraped into 10 mls of 2.times.TY, 20%
glycerol, shaken for 10 minutes, aliquoted and stored. These
bacteria and rescued phage derived from them are termed THYPAN1,
and used to inoculate a fresh culture for rescue with M13KO7gIII
No. 3 to give a polyclonal rescued phage preparation. Material
similarly derived from second and third round pannings are termed
THYPAN2 and THYPAN3 respectively. Second and their round pannings
with thyroglobulin were as described for second and third round
OX-BSA panning. The eluate from the second round panning contained
8.times.10.sup.7 transducing units and the eluate from the third
round panning contained 6.times.10.sup.7 infectious particles.
ELISA Screening of Clones Derived by Panning
[0662] 40 colonies derived form the third round of panning against
thyroglobulin (THYPAN3) were picked into a 96 well plate and grown
overnight at 37.degree. C. in 200 .mu.l of TY/Amp/clu. Similarly 48
colonies from two rounds and 48 colonies from three rounds of
panning against OX-BSA were grown (OX-PAN2 and OX-PAN3). Polyclonal
phage were prepared at the same time. Next day 5 .mu.l from each
culture was transferred to 100 .mu.l of fresh prewarmed TY/Amp/Glu
grown for 1.5 hours and M13KO7gIII No. 3 added (2.times.10.sup.5
infectious phage per well in 100 .mu.l of TY/Amp/Glu). These were
incubated for 1 hour at 37.degree. C. without shaking, centrifuged
at 4,000 r.p.m. for 10 minutes, resuspended in 150 .mu.l of
2.times.TY medium containing 100 .mu.g/ml ampicillin and incubated
for a further hour with shaking before adding to 2mls of medium
containing 100 .mu.g/ml ampicillin, 50 .mu.g/ml kanamycin. After
overnight growth the cultures were centrifuged at 4,000 r.p.m. for
10 minutes and the supernatants collected. ELISA plates used to
screen THYPAN3 clones were coated at 37.degree. C. overnight with
200 .mu.g/ml thyroglobulin in 50 mM NaHCO3pH9.6. Plates used for
OXPAN2 and OXPAN3 were coated at 100 .mu.g/ml OX-BSA in PBS at
37.degree. C. overnight.
[0663] 120 .mu.l of culture supernatant was mixed with 30 .mu.l of
5.times.PBS, 10% milk powder and incubated at room temperature for
2 hours at room temperature. ELISAs were carried out as described
in example 18.
[0664] For thyroglobulin, 18 out of 40 clones were positive
(0.3-2.0 O.D. after 30 minutes). (A phage control (vector pCAT3)
gave a reading of 0.07 O.D.). In addition, positives were also seen
on the polyclonal phage preparations THYPAN1 (0.314 O.D.) and
THYPAN2 (0.189 O.D.) compared with phage derived from the original
non-panned phagemid library (0.069 O.D.). All polyclonal phage were
PEG precipitated and used at a 10 fold concentration.
[0665] PCR reactions and BstN1 digests were carried out on the
positive clones as described above and six different patterns of
DNA fragments were obtained showing that at least six different
clones had been isolated.
[0666] For OX-BSA after two rounds of panning, 30 of 48 clones were
positive by ELISA and after three rounds, 42 of 48 were positive.
In a separate experiment, positive signal was obtained from the
polyclonal phage preparations OXPAN1 (0.988 OD) and OXPAN2 (1.717
OD) compared with phage derived from the original non-panned
phagemid library (0.186 O.D.) after 30 minutes.
Specificity of Clones for Thyroglobulin or OX-BSA
[0667] Selected clones (11 anti-thyroglobulin, 5 anti-OX-BSA)
representing each of the different BstNI restriction digest
patterns were assayed for binding to a panel of irrelevant
antigens. ELISA plates were coated with antigen (100 .mu.l/ml in 50
mM NaHCO3, pH 9.6) by overnight incubation at 37.degree. C. The
panel of antigens consisted of keyhole limpet haemocyanin, hen egg
lysozyme, bovine serum albumin, ovalbumin, cytochrome c,
chymotrysinogen, trypsin inhibitor, GAP-D11
(glyceraldehyde-3-phosphate dehydrogenase), bovine thyroglobulin
and oxazolone-BSA. Duplicate samples of phage supernatant (80
.mu.l+20 .mu.l 5.times.PBS, 10% milk powder) were added to each
antigen and incubated for 1 hour at room temperature. The ELISA was
carried out as described in example 18.
[0668] Each of the thyroglobulin specific clones (11 from 11) were
positive for thyroglobulin (OD 0.12-0.76) but after 60 minutes
showed no binding (OD<0.03) to any of the 9 irrelevant antigens.
Similarly of the 5 OX-BSA specific clones 3 had an OD 0.07-0.52
compared to ODs <0.02 for the irrelevant antigens. None of the 5
clones had any binding to BSA alone.
[0669] Thus positive clones can be isolated after only two rounds
of panning by rescuing with M13KO7gIII No. 3. In addition there is
a greater likelihood with this helper of generating phage particles
with more than one intact antibody molecule. This will potentially
increase the avidity of phage-antibodies and may enable isolation
of clones of weaker affinity.
Example 45
Alteration of Fine Specificity of scFv D1.3 Displayed on Phage by
Mutagenesis and Selection on Immobilised Turkey Lysozyme
[0670] The D1.3 antibody binds hen egg lysozyme (HEL) with an
affinity constant of 4.5.times.10.sup.7M.sup.-1 whereas it binds
turkey egg lysozyme (TEL) with an affinity of
<1.times.10.sup.5M.sup.-1. (Harper et al (1987) Molecular
Immunology 24 p 97-108, Amit et al (1986) Science 233 p
747-753).
[0671] It has been suggested that this is because the glutamine
residue present at position 121 of HEL (gln121) is represented by
histidine residue at the same position in TEL. Thus mutagenising
the D1.3 antibody residues which interact with gln121 of HEL may
facilitate binding to TEL.
[0672] According to Amit et al, supra, tyrosine at amino acid
position 32, phenylalanine at position 91 and tryptophan at
position 92 of the light chain interact with gln121 of HEL. In
addition tyrosine at position 101 of the heavy chain also
interacts. None of these residues are predicted to be involved in
determining the main chain conformation of the antibody variable
regions (Chothia and Lesk (1987) Journal of Molecular Biology 196,
p 901-917).
Mutagenesis of pCAT3SCFvD1.3
[0673] The oligonucleotides mutL91,92, was prepared to randomise
phenylalanine at position 91 (L91) and tryptophan at position 92
(L92) of the light chain. The oligonucleotides mutL32, was prepared
to randomise tyrosine at light chain position 32 (L32) and the
oligonucleotides mutH101 was prepared to randomise tyrosine at
position 101 of the heavy chain (H101). TABLE-US-00024 mutL91, 92:
5' CGT CCG AGG AGT ACT NNN NNN ATG (SEQ ID NO:75) TTG ACA GTA ATA
3' mutL32: 5' CTG ATA CCA TGC TAA NNN ATT GTG (SEQ ID NO:76) ATT
ATT CCC 3' mutH101: 5' CCA GTA GTC AAG CCT NNN ATC TCT (SEQ ID
NO:77) CTC TCT GGC 3'
(N represents a random insertion of equal amounts of A, C, G or T)
in vitro mutagenesis of the phagemid vector, pCAT3scFvD1.3 (example
17) with the oligonucleotide mutL91,92 was carried out using an in
vitro mutagenesis kit (Amersham). The resultant DNA was transformed
by electroporation into TG1 cells using a Bio-Rad electroportor.
78,000 clones were obtained and these were scraped into 15 mls of
2.times.TY/20% glycerol. This pool was called D1.3L91L92. Single
stranded DNA was prepared by rescue with M13K07 as described in
Sambrook et al, 1989 supra, and sequenced with the primer FDTSEQ1,
using a Sequenase sequencing kit (United States Biochemical
Corporation).
[0674] This revealed that the DNA had been successfully mutagenised
as judged by the presence of bands in all four DNA sequencing
tracks at the nucleotide positions encoding L91 and L92. This
mutagenised single stranded DNA was subjected to a further round of
mutagenesis as above using either mutL32 or mutH101
oligonucleotides. Mutagenesis with mutL32 gave rise to 71,000
clones (pool called D1.3L32) while mutH101 gave 102,000 clones
(pool called D1.3H101). These clones were scraped into 15 mls of
2.times.TY/20% glycerol. Single stranded DNA derived from each pool
was sequenced with the oligonucleotides D1.3L40 and LINKSEQ1
respectively, as described above, and shown to be correctly
randomised. TABLE-US-00025 D1.3L40: 5' CAG GAG CTG AGG AGA TTT TCC
3' LINKSEQ1: 5' TCC GCC TGA ACC GCC TCC ACC 3'
Preparation of Rescued Phage for Affinity Purification
[0675] 10-20 .mu.l of bacteria derived from each mutagenised pool
(plate scrapes) was used to inoculate 5 mls of TY/Glu/Amp. All
bacterial growth was at 37.degree. C. After 2-3 hours growth, 1 ml
was diluted in 5 mls of prewarmed TY/Glu/Amp and infected by
addition of 0.5 mls of a 200 fold concentrate of the M13K07gIII
.DELTA. No. 3 preparation described in example 34. After 1 hour of
infection the cultures were centrifuged at 4,000 r.p.m. for 10
minutes, resuspended in 2.times.TY, 100 .mu.g/ml ampicillin,
incubated for a further hour, transferred to 500 mls of 2.times.TY
medium containing 100 .mu.g/ml ampicillin, 50 .mu.g/ml kanamycin
and grown for 16 hours. The remaining steps of phage preparation
were as described in example 44. Phage were finally dissolved in 10
mM Tris, 1 mM EDTA pH7.4 at 1/100th the original culture
volume.
Affinity Purification
[0676] 10 mls of turkey egg lysozyme at a concentration of 10 mg/ml
in 0.1M NaHCO3, 0.5MNaC1 pH8.3 was mixed with an equal volume of
swollen Cyanogen Bromide Activated Sepharose 4B (Pharmacia),
covalently linked and washed according to manufacturers
instructions. Before use this matrix (TEL-Sepharose) was washed
with 100 volumes of PBS followed by 10 volumes of PBSM. The
TEL-Sepharose was resuspended in an equal volume of PBSM and 1 ml
was added to 1 ml of a 50 fold concentrate of phage in PBSM and
incubated on a rotating platform for 30 minutes at room
temperature. The actual phage used for this step was prepared by
mixing equal volumes of the independent preparations of the three
randomised pools (D1.3L9192, D1.3H101 and D1.3L32). After this
binding step, the suspensions were loaded onto a disposable
polypropylene column (Poly-Prep columns, Bio-Rad) and washed with
200 volumes of PBS containing 0.1% Tween 20. Bound phage were
eluted with 1 ml of 100 mM triethylamine and neutralised with 0.5
ml 1M Tris (pH7.4). A dilution series was prepared from the eluate
and used to infect TG1 cells and plated out on TY plates containing
100 .mu.g/ml ampicillin, 2% glucose. Plates carrying approximately
10.sup.6 colonies were scraped into 3 mls of 2.times.TY, 20%
glycerol and stored at -70.degree. C. 10 .mu.l of this was used to
initiate a second round culture which was rescued with
M13K07gIII.DELTA. No. 3 as described above (using a final culture
volume of 100 mls). Second and third round affinity column
purification steps were carried out as described above for the
first round.
Analysis by ELISA
[0677] 40 colonies derived from the third round of column
purification on TEL-Sepharose were picked into a 96 well plate and
grown overnight at 37.degree. C. in 200 .mu.l of TY/Amp/Glu.
Phagemid particles were rescued and prepared for ELISA as described
in example 18. ELISA plates were coated overnight at 37.degree. C.
with hen egg lysozyme (HEL) or turkey egg lysozyme (TEL) at a
concentration of 200 .mu.g/ml in 50 mM NaHCO.sub.3 pH9.6 ELISAs
were carried out as described in example 18.
[0678] After 15 minutes incubation in substrate, 13 clones were
found to be negative (OD<0.05 on HEL and TEL). In all positives,
a signal of 0.1-0.78 was scored on HEL with the exception of one
where signal on HEL was 0.078 but signal on TEL (OD 0.169) brought
it in to the positive group. The control phagemid preparation had a
percentage ratio of signal TEL:HEL of 22%. Clones were deemed to
have an unaltered binding if the ratio of TEL:HEL was less than
40%. 9 clones fell into this category. 18 samples were scored as
having altered binding with a ratio of signal on TEL:HEL of between
40-200%.
[0679] A dilution series was made on 10 clones which were analysed
by ELISA in 6 of these clones the profile of binding to HEL was the
same as the original clone (pCAT3SCFvD1.3) while the signal with
TEL was increased (see FIG. 50a clone B1). In the remaining 4
clones, the increased signal with TEL was accompanied by a decrease
in signal on HEL (see FIG. 50 clone A4).
Competition with Soluble Antigen
[0680] All of the isolated clones retained binding to HEL to
varying extents. In order to determine whether a soluble antigen
could compete with the immobilised antigen, a parallel experiment
was carried out, as above, but with the addition of hen egg
lysozyme (1 mg/ml) to TEL-Sepharose before incubating with the
phage preparation. This experiment was carried through 3 rounds of
column purification and 40 colonies were picked. None of these
clones bound HEL or GEL demonstrating that the soluble antigen had
been successful in competing out binding to the immobilised
antigen.
Example 46
Modification of the Specificity of an Antibody by Replacement of
the VLK Domain by a VLK Library Derived from an Unimmunised
Mouse
[0681] When an antibody specificity is isolated it will often be
desirable to alter some of its properties particularly its affinity
or specificity. This example demonstrates that the specificity of
an antibody can be altered by use of a different VL domain derived
form a repertoire of such domains. This method using display on
phage would be applicable to improvement of existing monoclonal
antibodies as well as antibody specificities derived using phage
antibodies. This example shows that replacement of the VL domain of
scFvD1.3 specific for Hen eggwhite lysozyme (HEL) with a library of
VL domains allows selection of scFv fragments with bind also to
Turkey eggwhite lysozyme (TEL). More generally this experimental
approach shows that specificities of antibodies can be modified by
replacement of a variable domain and gives a further example of the
hierarchical approach to isolating antibody specificities.
[0682] The D1.3 heavy chain was amplified from an existing
construct (pSW1-VHD1.3, Ward et al., 1989 supra) by PCR using the
primers VH1BACK and VH1FOR, the light chain library was amplified
from a cDNA library derived from the spleen of an unimmunised
mouse, which was synthesized by using the MJKFONX primers 1, 2, 4,
5 for the first strand as in example 14. The subsequent
amplification was performed with the same forward primers and the
VK2BACK primer. The PCR assembly of the D1.3 heavy chain with the
light chain library was mediated by the signal chain Fv linker as
described in example 14.
[0683] Cloning the assembled PCR products (scFv sequences) was done
after an additional PCR step (pull-through) using a BACK primer
providing an ApaLI site and forward primers which contained a Not 1
site as described in example 14. ApaL1/Not 1 digested PCR fragments
were cloned into the similarly digested vector fdCAT2 as in example
11. 5.times.10.sup.5 transformations were obtained after
electroporation of the ligation reaction into MC1061 cells.
[0684] Screening of the phage library for TEL binders was performed
by panning. Polystyrene Falcon 2058 tubes were coated (16 hrs) with
2 ml of TEL-PBS (3 mg/ml) and blocked for 2 hrs with 4 ml MPBS (PBS
containing 2% skimmed milk powder). Phage derived from the library
(5.times.10.sup.10 transducing unites) in 2 ml of MPBS (2%) were
incubated in these tubes for 2 hrs at room temperature. The tubes
were washed 3.times. with PBS, 1.times. with 50 mM Tris-HCl, pH
7.5, 0.5 M NaCl; 1.times. with 50 mM Tris-HCl, pH8.5, 0.5 M NaCl,
50 mM Tris-HCl, pH 9.5 M NaCl. Finally phage were eluted with 100
mM triethylamine. Eluted phages were taken to infect TG1 cells, the
cells were plated on 2.times.TY plates containing 15 .mu.g/ml
tetracycline and grown for 16 h. The colonies were scraped into 25
ml of 2.times.Ty medium and the phages were recovered by PEG
precipitation. After a second round of selection for TEL binders
ELISAs were performed as described (example 2).
[0685] Analysis of 100 clones from the library before affinity
selection by ELISA on plates coated with TEL showed no binders. In
contrast, after two rounds of selection for TEL binding phages
about 10% of the phage clones showed positive ELISA signals. ELISA
signals were scored positive with values at least two fold higher
than the fdCAT2 vector without insert. A more detailed analysis of
binding properties of TEL binding phages is shown in FIG. 51.
[0686] As shown in FIG. 51, several clones were found which bind
equally to TEL and HEL in contrast to the original D1.3 scFv, which
binds almost exclusively to HEL. None of the clones bound to BSA.
These findings indicate that the specificity of these scFvs was
broader in comparison to D1.3, since both lysozymes (HEL and TEL)
are recognized, but specificity for lysozyme was retained since
other BSA was not recognized. The deduced amino acid sequences
(derived by DNA sequencing) of two light chains from clones MF1 and
M21, which correspond to clones 3 and 9 in FIG. 51 are shown in
FIG. 52.
[0687] In the case of isolated antibodies the experimental approach
as described in this study may be particularly useful if
recognition of a wider range of different but closely related
antigens is desired. For example, monoclonal antibodies against
viral antigens viral antigens like V3 loop of HIV-1 gp120 are in
most cases quite specific for one particular virus isolate because
of the variability in this part of the HIV-1 env gene. The
modification of such antibodies in the way described in this
example may lead to antibodies which cross react with a wider range
of HIV-1 isolates, and would therefore be of potentially higher
therapeutic or diagnostic value.
[0688] A similar approach could be taken in which a light chain
variable domain of desired properties is kept fixed and combined
with a library of heavy chain variable domains. Some heavy chains,
for example VHD1.3 retain binding activity as single domains. This
may allow a strategy where VH domains are screened for binding
activity when expressed on phage and then binding domains combined
with a library of VL domains for selection of suitable light chain
partners.
Example 47
Selection of a Phage Antibody Specificity by Binding to an Antigen
Attached to Magnetic Beads. Use of a Cleavable Reagent to Allow
Elution of Bound Phage Under Mild Conditions
[0689] When a phage antibody binds to its antigen with high
affinity or avidity it may not be possible to elute the phage
antibody from an affinity matrix with a molecule related to the
antigen. Alternatively, there may be no suitable specific eluting
molecule that can be prepared in sufficiently high concentration.
In these cases it is necessary to use an elution method which is
not specific to the antigen-antibody complex. Unfortunately, some
of the non-specific elution methods disrupt phage structure, for
instance phage viability is reduced with time at pH12 (Rossomando,
E. F. and Zinder, N. D. J. Mol. Biol. 36 387-399 1968). A method
was therefore devised which allows elution of bound phage
antibodies under mild conditions (reduction of a dithiol group with
dithiothreitol) which do not disrupt phage structure.
[0690] Target antigen was biotinylated using a cleavable
biotinylation reagent. BSA conjugated with 2-phenyl-5-oxazolone (O.
Makela et al. supra) was modified using a biotinylation reagent
with a cleavable dithiol group
(sulphosuccinimidyl2-(biotinamido)ethyl-1,3-dithiopropionate from
Pierce) according to the manufacturers instructions. This
biotinylated antigen was bound to streptavidin coated magnetic
beads and the complex used to bind phage. Streptavidin coated
magnetic beads (Dynal) were precoated with antigen by mixing 650
.mu.g of biotinylated OX-BSA in 1 ml PBS, with 200 .mu.l of beads
for at least 1 hour at room temperature. Free antigen was removed
by washing in PBS. One fortieth of the complex (equivalent to 5
.mu.l of beads and an input of 17.5 .mu.g of OX-BSA) was added to
0.5 ml of phage in PBSM (PBS containing 2% skimmed milk powder)
containing 1.9.times.10.sup.10 phage particles mixed at the ratios
of pAbD1.3 directed against lysozyme (example 2) to pAbNQ11
directed against 2-phenyl-5-oxazolone (example 11) shown in Table
12.After 1 hour of incubation with mixing at room temperature,
magnetic beads were recovered using a Dynal MPC-E magnetic
desperation device. They were then washed in PBS containing 0.5%
Tween 20, (3.times.10 minutes, 2.times.1 hour, 2.times.10 minutes)
and phage eluted by 5 minutes incubation in 50 .mu.l PBS containing
10 mM dithiothreitol. The eluate was used to infect TG1 cells and
the resulting colonies probed with the oligo NQ11CDR3 (5'
AAACCAGGCCCCGTAATCATAGCC 3') (SEQ ID NO:80) derived from CDR3 of
the NQ11 antibody (This hybridises to pAbNO11 but not pAb
D1.3).
[0691] A 670 fold enrichment of pAbNQ11 (table 12) was achieved
form a background of pAbD1.3 in a single round of purification
using the equivalent of 17.5 .mu.g of biotinylated OX-BSA.
[0692] This elution procedure is just one example of an elution
procedure under mild conditions. A particularly advantageous method
would be to introduce a nucleotide sequence encoding amino acids
constituting a recognition site for cleavage by a highly specific
protease between the foreign gene inserted, in this instance a gene
for an antibody fragment, and the sequence of the remainder of gene
III. Examples of such highly specific proteases are Factor X and
thrombin. After binding of the phage to an affinity matrix and
elution to remove non-specific binding phage and weak binding
phage, the strongly bound phage would be removed by washing the
column with protease under conditions suitable for digestion at the
cleavage site. This would cleave the antibody fragment from the
phage particle eluting the phage. These phage would be expected to
be infective since the only protease site should be the one
specifically introduced. Strongly binding phage could then be
recovered by infecting, e.g., E. coli TG1 cells.
Example 48
Use of Cell Selection to Provide an Enriched Pool of Antigen
Specific Antibody Genes, Application to Reducing the Complexity of
Repertoires of Antibody Fragment Displayed on the Surface of
Bacteriophage
[0693] There are approximately 10.sup.14 different combinations of
heavy and light chains derived from the spleen of an immunised
mouse. If the random combinatorial approach is used to clone heavy
and light chain fragments into a single vector to display scFv, Fv
or Fab fragments on phage, it is not a practical proposition to
display all 10.sup.14 combinations. One approach, described in this
example, to reducing the complexity is to clone genes only from
antigen selected cells. (An alternative approach, which copes with
the complexity is the dual combinatorial library described in
example 26).
[0694] The immune system uses the binding of antigen by surface
immunoglobulin to select the population of cells that respond to
produce specific antibody. This approach of selecting antigen
binding cells has been investigated to reduce the number of
combinatorial possibilities and so increase the chance of
recovering the original combination of heavy and light chains.
[0695] The immunological response to the hapten
4-hydroxy-3-nitrophenylacetic acid (NP) has been extensively
studied. Since the primary immune response to NP uses only a single
light chain the applicants were able to examine the use of the
combinatorial method using a fixed light chain and a library of
heavy chains to examine the frequencies genes that code for
antibodies binding to NIP (4-hydroxy-3-iodo-5-nitrophenylacetic
acid). The applicants have thus used this system to investigate the
merits of selecting cell populations prior to making combinatorial
libraries for display on phage.
Methods
2.1 Hapten Conjugates
[0696] Chick gamma globulin (CGG, Sigma, Poole, UK) and Bovine
serum albumen (BSA, Boehringer, Mannheim, Germany) were conjugated
with NP--O-succinimide or NIP-caproate-O-succinimide (Cambridge
Research Biochemicals, Northwich, UK) based on the method described
by Brownstone (Brownstone, A., Mitchison, N. A. and Pitt-Rivers,
R., Immunology 1966. 10: 465-492). The activated compounds were
dissolved in dimethylformamide and added to proteins in 0.2 M
sodium hydrogen carbonate. They were mixed with constant agitation
for 16 hours at 4.degree. C. and then dialysed against several
changes of 0.2 M sodium hydrogen carbonate. They were finally
dialysed into phosphate buffered saline (PBS). The conjugates made
were NP.sub.12CGG, NIP.sub.10BSA. The NIP.sub.10BSA derivative was
subsequently biotinylated using a biotinylation kit purchased from
Amersham (Amersham International, Amersham, UK).
2.2 Animals and Immunisation
[0697] Mice of the strain C57BL/6 were immunised by intraperitoneal
injection of 100 .mu.g NP-CGG in Complete Freunds Adjuvant at 10
weeks of age.
2.3 Spleen Preparation
[0698] Seven days after immunization cells from the spleen were
prepared as described by Galfre and Milstein (Galfre, G. and
Milstein, C. Methods Enzymol. 1981. 73:3-46). Red cells were lysed
with ammonium chloride (Boyle, W. Transplantation 1968.6:71) and
when cell selection was performed dead cells were removed by the
method described by von Boehmer and Shortman (von Boehmer, H. and
Shortman, K, J. Immunol, Methods 1973:1:273). The cells were
suspended in phosphate buffered saline (PBS), 1% Bovine serum
albumen, 0.01% sodium azide; throughout all cell selection
procedures the cells were kept at 4.degree. C. in this medium.
2.4 Cell Solution
[0699] Biotinylated NIP-BSA was coupled to streptavidin coupled
magnetic beads (Dynabeads M280 Streptavidin, Dynal, Oslo, Norway)
by incubating 10.sup.8 beads with 100 .mu.g of biotinylated protein
for 1 hour, with occasional agitation, and then washing five times
to remove unbound antigen. The coupled beads were stored at
4.degree. C. in medium until required. For selection of antigen
binding cells the cells (2-4.times.10.sup.7/ml) were first
incubated for 30 minutes with uncoupled beads, at a bead: cell
ratio of 1:1, to examine the degree of non-specific binding. The
beads were then separated by placing the tube in a magnetic device
(MPC-E Dynal) for 3-5 minutes. The unbound cells were removed and
then incubated with NIP-BSA coupled magnetic beads, at a bead:cell
ratio of 0.1:1, for 60 minutes, with occasional agitation. The
beads and rosetted cells were separated as described above. The
beads were then resuspended in 1 ml of medium and the separation
repeated; this process was repeated 5-7 times until no unbound
cells could be detected when counted on a haemocytometer.
[0700] For the depletion of surface immunoglobulin positive cells
the cells were incubated with 20 .mu.g biotinylated goat anti-mouse
polyvalent immunoglobulin (Sigma, Poole, UK). The cells were then
washed twice with medium and added to streptavidivin coupled
magnetic beads at a bead to cell ratio of 30:1. After 30 minutes
incubation the beads and rosetted cells were separated by applying
the magnetic device three times - taking the supernatant each
time.
2.4 DNA/cDNA Preparation, PCR Amplification and Cloning
[0701] DNA was prepared by a simple proteinase-K digest method that
was particularly convenient for small numbers of cells (PCR
Protocols: A Guide to Methods and Applications. Ed Innis M. A.,
Gelfand D. H., Sninsky J. J. and White T. J. Academic Press). RNA
preparation and subsequent cDNA synthesis was performed as
described by Gherardi et al (Gherardi E., Pannell R. and Milstein
C. J. Immunol. Methods, 1990. 126:61-68). PCR and cloning of the
heavy chain libraries was performed using the primers and
conditions described by Ward et al (Ward, E. S., Gussow, D.,
Griffiths, A. D., Jones, P. T. and Winter, G., Nature, 1989. 341:
544-546); 40 cycles of PCR amplification were performed. The VH and
Fv expression vectors used were adapted from those previously
described by Ward et al. They were both subcloned into pUC119
(Veira and Messing see later) and the Fv expression vector was
modified to include a germline lambda-1 light chain (obtained as a
gift from T. Simon (originally cloned by Siegfried Weiss, Basel
Institute of Immunology)). THe vector is shown in FIG. 53.
2.5 Expression and ELISA
[0702] For screening single colonies were picked into individual
wells of microtitre plates (Bibby) in 200 .mu.l
2.times.TY/Ampicillin 100 .mu.g/ml/0.1% glucose and then incubated
at 37.degree. C. for 5-6 hours with agitation,
Isopropyl-.beta.-D-thiogalactopyranoside (IPTG, Sigma, Poole, UK)
was then added to a final concentration of 1 mM and the incubation
continued for a further 16 hours at 30.degree. C. before harvesting
the supernatants. The wells of Falcon ELISA plates (Becton
Dickenson, N.J., USA) were coated overnight at room temperature
with NIP.sub.10-BSA (40 .mu.g/ml in PBS) and then blocked with 2%
skimmed milk powder in PBS for 2 hours at room temperature. The
bacterial supernatants were added and incubated at room temperature
for 1 hour and then the plates were washed three times with PBS.
Peroxidase conjugated-Goat anti-mouse lambda-chain (Southern
Biotechnology, Birmingham, USA) was added and again incubated for 1
hour at room temperature before washing six times with PBS and then
developing with 2,2'-Azino-bis (3-ethylbenzthiazoline-6-sulfonic
acid) (Sigma, Poole, UK) as the peroxidase substrate. The optical
density at 405 nm was measured using a Thermomax microplate reader
(Molecular Devices, Menlo Park, USA) after 30 minutes. Western
blotting using the C-terminal myc tag as described in example
27.
3.1 Comparison of RNA/DNA and Antigen Selected Cells
[0703] The results of antigen selection are shown in Table 13. Less
than 1% of cells bind to NIP-BSA coated beads and the non-specific
binding is very low. Assessment of the proportion of expressed
genes from each VH library using western blotting showed that full
length VH domains were expressed in 95% ( 19/20) of all clones when
RNA was used as the starting material but only 60% ( 12/20) of
clones when DNA (either selected cells or from total spleen) was
used as the starting material. This difference probably results
from the fact that many re-arranged pseudogenes could be amplified
with our primers and it appears that there must be some degree of
selection, at the level of transcription, for functional genes.
[0704] A variable number of clones from each type of library were
screened for the production of Fv fragments that bound to NIP.
Initial screening ELISAs were performed and positives taken to
include those with an optical density of at least twice the
background. The initial positives were retransformed and the
binding checked in duplicate; it was confirmed that the binding was
specific to NIP and not to BSA. The frequency of confirmed positive
NIP binding clones for each starting material are shown in Table
14. Using DNA as the starting material for the PCR amplification is
approximately equivalent to sampling the cells present as there is
only one functional re-arranged heavy chain gene and at most one
re-arranged pseudogene per B-cell. Amplifying from the RNA of an
animal of course biases the repertoire to the reacting B-cells and
in a recently immunised animal this would be expected to give some
bias towards the immunogen. The data in Table 14 clearly shows how
powerful this selection is with the number of antigen specific
genes being enriched at least 96 fold when RNA made one week after
primary immunisation is used as the starting material. The data
also show that selection for antigen binding cells also provides an
alternative powerful method of selection for the required genetic
starting material.
3.2 Comparison of Total Spleen/Surface Immunoglobulin Depleted
Spleen
[0705] To examine the cellular basis of the selection achieved by
using RNA as the starting material we depleted the spleen of
surface immunoglobulin positive cells using biotinylated
anti-polyvalent immunoglobulin and streptavidin conjugated magnetic
beads. Prior FACS analysis had demonstrated that this method
removed over 96% of surface immunoglobulin positive cells. RNA was
prepared from both surface immunoglobulin depleted and non-depleted
factions of a spleen and VH libraries made from each. The ELISA
results (Table 14) show that the number of positives is certainly
not decreased by this depletion suggesting that the major portion
of the selective effect of using RNA may come from surface
immunoglobulin negative G-cells (probably plasma cells).
CONCLUSIONS
[0706] The applicants have demonstrated the importance of the
amplification of specific RNA produced by immunisation to enable
binding activity to be obtained with any reasonable frequency from
a combinatorial library. The applicants have also demonstrated an
alternative strategy which mimics that of the immune system itself.
Using a simple method of selecting for antigen binding cells gave
comparable enrichment and has the added advantage of using a
broader range of genes. At first sight the random combinatorial
approach would appear unlikely to produce the original combination
of heavy and light chain because of the vast diversity of the
immunoglobulin genes. The applicants show here, however, that
following immunisation, with a good antigen, 10% of the VH genes
from total splenic RNA isolated come from antigen specific cells so
the effective size of the repertoire is greatly reduced. This
together with the fact that promiscuity of the heavy and light
chains occurs (examples 21 and 22) accounts for the fact that
combinatorial system does produce antigen binding clones with
reasonable frequency. The data also suggests that the bulk of the
antigen specific RNA comes from surface immunoglobulin negative
cells which are most likely plasma cells.
[0707] The data also show that this simple method of antigen
selection may be useful in reducing the complexity of the
combinatorial library. In this case an enrichment of antigen
specific genes of at least 56 fold has been achieved which in the
normal case where heavy and light chains are unknown would result
in a reduction of the complexity of the combinatorial library by a
factor of over 3000. A further advantage of using antigen selected
cells (and amplifying from DNA to reduce any bias due to the state
of the cell) is that this results in a broader range of antibody
genes amplified. It may be that a simple cell selection such as
that the applicants have described here in combination with phage
selection would be ideal. From this example it can be seen that by
combining cell and phage selection methods one could reasonably
expect to screen all the combinations of heavy and light chain
(approximately 4.times.10.sup.10) and would thus be able to screen
all binding combinations although this would not, at present, be
possible from whole spleen (approximately 4.times.10.sup.14
combinations, assuming 50% B-cells). TABLE-US-00026 TABLE 1
Enrichment of pAb (D1.3) from vector population OUTPUT RATIO
ELISA.sup.c INPUT RATIO.sup.a oligo.sup.b pAb:total pAb:fd-CAT1
pAb:total phage phage ENRICHMENT.sup.d Single Round 1:4 .times.
10.sup.3 43/124 1.3 .times. 10.sup.3 1:4 .times. 10.sup.4 2/82 1.0
.times. 10.sup.3 Two Rounds 1:4 .times. 10.sup.4 197/372 2.1
.times. 10.sup.4 1:4 .times. 10.sup.5 90/356 3/24 1.0 .times.
10.sup.5 1:4 .times. 10.sup.6 27/183 5/26 5.9 .times. 10.sup.5 1:4
.times. 10.sup.7 13/278 1.8 .times. 10.sup.6 Footnotes:
.sup.aApproximately 10.sup.12 phage with the stated ratio of pAb
(D1.3):FDTPs/Bs were applied to 1 ml lysozyme-sepharose columns,
washed and eluted. .sup.bTG1 cells were infected with the eluted
specific binding phage and plated onto TY-tet plates. After
overnight incubation at 30-37.degree. C., the plates were analysed
by hydridisation to the .sup.32p, labelled oligonucleotide VH1FOR
(Ward et al op cit) which is specific to pAb D1.3. .sup.cSingle
colonies from overnight plates were grown, phage purified, and
tested for lysozyme binding. .sup.dEnrichment was calculated from
the oligonucleotide probing data.
[0708] TABLE-US-00027 TABLE 2 Enrichment of pAb (D1.3) from mixed
pAb population Input Ratio1 Output Ratio.sup.2 (pAbD1.3:pAbNQ11)
(pAb D1.3:Total phage) Enrichment Single Round 1:2.5 .times.
10.sup.4 18/460 0.98 .times. 10.sup.3 1:2.5 .times. 10.sup.5 3/770
0.97 .times. 10.sup.3 1:2.5 .times. 10.sup.6 0/112 -- pAb NQ11 only
0/460 -- Second Round 1:2.5 .times. 10.sup.4 119/170 1.75 .times.
10.sup.4 1:2.5 .times. 10.sup.5 101/130 1.95 .times. 10.sup.5 1:2.5
.times. 10.sup.6 102/204 1.26 .times. 10.sup.6 1:2.5 .times.
10.sup.7 0/274 -- 1:2.5 .times. 10.sup.8 0/209 -- pAb NQ11 only
0/170 -- Notes .sup.110.sup.10 phage applied to a lysozyme column
as in table 1. .sup.2Plating of cells and probing with
oligonucleotide as in table 1, except the oligonucleotide was
D1.3CDR3A.
[0709] TABLE-US-00028 TABLE 3 Enzyme activity of phage-enzyme No.
of molecules of Enzyme ng of enzyme Rate equivalent Input or No. of
phage (OD/hr) (.times.10.sup.-11) Pure Enzyme 335 34 24.5 Pure
Enzyme 177.5 17.4 12.25 Pure Enzyme 88.7 8.7 6.125 Pure Enzyme 44.4
4.12 3.06 Pure Enzyme 22.2 1.8 1.5 Pure Enzyme 11.1 0.86 0.76 No
Enzyme 0 0.005 0 fd-phoAla166/TG1 1.83 .times. 10.sup.11 5.82 4.2
fd-CAT2/TG1 1.0 .times. 10.sup.12 0.155 0.112 fd-phoAla166/KS272
7.1 .times. 10.sup.10 10.32 7.35 fd-CAT2/KS272 8.2 .times.
10.sup.12 0.038 0.027
[0710] TABLE-US-00029 TABLE 4 Affinity selection of hapten-binding
phage. Clones binding to phOx.sup..dagger. Pre-column After first
round After second round After third round A Random Combinatorial
Libraries phOx-immunised mice 0/568 (0%) 48/376 (13%) 175/188 (93%)
Unimmunised mice 0/388 (0%) B Hierarchical Libraries
VH-B/V.kappa.-rep library 6/190 (3%) 348/380 (92%)
VH-rep/V.kappa.-d library 0/190 (0%) 23/380 (7%) C Fractionation of
VH-B/V.kappa.-d and VH-B/V.kappa.-b phage.sup..dagger. Mixture of
clones 88/1896 (4.6%) 55/95 (57.9%) 1152/1156 (99.7%) 1296/1299
(99.8%) [44/1740 (2.5%)*] .sup..dagger.In panel C, numbers refer to
VH-B/V.kappa.-d colonies. *Numbers after three reinfections and
cycles of growth. This control, omitting the column steps, confirms
that a spurious growth or infectivity advantage was not responsible
for the enrichment for clone VH-B/V.kappa.-d.
[0711] TABLE-US-00030 TABLE 5 Binding to Chain(s) Chain as Soluble
Phage/Phagemid.sup..dagger. Helper Phage phOx* displayed.sup.# gene
III fusion.sup.# chain(s).sup.# A fd CAT2 non binding none fd
CAT2-I binding scFv scFv fd CAT2-II binding Fab light chain heavy
chain pHEN1 VCSMB non binding none pHEN1 I VCSMB binding scFv scFv
pHEN1 II VCSMB binding Fab light chain heavy chain B pHEN1 I
(HB2151) binding scFv.sup..sctn. pHEN1 II (HB2151) binding
Fab.sup..sctn. C fd CAT2-III non binding heavy chain heavy chain fd
CAT2-IV non binding light chain light chain pHEN1 III (HB2151)
VCSMB non binding none heavy chain pHEN1 III (HB2151) fd-tet-DOG1
IV binding Fab light chain heavy chain pHEN1 IV (HB2151) VCSMB non
binding none light chain pHEN1 IV (HB2151) fd-tet-DOG1 III binding
Fab heavy chain light chain Overview of phOx-BSA ELISA results of
phage and phagemid constructions. *Phase were considered to be
`binding` if OD.sub.405 of sample was at least 10 fold greater than
background in ELISA; .sup..dagger.E. coli TG1 was used for the
growth of the phage unless the use of E. coli HB2151 is
specifically indicated; .sup.#Information deduced from genetic
structure and in accordance with binding data; .sup..sctn.Result
confirmed experimentally by Western blot (for Fab, see FIG. 29.
[0712] TABLE-US-00031 TABLE 6 Kinetic parameters of soluble and
phage-bound alkaline phosphase. Relative values of k.sub.cat and
K.sub.m for the soluble enzyme and for the phage enzyme were
derived by comparing with the values for wild type enzyme
(phoArg166) and the phage-wild type enzyme (fdphoArg166). Soluble
enzyme (Data from Chaidaroglu Phage enzyme et al 1988) (Data from
this study) phoArg166 phoAla166 phoArg166 phoAla166 K.sub.m (.mu.M)
12.7 1620 73 1070 Relative K.sub.m 1 127 1 14.6 Relative 1 0.397 1
0.360 k.sub.cat Relative 1 0.0032 1 0.024 k.sub.cat/K.sub.m
[0713] TABLE-US-00032 TABLE 7 Enzyme Activity of Phage Samples
SPECIFIC INPUT ACTIVITY PHAGE RATE (mol substrate SAMPLE PARTICLE
(pmol substrate converted/mol (Construct:host) (pmol converted/min)
phage/min) fdphoArg166:TG1 2.3 8695 3700 fdphoAla166:TG1 5.6 2111
380 fdphoAla166:KS272 1.8 2505 1400 fdCAT2:TG1 3.3 <1 <0.3
fdCAT2:KS272 5.6 70 12
[0714] TABLE-US-00033 TABLE 8 Affinity chromatography of
phage-enzymes INFECTIVITY (Percentage of phage particles INPUT
PHAGE OUTPUT PHAGE which are PARTICLE PARTICLE SAMPLE infectious)
(.times.10.sup.9) (.times.10.sup.9) fdphoArg166 0.37% 5160 30
fdphoAla166 0.26% 3040 90 fdCAT2 4.75% 4000 2
[0715] TABLE-US-00034 TABLE 9 Mutations in scFvB18 selected by
display on phage following growth in mutator strains Nucleotide
mutation (base position) Amino acid mutation Number 308 Ala->Val
(VH FR3) 3 703 Tyr->Asp (VL CDR3) 1 706 Ser->Gly (VL CDR3) 1
724 Gly->Ser (VL FR4) 21 725 Gly->Asp (VL FR4) 3 734
Thr->Ile (VL FR4) 1
[0716] TABLE-US-00035 TABLE 10 Oligonucleotide primers used for PCR
of human immunoglobulin genes Oligo Name Sequence Human VH Back
Primers HuVH1aBACK 5'-CAG GTG CAG CTG GTG CAG TCT GG-3' (SEQ ID
NO:81) HuVH2aBACK 5'-CAG GTC AAC TTA AGG GAG TCT GG-3' (SEQ ID
NO:82) HuVH3aBACK 5'-GAG GTG CAG CTG GTG GAG TCT GG-3' (SEQ ID
NO:83) HuVH4aBACK 5'-CAG GTG CAG CTG CAG GAG TCG GG-3' (SEQ ID
NO:84) HuVH5aBACK 5'-GAG GTG CAG CTG TTG CAG TCT GC-3' (SEQ ID
NO:85) HuVH6aBACK 5'-CAG GTA CAG CTG CAG CAG TCA GG-3' (SEQ ID
NO:86) HuVH1aBACKSfi 5'-GTC CTC GCA ACT GCG GCC CAG CCG GCC ATG GCC
CAG (SEQ ID NO:87) GTG CAG CTG GTG CAG TCT GG-3' HuVH2aBACKSfi
5'-GTC CTC GCA ACT GCG GCC CAG CCG GCC ATG GCC CAG (SEQ ID NO:88)
GTC AAC TTA AGG GAG TCT GG-3' HuVH3aBACKSfi 5'-GTC CTC GCA ACT GCG
GCC CAG CCG GCC ATG GCC GAG (SEQ ID NO:89) GTG CAG CTG GTG GAG TCT
GG-3' HuVH4aBACKSfi 5'-GTC CTC GCA ACT GCG GCC CAG CCG GCC ATG GCC
CAG (SEQ ID NO:90) GTG CAG CTG CAG GAG TCG GG-3' HuVH5aBACKSfi
5'-GTC CTC GCA ACT GCG GCC CAG CCG GCC ATG GCC CAG (SEQ ID NO:91)
GTG CAG CTG TTG CAG TCT GC-3' HuVH6aBACKSfi 5'-GTC CTC GCA ACT GCG
GCC CAG CCG GCC ATG GCC CAG (SEQ ID NO:92) GTA CAG CTG CAG CAG TCA
GG-3' Human JH Forward Primers HuJH1-2FOR 5'-TGA GGA GAC GGT GAC
CAG GGT GCC-3' (SEQ ID NO:93) HuJH3FOR 5'-TGA AGA GAC GGT GAC CAT
TGT CCC-3' (SEQ ID NO:94) HuJH4-5FOR 5'-TGA GGA GAC GGT GAC CAG GGT
TCC-3' (SEQ ID NO:95) HuJH6FOR 5'-TGA GGA GAC GGT GAC CGT GGT
CCC-3' (SEQ ID NO:96) Human Heavy Chain Constant Region Primers
HuIgG1-4CH1FOR 5'-GTC CAC CTT GGT GTT GCT GGG CTT-3' (SEQ ID NO:97)
HUIgMFOR 5'-TGG AAG AGG CAC GTT CTT TTC TTT-3' (SEQ ID NO:98) Human
V Back Primers HuV 1aBACK 5'-GAC ATC CAG ATG ACC CAG TCT CC-3' (SEQ
ID NO:99) HuV 2aBACK 5'-GAT GTT GTG ATG ACT CAG TCT CC-3' (SEQ ID
NO:100) HuV 3aBACK 5'-GAA ATT GTG TTG ACG CAG TCT CC-3' (SEQ ID
NO:101) HuV 4aBACK 5'-GAC ATC GTG ATG ACC CAG TCT CC-3' (SEQ ID
NO:102) HuV 5aBACK 5'-GAA ACG ACA CTC ACG CAG TCT CC-3' (SEQ ID
NO:103) HuV 6aBACK 5'-GAA ATT GTG CTG ACT CAG TCT CC-3' (SEQ ID
NO:104) Human J Forward Primers HuJ 1FOR 5'-ACG TTT GAT TTC CAC CTT
GGT CCC-3' (SEQ ID NO:105) HuJ 2FOR 5'-ACG TTT GAT CTC CAG CTT GGT
CCC-3' (SEQ ID NO:106) HuJ 3FOR 5'-ACG TTT GAT ATC CAC TTT GGT
CCC-3' (SEQ ID NO:107) HuJ 4FOR 5'-ACG TTT GAT CTC CAC CTT GGT
CCC-3' (SEQ ID NO:108) HuJ 5FOR 5'-ACG TTT AAT CTC CAG TCG TGT
CCC-3' (SEQ ID NO:109) HuJ 1BACKNot 5'-GAG TCA TTC TCG ACT TGC GGC
CGC ACG TTT GAT TTC CAC CTT (SEQ ID NO:110) GGT CCC-3' HuJ 2BACKNot
5'-GAG TCA TTC TCG ACT TGC GGC CGC ACG TTT GAT CTC CAG CTT (SEQ ID
NO:111) GGT CCC-3' HuJ 3BACKNot 5'-GAG TCA TTC TCG ACT TGC GGC CGC
ACG TTT GAT ATC CAC TTT (SEQ ID NO:112) GGT CCC-3' HuJ 4BACKNot
5'-GAG TCA TTC TCG ACT TGC GGC CGC ACG TTT GAT CTC CAC CTT (SEQ ID
NO:113) GGT CCC-3' HuJ 5BACKNot 5'-GAG TCA TTC TCG ACT TGC GGC CGC
ACG TTT AAT CTC CAG TCG (SEQ ID NO:114) TGT CCC-3' Human Constant
Region Primers HuC FOR 5'-AGA CTC TCC CCT GTT GAA GCT CTT-3' (SEQ
ID NO:115) HuC FORNot1 5'-GAG TCA TTC TCG ACT TGC GGC CGC TTA TTA
AGA CTC TCC CCT (SEQ ID NO:116) GTT GAA GCT CTT-3' HuC FORNot2
5'-GAG TCA TTC TCG ACT TGC GGC CGC AGA CTC TCC CCT GTT GAA (SEQ ID
NO:117) GCT CTT-3' Human Back Primers HuV 1BACK 5'-CAG TCT GTG TTG
ACG CAG CCG CC-3' (SEQ ID NO:118) HuV 2BACK 5'-CAG TCT GCC CTG ACT
CAG CCT GC-3' (SEQ ID NO:119) HuV 3aBACK 5'-TCC TAT GTG CTG ACT CAG
CCA CC-3' (SEQ ID NO:120) HuV 3bBACK 5'-TCT TCT GAG CTG ACT CAG GAC
CC-3' (SEQ ID NO:121) HuV 4BACK 5'-CAC GTT ATA CTG ACT CAA CCG
CC-3' (SEQ ID NO:122) HuV 5BACK 5'-CAG GCT GTG CTC ACT CAG CCG
TC-3' (SEQ ID NO:123) HuV 6BACK 5'-AAT TTT ATG CTG ACT CAG CCC
CA-3' (SEQ ID NO:124) Human Forward Primers HuJ 1FOR 5'-ACC TAG GAC
GGT GAC CTT GGT CCC-3' (SEQ ID NO:125) HuJ 2-3FOR 5'-ACC TAG GAC
GGT CAG CTT GGT CCC-3' (SEQ ID NO:126) HuJ 4-5FOR 5'-ACC TAA AAC
GGT GAG CTG GGT CCC-3' (SEQ ID NO:127) HuJ FORNOT 5'-GAG TCA TTC
TCG ACT TGC GGC CGC ACC TAG GAC GGT GAC CTT (SEQ ID NO:128) GGT
CCC-3' HuJ 2-3FORNOT 5'-GAG TCA TTC TCG ACT TGC GGC CGC ACC TAG GAC
GGT CAG CTT (SEQ ID NO:129) GGT CCC-3' HuJ 4-5FORNOT 5'-GAG TCA TTC
TCG ACT TGC GGC CGC ACY TAA AAC GGT GAG CTG (SEQ ID NO:130) GGT
CCC-3' Human Constant Region Primers HuC FOR 5'-TGA AGA TTC TGT AGG
GGC CAC TGT CTT-3' (SEQ ID NO:131) HuC FORNot1 5'-GAG TCA TTC TCG
ACT TGC GGC CGC TTA TTA TGA AGA TTC TGT (SEQ ID NO:132) AGG GGC CAC
TGT CTT-3' HuC FORNot2 5'-GAG TCA TTC TCG ACT TGC GGC CGC TGC AGA
TTC TGT AGG GGC (SEQ ID NO:133) TGT CTT-3' Linker oligos Reverse JH
for scFv linker RHuJH1-2 5'-GCA CCC TGG TCA CCG TCT CCT CAG GTG
G-3' (SEQ ID NO:134) RHuJH3 5'-GGA CAA TGG TCA CCC TCT CTT CAG GTG
G-3' (SEQ ID NO:135) RHuJH4-5 5'-GAA CCC TGG TCA CCG TCT CCT CAG
GTG G-3' (SEQ ID NO:136) RHuJH6 5'-GGA CCA CGG TCA CCG TCT CCT CAG
GTG C-3' (SEQ ID NO:137) Reverse IgG1-4CH1 primer for Fab linker
RhuIgG1-4CH1FOR 5'-AAG CCC AGC AAC ACC AAG GTG GAC-3' (SEQ ID
NO:138) Reverse V for scFv linker RhuV 1aBACKFv 5'-GGA GAC TGG GTC
ATC TGG ATG TCC GAT CCG CC-3' (SEQ ID NO:139) RhuV 2aBACKFv 5'-GGA
GAC TGA GTC ATC ACA ACA TCC GAT CCG CC-3' (SEQ ID NO:140) RhuV
3aBACKFv 5'-GGA GAC TGC GTC AAC ACA ATT TCC GAT CCG CC-3' (SEQ ID
NO:141) RhuV 4aBACKFv 5'-GGA GAC TGG GTC ATC ACG ATG TCC GAT CCG
CC-3' (SEQ ID NO:142) RhuV 5aBACKFv 5'-GGA GAC TGC GTG AGT GTC GTT
TCC GAT CCG CC-3' (SEQ ID NO:143) RhuV 6aBACKFv 5'-GGA GAC TGA GTC
AGC ACA ATT TCC GAT CCG CC-3' (SEQ ID NO:144) Reverse V for Fab
linker RHuV 1aBACKFab 5'-GGA GAC TGG GTC ATC TGG ATG TCG GCC ATC
GCT GG-3' (SEQ ID NO:145) RHuV 2aBACKFab 5'-GGA GAC TGC GTC ATC ACA
ACA TCG GCC ATC GCT GG-3' (SEQ ID N0:146) RHuV 3aBACKFab 5'-GGA GAC
TGC GTC AAC ACA ATT TCG GCC ATC GCT GG-3' (SEQ ID NQ:147) RHuV
4aBACKFab 5'-GGA GAC TGG GTC ATC ACG ATG TCG GCC ATC GCT GG-3' (SEQ
ID NO:148) RHuV 5aBACKFab 5'-GGA GAC TGC GTG AGT GTC GTT TCG GCC
ATC GCT GG-3' (SEQ ID NO:149) RHuV 6aBACKFab 5'-GGA GAC TGC GTC AGC
ACA ATT TCG GCC ATC GCT GG-3' (SEQ ID NO:150) Reverse V for svFv
linker RHuV BACK1Fv 5'-GGC GGC TGC GTC AAC ACA GAC TGC GAT CCG CCA
CCG CCA GAG-3' (SEQ ID NO:151) RHuV BACK2Fv 5'-GCA GGC TGA GTC AGA
GCA GAC TGC GAT CCG CCA CCG CCA GAG-3' (SEQ ID NO:152) RHuV
BACK3aFv 5'-GGT GGC TGA GTC AGC ACA TAG GAC GAT CCG CCA CCC CCA
GAG-3' (SEQ ID NO:153) RHuV BACK3bFv 5'-GGG TCC TGA GTC AGC TCA GAA
GAC GAT CCG CCA CCG CCA GAG-3' (SEQ ID NO:154) RHuV BACK4Fv 5'-GGC
GGT TGA GTC AGT ATA ACG TGC GAT CCG CCA CCG CCA GAG-3' (SEQ ID
NO:155) RHuV BACK5Fv 5'-GAC GGC TGA GTC AGC ACA GAC TGC GAT CCG CCA
CCG CCA GAG-3' (SEQ ID NO:156) RHuV BACK6Fv 5'-TGG GGC TGA GTC AGC
ATA AAA TTC GAT CCG CCA CCG CCA GAG-3' (SEQ ID NO:157) Reverse V
for Fab linker RHuV BACK1Fab 5'-GGC GGC TGC GTC AAC ACA GAC TGG GCC
ATC GCT GGT TGG GCA-3' (SEQ ID NO:158) RHuV BACK2Fab 5'-GCA GGC TGA
GTC AGA GCA GAC TGG GCC ATC GCT GGT TGG GCA-3' (SEQ ID NO:159) RHuV
BACK3aFab 5'-GGT GGC TGA GTC AGC ACA TAG GAG GCC ATC GCT GGT TGG
GCA-3' (SEQ ID NO:160) RHuV BACK3bFab 5'-GGG TCC TGA GTC AGC TCA
GAA GAG GCC ATC GCT GGT TGG GCA-3' (SEQ ID NO:161) RHuV BACK4Fab
5'-GGC GGT TGA GTC AGT ATA ACG TGG GCC ATC GCT GGT TGG GCA-3' (SEQ
ID NO:162) RHuV BACK5Fab 5'-GAC GGC TGA GTC AGC ACA GAC TGG GCC ATC
GCT GGT TGG GCA-3' (SEQ ID NO:163) RHuV BACK6Fab 5'-TGG GGC TGA GTC
AGC ATA AAA TTG GCC ATC GCT GGT TGG GCA-3' (SEQ ID NO:164)
[0717] TABLE-US-00036 TABLE 11 Deduced protein sequences of heavy
and light chains selected from unimmunized library Oxazolone binder
HEAVY CHAIN VH15.4 QVQLVQSGAEVKKPGASVKVSCKASGYTFT SYGIS
KVRQAPGQGLEWMG WISAYNGNTKYAQKLQG (SEQ ID NO:165)
RVTMITDTSTSTAYMELRSLRSDDTAVYYCVR LLPKRTATLH YYIDVWGKGT LIGHT CHAIN
VL15.4 NNYVS WYQHLPGTAPNLLIY DNNKRPS
GIPDRFSGSKSGTSATLGITGLQTGDEADYYC GIWDGR (SEQ ID ND:166) BSA Binders
HEAVY CHAINS VH3.5 QVQLVQSGGGVVQPGRSLRLSCAASGFTPS SYGMH
WVNQAPGKGLEWVA VISYDGSNKYYADSVKG (SEQ ID NO:167)
RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK TGYSSGWGY FDYWSQGT LIGHT CHAINS
VL3.5 SSELTQDPAVSVALGQTVRITC QGDSLRSYYAS WYQQKPGQAPVLVIY GKNNRPS
(SEQ ID NO:168) GIPDRFSGSSSGNTASLTITGAQAEDEADYYC NSRDSSGNH VVFGG
Lysozyme binders: HEAVY CHAINS VH10.1 SLTCSVSGDSIS SGGYS
WIRQPSGKDLEWIG SVHHSGPTYYNPSLKS (SEQ ID NO:169)
RVTMSVDTSKNQFSLKLKSVTAADTAMYFCAR LGGSTWRSLYKH YYMDVWGK VH14.1
QVQLQESGPGLVKPSETLSLVCTVSGGSLS FSYWG WIRQPPGKGLEWDG YISHRGTDYNSSLQS
(SEQ ID NO:175) RVTISADTSKNQFSLKLSSVTAADTAYYYCAR SFSNSFFFGY WGQTGT
VH13.1 QVQLVQSGAEVKKPGQSLMISCQGSGYSFS NYWIG WVRQMPGKGLEWMG
IIYPGDSDTRYSPSFQG (SEQ ID NO:171) QVTISADKSISTAYLHWSSLKASDTALYYCAR
LVGGTPAY WGQGT VH16.1 QVQLVQSGAEVKKPGQSLRISCKGAGYSFS TYWIG
WVRQMPGKGGEWMG IIYPDDSDTRYSPSFEG (SEQ ID NO:172)
QVTISVDKSITTAYLHWSSLKA LIGHT CHAINS VK10.1 EIVLTQSPSSLSASVGDRVTITC
RASQSISNYLN WTQQKPGKAPKLLIY AASTLQS (SEQ ID NO:173)
GVPSRFSGSGSGTDFTLTINSLQPEDFATYYC QQTIISFP LTFGGG VL14.1
SSELTQDPAVSVAFGQTVRITC QGDSLRSSYAS WYQQEPGQAPLLVIY GENSRPS (SEQ ID
NO:174) GIPDRFSGSSSGNTASLTITGAQAEDEADYYC NSRDSRGTHL EVPGG VL13.1
HVILTQPASVSGSPGQSITISC TGSSRDVGGYNYVS WYQHHPGEAPKLLTS EVTNRPS (SEQ
ID NO:175) GVSNRFSGSKSGNTASLTISGLQAEDEADYFC ASYTSSKT YVFGG VL16.1
QSALTQPASVSGSPGQSITISC SGSSSDTGRYDYVS NYQHYPDKAPKLLIY EVKHRPS (SEQ
ID NO:176) GISERFSASKSGNTASLTISELQPGDEADYYC ASYT
[0718] TABLE-US-00037 TABLE 12 Enrichment of pAbNQ11 from pAbD1.3
background by affinity selection using Ox-BSA biotinylated with a
cleavable reagent and binding to streptavidin magnetic beads Input
Ratio.sup.1 Output Ratio.sup.2 (pAbD1.3:pAbNQ11) (pAb NQ11:Total
phage) Enrichment 2235:1 61/197 690 22350:1 5/202 544 .sup.11.9
.times. 10.sup.10 phage in 0.5 ml mixed for 1 hour with 5 .mu.l
streptavidin-magnetic beads precoated with antigen (OX-BSA).
.sup.2Colonies probed with the oligonucleotide NQ11CDR3
[0719] TABLE-US-00038 TABLE 13 Results of antigenic cell selection
Number % of total of Cells cells Total spleen cells 4 .times.
10.sup.7 Cells bound to 0.8 .times. 10.sup.4 0.02 uncoated beads
Cells bound to NIP-BSA 22 .times. 10.sup.4 0.55 coated beads
[0720] TABLE-US-00039 TABLE 14 Results of Fv NIP binding ELISAs
from selected cell populations: *Degree of Positives Enrichment
Cell Population DNA from total spleen 0/940 -- RNA from total
Spleen 29/282 >96 DNA from antigen 17/282 >56 binding cells
Surface Ig Selection RNA fromSurface Ig 8/94 -- negative fraction
RNA from total Spleen 4/94 -- *Degree of enrichment compared to
total DNA.
[0721]
Sequence CWU 1
1
272 1 5 PRT Bacteriophage fd 1 Gln Val Gln Leu Gln 1 5 2 5 PRT
Bacteriophage fd 2 Val Thr Val Ser Ser 1 5 3 5 PRT Bacteriophage fd
3 Leu Glu Ile Lys Arg 1 5 4 75 DNA Artificial Sequence
oligonucleotide for mutagensis 4 actttcaaca gtttctgcgg ccgcccgttt
gatctcgagc tcctgcagtt ggacctgtgc 60 actgtgagaa tagaa 75 5 22 DNA
Artificial Sequence PCR primer 5 aggtgcagct gcaggagtca gg 22 6 34
DNA Artificial Sequence PCR primer 6 ggtgacctcg agtgaagatt
tgggctcaac tttc 34 7 27 DNA Artificial Sequence PCR primer 7
tgaggacwcw gccgtctact actgtgc 27 8 24 DNA Artificial Sequence
oligonucleotide probe distinguishing between pAb D1.3 and pAB NQ11
8 gtagtcaagc ctataatctc tctc 24 9 51 DNA Artificial Sequence PCR
primer 9 tattctcaca gtgcacaaac tgttgaacgg acaccagaaa tgcctgttct g
51 10 39 DNA Artificial Sequence PCR primer 10 acatgtacat
gcggccgctt tcagccccag agcggcttt 39 11 33 DNA Artificial Sequence
PCR primer 11 tttaatgagg atccacaggt gcagctgcaa gag 33 12 30 DNA
Artificial Sequence PCR primer 12 aacgaatgga tcccgtttga tctcaagctt
30 13 24 DNA Artificial Sequence oligonucleotide for mutagensis -
removal of a BamH1 site 13 caaacgaatg ggtcctcctc atta 24 14 26 DNA
Artificial Sequence oligonucleotide for mutagensis - introduction
of a BamH1 site 14 ccrccaccct cggatccrcc accctc 26 15 15 PRT
Artificial Sequence linker between VH and VLK 15 Gly Gly Gly Gly
Ser Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser 1 5 10 15 16 23 DNA
Artificial Sequence primer for reverse transcription 16 ctggacaggg
atccagagtt cca 23 17 23 DNA Artificial Sequence primer for reverse
transcription 17 ctggacaggg ctccatagtt cca 23 18 32 DNA Artificial
Sequence PCR primer 18 tgaggagacg gtgaccgtgg tcccttggcc cc 32 19 22
DNA Artificial Sequence PCR primer 19 aggtsmarct gcagsagtcw gg 22
20 24 DNA Artificial Sequence PCR primer 20 ccgtttgatt tccagcttgg
tgcc 24 21 24 DNA Artificial Sequence PCR primer 21 ccgttttatt
tccagcttgg tccc 24 22 24 DNA Artificial Sequence PCR primer 22
ccgttttatt tccaactttg tccc 24 23 24 DNA Artificial Sequence PCR
primer 23 ccgtttcagc tccagcttgg tccc 24 24 24 DNA Artificial
Sequence PCR primer 24 gacattgagc tcacccagtc tcca 24 25 24 DNA
Artificial Sequence PCR primer 25 tggagactcg gtgagctcaa tgtc 24 26
24 DNA Artificial Sequence PCR primer 26 gggaccacgg tcaccgtctc ctca
24 27 38 DNA Artificial Sequence PCR primer 27 catgaccaca
gtgcacaggt smarctgcag sagtcwgg 38 28 42 DNA Artificial Sequence PCR
primer 28 gagtcattct gcggccgccc gtttgatttc cagcttggtg cc 42 29 42
DNA Artificial Sequence PCR primer 29 gagtcattct gcggccgccc
gttttatttc cagcttggtc cc 42 30 42 DNA Artificial Sequence PCR
primer 30 gagtcattct gcggccgccc gttttatttc caactttgtc cc 42 31 42
DNA Artificial Sequence PCR primer 31 gagtcattct gcggccgccc
gtttcagctc cagcttggtc cc 42 32 69 DNA Artificial Sequence PCR
primer 32 cacagtgcac tggtcgtcac acccccgggg ccagagcttg tcctcaatgt
ctccagcacc 60 ttcgttctg 69 33 33 DNA Artificial Sequence PCR primer
33 gatctcgagc ttaaagggca aggagtgtgg cac 33 34 40 DNA Artificial
Sequence PCR primer 34 tgcgaagctt tggagccttt ttttttggag attttcaacg
40 35 43 DNA Artificial Sequence PCR primer 35 cagtgaattc
ctattaagac tccttattac gcagtatgtt agc 43 36 17 DNA Artificial
Sequence sequencing primer 36 gaattttctg tatgagg 17 37 5 PRT Homo
sapiens misc_feature (2)..(2) X = A, C, D, E, F, G, H, I, K, L, M,
N, P, Q, R, S, T, V, W or Y misc_feature (4)..(5) X = A, C, D, E,
F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W or Y 37 Asp Xaa Gly Xaa
Xaa 1 5 38 5 PRT Homo sapiens MISC_FEATURE (1)..(1) X = D or, N
MISC_FEATURE (2)..(2) X = A, C, D, E, F, G, H, I, K, L, M, N, P, Q,
R, S, T, V, W or Y MISC_FEATURE (4)..(5) X = A, C, D, E, F, G, H,
I, K, L, M, N, P, Q, R, S, T, V, W or Y 38 Xaa Xaa Gly Xaa Xaa 1 5
39 45 DNA Artificial Sequence PCR primer 39 tcgcggccca gccggccatg
gccsaggtsm arctgcagsg tcwgg 45 40 20 DNA Artificial Sequence
oilgonucleotide probe for Vk-b 40 gagcgggtaa ccactgtact 20 41 20
DNA Artificial Sequence oilgonucleotide probe for Vk-d 41
gaatggtata gtactaccct 20 42 43 DNA Artificial Sequence PCR primer
42 cagtgaattc ttattaagac tccttattac gcagtatgtt agc 43 43 40 DNA
Artificial Sequence PCR primer 43 tgcgaagctt tggagccttt ttttttggag
attttcaacg 40 44 38 DNA Artificial Sequence PCR primer 44
catgaccaca gtgcacaggt smarctgcag sagtcwgg 38 45 57 DNA Artificial
Sequence PCR primer 45 catgccatga ctcgcggccc agccggccat ggccsaggts
marctgcags agtcwgg 57 46 48 DNA Artificial Sequence PCR primer 46
ccacgattct gcggccgctg aagatttggg ctcaactttc ttgtcgac 48 47 48 DNA
Artificial Sequence PCR primer 47 ccacgattct gcggccgctg actctccgcg
gttgaagctc tttgtgac 48 48 36 DNA Artificial Sequence PCR primer 48
cacagtgcac tcgacattga gctcacccag tctcca 36 49 54 DNA Artificial
Sequence PCR primer 49 catgaccacg cggcccagcc ggccatggcc gacattgagc
tcacccagtc tcca 54 50 36 DNA Artificial Sequence PCR primer 50
ttctgcggcc gcccgtttca gctcgagctt ggtccc 36 51 21 DNA Artificial
Sequence oligonucleotide for mutagensis - Ala166 to Arg 51
tagcatttgc gcgaggtcac a 21 52 42 DNA Artificial Sequence PCR primer
52 tggagactgg gtgagctcaa tgtcggagtg agaatagaaa gg 42 53 72 DNA
Artificial Sequence PCR primer 53 aagcccagca acaccaaggt ggacaagaaa
gttgagccca aatctagctg ataaaccgat 60 acaattaaag gc 72 54 21 DNA
Artificial Sequence PCR primer 54 cggaataccc aaaagaactg g 21 55 33
DNA Artificial Sequence PCR primer 55 cacagtgcac aggtccaact
gcaggagagc ggt 33 56 24 DNA Artificial Sequence PCR primer 56
cggtgacgag gctgccttga cccc 24 57 24 DNA Artificial Sequence PCR
primer 57 ggggtcaggg cagcctcgtc accg 24 58 28 DNA Artificial
Sequence PCR primer 58 tgggctctgg gtcatctgga tgtccgat 28 59 24 DNA
Artificial Sequence PCR primer 59 gacatccaga tgacccagag ccca 24 60
42 DNA Artificial Sequence PCR primer 60 gagtcattct gcggccgcac
gtttgatttc caccttggtc cc 42 61 17 DNA Artificial Sequence PCR
primer 61 gaggagattt tccctgt 17 62 17 DNA Artificial Sequence PCR
primer 62 ttggagcctt acctggc 17 63 24 DNA Artificial Sequence PCR
primer 63 tagccccctt attagcgttt gcca 24 64 24 DNA Artificial
Sequence PCR primer 64 gcgatgggtg ttgtcattgt cggc 24 65 40 DNA
Artificial Sequence PCR primer 65 ggaattcgtg cacagagtgc aacttcaact
aaaaaattac 40 66 40 DNA Artificial Sequence PCR primer 66
gggatccgcg gccgcttgac ctgaatcagc gttgtcttcg 40 67 43 DNA Artificial
Sequence PCR primer 67 ggaattcgtg cacagaagaa agtggtgctg ggcaaaaaag
ggg 43 68 45 DNA Artificial Sequence PCR primer 68 gggatccgcg
gccgcagcta gcaccacgat gtctattttg aactc 45 69 17 DNA Artificial
Sequence sequencing primer 69 gaattttctg tatgagg 17 70 17 DNA
Artificial Sequence sequencing primer 70 gaagtttcct tggtccc 17 71
17 DNA Artificial Sequence sequencing primer 71 actaccaggg gggctct
17 72 45 DNA Artificial Sequence PCR primer 72 gggatccgcg
gccgcggtgt cagagttggc agtcaatccg aacac 45 73 31 DNA Artificial
Sequence primer for reverse transcription 73 ggaattctta tgaagattct
gtaggggcca c 31 74 33 DNA Artificial Sequence PCR primer 74
aaccagccat ggccagtctg tgttgacgca gcc 33 75 36 DNA Artificial
Sequence oligonuleotide for mutagenesis - randomization of Phe91
and Phe92 of the light chain misc_feature (16)..(21) n = a, c, g or
t 75 cgtccgagga gtactnnnnn natgttgaca gtaata 36 76 33 DNA
Artificial Sequence oligonuleotide for mutagenesis - randomization
of Tyr32 of the li ght chain misc_feature (16)..(18) n = a, c, g or
t 76 ctgataccat gctaannnat tgtgattatt ccc 33 77 33 DNA Artificial
Sequence oligonuleotide for mutagenesis - randomization of Tyr101
of the light chain misc_feature (16)..(18) n = a, c, g or t 77
ccagtagtca agcctnnnat ctctctctct ggc 33 78 21 DNA Artificial
Sequence sequencing primer 78 caggagctga ggagattttc c 21 79 21 DNA
Artificial Sequence sequencing primer 79 tccgcctgaa ccgcctccac c 21
80 24 DNA Artificial Sequence oligonucleotide probe for CD2 of the
NQ11 antibody 80 aaaccaggcc ccgtaatcat agcc 24 81 23 DNA Artificial
Sequence PCR Primer 81 caggtgcagc tggtgcagtc tgg 23 82 23 DNA
Artificial Sequence PCR Primer 82 caggtcaact taagggagtc tgg 23 83
23 DNA Artificial Sequence PCR Primer 83 gaggtgcagc tggtggagtc tgg
23 84 23 DNA Artificial Sequence PCR Primer 84 caggtgcagc
tgcaggagtc ggg 23 85 23 DNA Artificial Sequence PCR Primer 85
gaggtgcagc tgttgcagtc tgc 23 86 23 DNA Artificial Sequence PCR
Primer 86 caggtacagc tgcagcagtc agg 23 87 56 DNA Artificial
Sequence PCR Primer 87 gtcctcgcaa ctgcggccca gccggccatg gcccaggtgc
agctggtgca gtctgg 56 88 56 DNA Artificial Sequence PCR Primer 88
gtcctcgcaa ctgcggccca gccggccatg gcccaggtca acttaaggga gtctgg 56 89
56 DNA Artificial Sequence PCR Primer 89 gtcctcgcaa ctgcggccca
gccggccatg gccgaggtgc agctggtgga gtctgg 56 90 56 DNA Artificial
Sequence PCR Primer 90 gtcctcgcaa ctgcggccca gccggccatg gcccaggtgc
agctgcagga gtcggg 56 91 56 DNA Artificial Sequence PCR Primer 91
gtcctcgcaa ctgcggccca gccggccatg gcccaggtgc agctgttgca gtctgc 56 92
56 DNA Artificial Sequence PCR Primer 92 gtcctcgcaa ctgcggccca
gccggccatg gcccaggtac agctgcagca gtcagg 56 93 24 DNA Artificial
Sequence PCR Primer 93 tgaggagacg gtgaccaggg tgcc 24 94 24 DNA
Artificial Sequence PCR Primer 94 tgaagagacg gtgaccattg tccc 24 95
24 DNA Artificial Sequence PCR Primer 95 tgaggagacg gtgaccaggg ttcc
24 96 24 DNA Artificial Sequence PCR Primer 96 tgaggagacg
gtgaccgtgg tccc 24 97 24 DNA Artificial Sequence PCR Primer 97
gtccaccttg gtgttgctgg gctt 24 98 24 DNA Artificial Sequence PCR
Primer 98 tggaagaggc acgttctttt cttt 24 99 23 DNA Artificial
Sequence PCR Primer 99 gacatccaga tgacccagtc tcc 23 100 23 DNA
Artificial Sequence PCR Primer 100 gatgttgtga tgactcagtc tcc 23 101
23 DNA Artificial Sequence PCR Primer 101 gaaattgtgt tgacgcagtc tcc
23 102 23 DNA Artificial Sequence PCR Primer 102 gacatcgtga
tgacccagtc tcc 23 103 23 DNA Artificial Sequence PCR Primer 103
gaaacgacac tcacgcagtc tcc 23 104 23 DNA Artificial Sequence PCR
Primer 104 gaaattgtgc tgactcagtc tcc 23 105 24 DNA Artificial
Sequence PCR Primer 105 acgtttgatt tccaccttgg tccc 24 106 24 DNA
Artificial Sequence PCR Primer 106 acgtttgatc tccagcttgg tccc 24
107 24 DNA Artificial Sequence PCR Primer 107 acgtttgata tccactttgg
tccc 24 108 24 DNA Artificial Sequence PCR Primer 108 acgtttgatc
tccaccttgg tccc 24 109 24 DNA Artificial Sequence PCR Primer 109
acgtttaatc tccagtcgtg tccc 24 110 48 DNA Artificial Sequence PCR
Primer 110 gagtcattct cgacttgcgg ccgcacgttt gatttccacc ttggtccc 48
111 48 DNA Artificial Sequence PCR Primer 111 gagtcattct cgacttgcgg
ccgcacgttt gatctccagc ttggtccc 48 112 48 DNA Artificial Sequence
PCR Primer 112 gagtcattct cgacttgcgg ccgcacgttt gatatccact ttggtccc
48 113 48 DNA Artificial Sequence PCR Primer 113 gagtcattct
cgacttgcgg ccgcacgttt gatctccacc ttggtccc 48 114 48 DNA Artificial
Sequence PCR Primer 114 gagtcattct cgacttgcgg ccgcacgttt aatctccagt
cgtgtccc 48 115 24 DNA Artificial Sequence PCR Primer 115
agactctccc ctgttgaagc tctt 24 116 54 DNA Artificial Sequence PCR
Primer 116 gagtcattct cgacttgcgg ccgcttatta agactctccc ctgttgaagc
tctt 54 117 48 DNA Artificial Sequence PCR Primer 117 gagtcattct
cgacttgcgg ccgcagactc tcccctgttg aagctctt 48 118 23 DNA Artificial
Sequence PCR Primer 118 cagtctgtdt tgacgcagcc gcc 23 119 23 DNA
Artificial Sequence PCR Primer 119 cagtctgccc tgactcagcc tgc 23 120
23 DNA Artificial Sequence PCR Primer 120 tcctatgtgc tgactcagcc acc
23 121 23 DNA Artificial Sequence PCR Primer 121 tcttctgagc
tgactcagga ccc 23 122 23 DNA Artificial Sequence PCR Primer 122
cacgttatac tgactcaacc gcc 23 123 23 DNA Artificial Sequence PCR
Primer 123 caggctgtgc tcactcagcc gtc 23 124 23 DNA Artificial
Sequence PCR Primer 124 aattttatgc tgactcagcc cca 23 125 24 DNA
Artificial Sequence PCR Primer 125 acctaggacg gtgaccttgg tccc 24
126 24 DNA Artificial Sequence PCR Primer 126 acctaggacg gtcagcttgg
tccc 24 127 24 DNA Artificial Sequence PCR Primer 127 acctaaaacg
gtgagctggg tccc 24 128 48 DNA Artificial Sequence PCR Primer 128
gagtcattct cgacttgcgg ccgcacctag gacggtgacc ttggtccc 48 129 48 DNA
Artificial Sequence PCR Primer 129 gagtcattct cgacttgcgg ccgcacctag
gacggtcagc ttggtccc 48 130 48 DNA Artificial Sequence PCR Primer
130 gagtcattct cgacttgcgg ccgcacytaa aacggtgagc tgggtccc 48 131 27
DNA Artificial Sequence PCR Primer 131 tgaagattct gtaggggcca
ctgtctt 27 132 57 DNA Artificial Sequence PCR Primer 132 gagtcattct
cgacttgcgg ccgcttatta tgaagattct gtaggggcca ctgtctt 57 133 48 DNA
Artificial Sequence PCR Primer 133 gagtcattct cgacttgcgg ccgctgcaga
ttctgtaggg gctgtctt 48 134 28 DNA Artificial Sequence PCR Primer
134 gcaccctggt caccgtctcc tcaggtgg 28 135 28 DNA Artificial
Sequence PCR Primer 135 ggacaatggt caccgtctct tcaggtgg 28 136 28
DNA Artificial Sequence PCR Primer 136 gaaccctggt caccgtctcc
tcaggtgg 28 137 28 DNA Artificial Sequence PCR Primer 137
ggaccacggt caccgtctcc tcaggtgc 28 138 24 DNA Artificial Sequence
PCR Primer 138 aagcccagca acaccaaggt ggac 24 139 32 DNA Artificial
Sequence PCR Primer 139 ggagactggg tcatctggat gtccgatccg cc 32 140
32 DNA Artificial Sequence PCR Primer 140 ggagactgag tcatcacaac
atccgatccg cc 32 141 32 DNA Artificial Sequence PCR Primer 141
ggagactgcg tcaacacaat ttccgatccg cc
32 142 32 DNA Artificial Sequence PCR Primer 142 ggagactggg
tcatcacgat gtccgatccg cc 32 143 32 DNA Artificial Sequence PCR
Primer 143 ggagactgcg tgagtgtcgt ttccgatccg cc 32 144 32 DNA
Artificial Sequence PCR Primer 144 ggagactgag tcagcacaat ttccgatccg
cc 32 145 35 DNA Artificial Sequence PCR Primer 145 ggagactggg
tcatctggat gtcggccatc gctgg 35 146 35 DNA Artificial Sequence PCR
Primer 146 ggagactgcg tcatcacaac atcggccatc gctgg 35 147 35 DNA
Artificial Sequence PCR Primer 147 ggagactgcg tcaacacaat ttcggccatc
gctgg 35 148 35 DNA Artificial Sequence PCR Primer 148 ggagactggg
tcatcacgat gtcggccatc gctgg 35 149 35 DNA Artificial Sequence PCR
Primer 149 ggagactgcg tgagtgtcgt ttcggccatc gctgg 35 150 35 DNA
Artificial Sequence PCR Primer 150 ggagactgcg tcagcacaat ttcggccatc
gctgg 35 151 42 DNA Artificial Sequence PCR Primer 151 ggcggctgcg
tcaacacaga ctgcgatccg ccaccgccag ag 42 152 42 DNA Artificial
Sequence PCR Primer 152 gcaggctgag tcagagcaga ctgcgatccg ccaccgccag
ag 42 153 42 DNA Artificial Sequence PCR Primer 153 ggtggctgag
tcagcacata ggacgatccg ccaccgccag ag 42 154 42 DNA Artificial
Sequence PCR Primer 154 gggtcctgag tcagctcaga agacgatccg ccaccgccag
ag 42 155 42 DNA Artificial Sequence PCR Primer 155 ggcggttgag
tcagtataac gtgcgatccg ccaccgccag ag 42 156 42 DNA Artificial
Sequence PCR Primer 156 gacggctgag tcagcacaga ctgcgatccg ccaccgccag
ag 42 157 42 DNA Artificial Sequence PCR Primer 157 tggggctgag
tcagcataaa attcgatccg ccaccgccag ag 42 158 42 DNA Artificial
Sequence PCR Primer 158 ggcggctgcg tcaacacaga ctgggccatc gctggttggg
ca 42 159 42 DNA Artificial Sequence PCR Primer 159 gcaggctgag
tcagagcaga ctgggccatc gctggttggg ca 42 160 42 DNA Artificial
Sequence PCR Primer 160 ggtggctgag tcagcacata ggaggccatc gctggttggg
ca 42 161 42 DNA Artificial Sequence PCR Primer 161 gggtcctgag
tcagctcaga agaggccatc gctggttggg ca 42 162 42 DNA Artificial
Sequence PCR Primer 162 ggcggttgag tcagtataac gtgggccatc gctggttggg
ca 42 163 42 DNA Artificial Sequence PCR Primer 163 gacggctgag
tcagcacaga ctgggccatc gctggttggg ca 42 164 42 DNA Artificial
Sequence PCR Primer 164 tggggctgag tcagcataaa attggccatc gctggttggg
ca 42 165 118 PRT Homo sapiens 165 Gln Val Gln Leu Val Gln Ser Gly
Ala Glu Val Lys Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Val Ser Cys
Lys Ala Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30 Gly Ile Ser Trp
Val Arg Gln Ala Pro Gly Gln Gly Leu Glu Trp Met 35 40 45 Gly Trp
Ile Ser Ala Tyr Asn Gly Asn Thr Lys Tyr Ala Gln Lys Ile 50 55 60
Gln Gly Arg Val Thr Met Ile Thr Asp Thr Ser Thr Ser Thr Ala Tyr 65
70 75 80 Met Glu Leu Arg Ser Leu Arg Ser Asp Asp Thr Ala Val Tyr
Tyr Cys 85 90 95 Val Arg Leu Leu Pro Lys Arg Thr Ala Thr Leu His
Tyr Tyr Ile Asp 100 105 110 Val Trp Gly Lys Gly Thr 115 166 65 PRT
Homo sapiens 166 Asn Asn Tyr Val Ser Trp Tyr Gln His Leu Pro Gly
Thr Ala Pro Asn 1 5 10 15 Leu Leu Ile Tyr Asp Asn Asn Lys Arg Pro
Ser Gly Ile Pro Asp Arg 20 25 30 Phe Ser Gly Ser Lys Ser Gly Thr
Ser Ala Thr Leu Gly Ile Thr Gly 35 40 45 Leu Gln Thr Gly Asp Glu
Ala Asp Tyr Tyr Cys Gly Ile Trp Asp Gly 50 55 60 Arg 65 167 115 PRT
Homo sapiens 167 Gln Val Gln Leu Val Gln Ser Gly Gly Gly Val Val
Gln Pro Gly Arg 1 5 10 15 Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly
Phe Thr Phe Ser Ser Tyr 20 25 30 Gly Met His Trp Val Arg Gln Ala
Pro Gly Lys Gly Leu Glu Trp Val 35 40 45 Ala Val Ile Ser Tyr Asp
Gly Ser Asn Lys Tyr Tyr Ala Asp Ser Val 50 55 60 Lys Gly Arg Phe
Thr Ile Ser Arg Asp Asn Ser Lys Asn Thr Leu Tyr 65 70 75 80 Leu Gln
Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys 85 90 95
Ala Lys Thr Gly Tyr Ser Ser Gly Trp Gly Tyr Phe Asp Tyr Trp Gly 100
105 110 Gln Gly Thr 115 168 101 PRT Homo sapiens 168 Ser Ser Glu
Leu Thr Gln Asp Pro Ala Val Ser Val Ala Leu Gly Gln 1 5 10 15 Thr
Val Arg Ile Thr Cys Gln Gly Asp Ser Leu Arg Ser Tyr Tyr Ala 20 25
30 Ser Trp Tyr Gln Gln Lys Pro Gly Gln Ala Pro Val Leu Val Ile Tyr
35 40 45 Gly Lys Asn Asn Arg Pro Ser Gly Ile Pro Asp Arg Phe Ser
Gly Ser 50 55 60 Ser Ser Gly Asn Thr Ala Ser Leu Thr Ile Thr Gly
Ala Gln Ala Glu 65 70 75 80 Asp Glu Ala Asp Tyr Tyr Cys Asn Ser Arg
Asp Ser Ser Gly Asn His 85 90 95 Val Val Phe Gly Gly 100 169 100
PRT Homo sapiens 169 Ser Leu Thr Cys Ser Val Ser Gly Asp Ser Ile
Ser Ser Gly Gly Tyr 1 5 10 15 Ser Trp Ile Arg Gln Pro Ser Gly Lys
Gly Ile Glu Trp Ile Gly Ser 20 25 30 Val His His Ser Gly Pro Thr
Tyr Tyr Asn Pro Ser Leu Lys Ser Arg 35 40 45 Val Thr Met Ser Val
Asp Thr Ser Lys Asn Gln Phe Ser Leu Lys Ile 50 55 60 Lys Cys Ser
Val Thr Ala Ala Asp Thr Ala Met Tyr Phe Cys Ala Arg 65 70 75 80 Glu
Gly Gly Ser Thr Trp Arg Ser Leu Tyr Lys His Tyr Tyr Met Asp 85 90
95 Val Trp Gly Lys 100 170 111 PRT Homo sapiens 170 Gln Val Gln Leu
Gln Glu Ser Gly Pro Gly Leu Val Lys Pro Ser Glu 1 5 10 15 Thr Leu
Ser Leu Val Cys Thr Val Ser Gly Gly Ser Leu Ser Phe Ser 20 25 30
Tyr Trp Gly Trp Ile Arg Gln Pro Pro Gly Lys Gly Leu Glu Trp Ile 35
40 45 Gly Tyr Ile Ser His Arg Gly Thr Asp Tyr Asn Ser Ser Leu Gln
Ser 50 55 60 Arg Val Thr Ile Ser Ala Asp Thr Ser Lys Asn Gln Phe
Ser Leu Lys 65 70 75 80 Leu Ser Ser Val Thr Ala Ala Asp Thr Ala Val
Tyr Tyr Cys Ala Arg 85 90 95 Ser Phe Ser Asn Ser Phe Phe Phe Gly
Tyr Trp Gly Gln Gly Thr 100 105 110 171 111 PRT Homo sapiens 171
Gln Val Gln Leu Val Gln Ser Gly Ala Glu Val Lys Lys Pro Gly Gln 1 5
10 15 Ser Leu Met Ile Ser Cys Gln Gly Ser Gly Tyr Ser Phe Ser Asn
Tyr 20 25 30 Trp Ile Gly Trp Val Arg Gln Met Pro Gly Lys Gly Leu
Glu Trp Met 35 40 45 Gly Ile Ile Tyr Pro Gly Asp Ser Asp Thr Arg
Tyr Ser Pro Ser Phe 50 55 60 Gln Gly Gln Val Thr Ile Ser Ala Asp
Lys Ser Ile Ser Thr Ala Tyr 65 70 75 80 Leu His Trp Ser Ser Leu Lys
Ala Ser Asp Thr Ala Leu Tyr Tyr Cys 85 90 95 Ala Arg Leu Val Gly
Gly Thr Pro Ala Tyr Trp Gly Gln Gly Thr 100 105 110 172 88 PRT Homo
sapiens 172 Gln Val Gln Leu Val Gln Ser Gly Ala Glu Val Lys Lys Pro
Gly Gln 1 5 10 15 Ser Leu Arg Ile Ser Cys Lys Gly Ala Gly Tyr Ser
Phe Ser Thr Tyr 20 25 30 Trp Ile Gly Trp Val Arg Gln Met Pro Gly
Lys Gly Leu Glu Trp Met 35 40 45 Gly Ile Ile Tyr Pro Asp Asp Ser
Asp Thr Arg Tyr Ser Pro Ser Phe 50 55 60 Glu Gly Gln Val Thr Ile
Ser Val Asp Lys Ser Ile Thr Thr Ala Tyr 65 70 75 80 Leu Trp Trp Ser
Ser Leu Lys Ala 85 173 102 PRT Homo sapiens 173 Glu Ile Val Leu Thr
Gln Ser Pro Ser Ser Leu Ser Ala Ser Val Gly 1 5 10 15 Asp Arg Val
Thr Ile Thr Cys Arg Ala Ser Gln Ser Ile Ser Asn Tyr 20 25 30 Leu
Asn Trp Tyr Gln Gln Lys Pro Gly Lys Ala Pro Lys Leu Leu Ile 35 40
45 Tyr Ala Ala Ser Thr Leu Gln Ser Gly Val Pro Ser Arg Phe Ser Gly
50 55 60 Ser Gly Ser Gly Thr Asp Phe Thr Leu Thr Ile Asn Ser Leu
Gln Pro 65 70 75 80 Glu Asp Phe Ala Thr Tyr Tyr Cys Gln Gln Thr Ile
Ile Ser Phe Pro 85 90 95 Leu Thr Phe Gly Gly Gly 100 174 102 PRT
Homo sapiens 174 Ser Ser Glu Leu Thr Gln Asp Pro Ala Val Ser Val
Ala Phe Gly Gln 1 5 10 15 Thr Val Arg Ile Thr Cys Gln Gly Asp Ser
Leu Arg Ser Ser Tyr Ala 20 25 30 Ser Trp Tyr Gln Gln Lys Pro Gly
Gln Ala Pro Leu Leu Val Ile Tyr 35 40 45 Gly Glu Asn Ser Arg Pro
Ser Gly Ile Pro Asp Arg Phe Ser Gly Ser 50 55 60 Ser Ser Gly Asn
Thr Ala Ser Leu Thr Ile Thr Gly Ala Gln Ala Glu 65 70 75 80 Asp Glu
Ala Asp Tyr Tyr Cys Asn Ser Arg Asp Ser Arg Gly Thr His 85 90 95
Leu Glu Val Phe Gly Gly 100 175 103 PRT Homo sapiens 175 His Val
Ile Leu Thr Gln Pro Ala Ser Val Ser Gly Ser Pro Gly Gln 1 5 10 15
Ser Ile Thr Ile Ser Cys Thr Gly Ser Ser Arg Asp Val Gly Gly Tyr 20
25 30 Asn Tyr Val Ser Trp Tyr Gln His His Pro Gly Lys Ala Pro Lys
Leu 35 40 45 Leu Ile Ser Glu Val Thr Asn Arg Pro Ser Gly Val Ser
Asn Arg Phe 50 55 60 Ser Gly Ser Lys Ser Gly Asn Thr Ala Ser Leu
Thr Ile Ser Gly Leu 65 70 75 80 Gln Ala Glu Asp Glu Ala Asp Tyr Phe
Cys Ala Ser Tyr Thr Ser Ser 85 90 95 Lys Thr Tyr Val Phe Gly Gly
100 176 94 PRT Homo sapiens 176 Gln Ser Ala Leu Thr Gln Pro Ala Ser
Val Ser Gly Ser Pro Gly Gln 1 5 10 15 Ser Ile Thr Ile Ser Cys Ser
Gly Ser Ser Ser Asp Ile Gly Arg Tyr 20 25 30 Asp Tyr Val Ser Trp
Tyr Gln His Tyr Pro Asp Lys Ala Pro Lys Leu 35 40 45 Leu Ile Tyr
Glu Val Val His Arg Pro Ser Gly Ile Ser His Arg Phe 50 55 60 Ser
Ala Ser Lys Ser Gly Asn Thr Ala Ser Leu Thr Ile Ser Glu Leu 65 70
75 80 Gln Pro Gly Asp Glu Ala Asp Tyr Tyr Cys Ala Ser Tyr Thr 85 90
177 69 DNA Artificial Sequence oligonucleotide for mutagenesis 177
acaactttca acagttgagg agacggtgac cgtaagcttc tgcagttgga cctgagcgga
60 gtgagaata 69 178 51 DNA Artificial Sequence oligonucleotide for
mutagenesis 178 acaactttca acagtttccc gtttgatctc gagctcctgc
agttggacct g 51 179 21 DNA Artificial Sequence sequencing primer
179 gtcgtctttc cagacgttag t 21 180 26 DNA Bacteriophage fd 180
tctcactccg ctgaaactgt tgaaag 26 181 62 DNA Artificial Sequence
engineered insertion site for VH 181 tctcactccg ctcaggtcca
actgcagaag cttacggtca ccgtctcctc aactgttgaa 60 ag 62 182 59 DNA
Artificial Sequence engineered insertion site for Fv 182 tctcactccg
ctcaggtcca actgcaggag ctcgagatca aacgggaaac tgttgaaag 59 183 272
PRT Artificial Sequence scFv of genetically engineered anti-hen
egg-white lysozyme (HEL) monoclonal antibody D1.3 183 Met Lys Tyr
Leu Leu Pro Thr Ala Ala Ala Gly Leu Leu Leu Leu Ala 1 5 10 15 Ala
Gln Pro Ala Met Ala Gln Val Gln Leu Gln Glu Ser Gly Pro Gly 20 25
30 Leu Val Ala Pro Ser Gln Ser Leu Ser Ile Thr Cys Thr Val Ser Gly
35 40 45 Phe Ser Leu Thr Gly Tyr Gly Val Asn Trp Val Arg Gln Pro
Pro Gly 50 55 60 Lys Gly Leu Glu Trp Leu Gly Met Ile Trp Gly Asp
Gly Asn Thr Asp 65 70 75 80 Tyr Asn Ser Ala Leu Lys Ser Arg Leu Ser
Ile Ser Lys Asp Asn Ser 85 90 95 Lys Ser Gln Val Phe Leu Lys Met
Asn Ser Leu His Thr Asp Asp Thr 100 105 110 Ala Arg Tyr Tyr Cys Ala
Arg Glu Arg Asp Tyr Arg Leu Asp Tyr Trp 115 120 125 Gly Gln Gly Thr
Thr Val Thr Val Ser Ser Gly Gly Gly Gly Ser Gly 130 135 140 Gly Gly
Gly Ser Gly Gly Gly Gly Ser Asp Ile Glu Leu Thr Gln Ser 145 150 155
160 Pro Ala Ser Leu Ser Ala Ser Val Gly Glu Thr Val Thr Ile Thr Cys
165 170 175 Arg Ala Ser Gly Asn Ile His Asn Tyr Leu Ala Trp Tyr Gln
Gln Lys 180 185 190 Gln Gly Lys Ser Pro Gln Leu Leu Val Tyr Tyr Thr
Thr Thr Leu Ala 195 200 205 Asp Gly Val Pro Ser Arg Phe Ser Gly Ser
Gly Ser Gly Thr Gln Tyr 210 215 220 Ser Leu Lys Ile Asn Ser Leu Gln
Pro Glu Asp Phe Gly Ser Tyr Tyr 225 230 235 240 Cys Gln His Phe Trp
Ser Thr Pro Arg Thr Phe Gly Gly Gly Thr Lys 245 250 255 Leu Glu Ile
Lys Arg Glu Gln Lys Leu Ile Ser Glu Glu Asp Leu Asn 260 265 270 184
889 DNA Artificial Sequence nucleotide sequence encoding scFv of
genetically engineered anti-hen egg-white lysozyme (HEL) monoclonal
antibody D1.3 and surrounding sequence 184 gcatgcaaat tctatttcaa
ggagacagtc ataatgaaat acctattgcc tacggcagcc 60 gctggattgt
tattactcgc tgcccaacca gcgatggccc aggtgcagct gcaggagtca 120
ggacctggcc tggtggcgcc ctcacagagc ctgtccatca catgcaccgt ctcagggttc
180 tcattaaccg gctatggtgt aaactgggtt cgccagcctc caggaaaggg
tctggagtgg 240 ctgggaatga tttggggtga tggaaacaca gactataatt
cagctctcaa atccagactg 300 agcatcagca aggacaactc caagagccaa
gttttcttaa aaatgaacag tctgcacact 360 gatgacacag ccaggtacta
ctgtgccaga gagagagatt ataggcttga ctactggggc 420 caaggcacca
cggtcaccgt ctcctcaggt ggaggcggtt caggcggagg tggctctggc 480
ggtggcggat cggacatcga gctcactcag tctccagcct ccctttctgc gtctgtggga
540 gaaactgtca ccatcacatg tcgagcaagt gggaatattc acaattattt
agcatggtat 600 cagcagaaac agggaaaatc tcctcagctc ctggtctatt
atacaacaac cttagcagat 660 ggtgtgccat caaggttcag tggcagtgga
tcaggaacac aatattctct caagatcaac 720 agcctgcaac ctgaagattt
tgggagttat tactgtcaac atttttggag tactcctcgg 780 acgttcggtg
gagggaccaa gctcgagatc aaacgggaac aaaaactcat ctcagaagag 840
gatctgaatt aataatgatc aaacggtaat aaggatccag ctcgaattc 889 185 20
PRT Artificial Sequence amino acids encoded by the nucleotide
sequence around the cloning site in gene III of fd-CAT2 185 His Ser
Ala Gln Val Gln Leu Gln Glu Leu Glu Ile Lys Arg Ala Ala 1 5 10 15
Ala Glu Thr Val 20 186 60 DNA Artificial Sequence nucleotide
sequence around the cloning site in gene III of fd-CAT2 186
cacagtgcac aggtccaact gcaggagctc gagatcaaac gggcggccgc agaaactgtt
60 187 241 PRT Artificial Sequence VH of Fab D1.3 from genetically
engineered anti-hen egg-white lysozyme (HEL) monoclonal antibody
187 Met Lys Tyr Leu Leu Pro Thr Ala Ala Ala Gly Leu Leu Leu Leu Ala
1 5 10 15 Ala Gln Pro Ala Met Ala Gln Val Gln Leu Gln Glu Ser Gly
Pro Gly 20 25 30 Leu Val Ala Pro Ser Gln Ser Leu Ser Ile Thr Cys
Thr Val Ser Gly 35 40 45 Phe Ser Leu Thr Gly Tyr Gly Val Asn Trp
Val Arg Gln Pro Pro Gly 50 55 60 Lys Gly Leu Glu Trp Leu Gly Met
Ile Trp Gly Asp Gly Asn Thr Asp 65 70 75 80 Tyr Asn Ser Ala Leu Lys
Ser Arg Leu Ser Ile Ser Lys Asp Asn Ser 85 90 95 Lys Ser Gln Val
Phe Leu Lys Met Asn Ser Leu His Thr Asp Asp Thr 100 105 110 Ala Arg
Tyr Tyr Cys Ala Arg Glu Arg Asp Tyr Arg Leu Asp Tyr Trp 115 120 125
Gly Gln Gly Thr Thr Val Thr Val Ser Ser Ala Ser Thr Lys Gly Pro 130
135
140 Ser Val Phe Pro Leu Ala Pro Ser Ser Lys Ser Thr Ser Gly Gly Thr
145 150 155 160 Ala Ala Leu Gly Cys Leu Val Lys Asp Tyr Phe Pro Glu
Pro Val Thr 165 170 175 Val Ser Trp Asn Ser Gly Ala Leu Thr Ser Gly
Val His Thr Phe Pro 180 185 190 Ala Val Leu Gln Ser Ser Gly Leu Tyr
Ser Leu Ser Ser Val Val Thr 195 200 205 Val Pro Ser Ser Ser Leu Gly
Thr Gln Thr Tyr Ile Cys Asn Val Asn 210 215 220 His Lys Pro Ser Asn
Thr Lys Val Asp Lys Lys Val Glu Pro Lys Ser 225 230 235 240 Ser 188
236 PRT Artificial Sequence VL of Fab D1.3 from genetically
engineered anti-hen egg-white lysozyme (HEL) monoclonal antibody
188 Met Lys Tyr Leu Leu Pro Thr Ala Ala Ala Gly Leu Leu Leu Leu Ala
1 5 10 15 Ala Gln Pro Ala Met Ala Asp Ile Glu Leu Thr Gln Ser Pro
Ala Ser 20 25 30 Leu Ser Ala Ser Val Gly Glu Thr Val Thr Ile Thr
Cys Arg Ala Ser 35 40 45 Gly Asn Ile His Asn Tyr Leu Ala Trp Tyr
Gln Gln Lys Gln Gly Lys 50 55 60 Ser Pro Gln Leu Leu Val Tyr Tyr
Thr Thr Thr Leu Ala Asp Gly Val 65 70 75 80 Pro Ser Arg Phe Ser Gly
Ser Gly Ser Gly Thr Gln Tyr Ser Leu Lys 85 90 95 Ile Asn Ser Leu
Gln Pro Glu Asp Phe Gly Ser Tyr Tyr Cys Gln His 100 105 110 Phe Trp
Ser Thr Pro Arg Thr Phe Gly Gly Gly Thr Lys Leu Glu Ile 115 120 125
Lys Arg Thr Val Ala Ala Pro Ser Val Phe Ile Phe Pro Pro Ser Asp 130
135 140 Glu Gln Leu Lys Ser Gly Thr Ala Ser Val Val Cys Leu Leu Asn
Asn 145 150 155 160 Phe Tyr Pro Arg Glu Ala Lys Val Gln Trp Lys Val
Asp Asn Ala Leu 165 170 175 Gln Ser Gly Asn Ser Gln Glu Ser Val Thr
Glu Gln Asp Ser Lys Asp 180 185 190 Ser Thr Tyr Ser Leu Ser Ser Thr
Leu Thr Leu Ser Lys Ala Asp Tyr 195 200 205 Glu Lys His Lys Val Tyr
Ala Cys Glu Val Thr His Gln Gly Leu Ser 210 215 220 Ser Pro Val Thr
Lys Ser Phe Asn Arg Gly Glu Ser 225 230 235 189 1526 DNA Artificial
Sequence nucleotide sequence of Fab D1.3 from genetically
engineered anti-hen egg-white lysozyme (HEL) monoclonal antibody
189 gcatgcaaat tctatttcaa ggagacagtc ataatgaaat acctattgcc
tacggcagcc 60 gctggattgt tattactcgc tgcccaacca gcgatggccc
aggtgcagct gcaggagtca 120 ggacctggcc tggtggcgcc ctcacagagc
ctgtccatca catgcaccgt ctcagggttc 180 tcattaaccg gctatggtgt
aaactgggtt cgccagcctc caggaaaggg tctggagtgg 240 ctgggaatga
tttggggtga tggaaacaca gactataatt cagctctcaa atccagactg 300
agcatcagca aggacaactc caagagccaa gttttcttaa aaatgaacag tctgcacact
360 gatgacacag ccaggtacta ctgtgccaga gagagagatt ataggcttga
ctactggggc 420 caaggcacca cggtcaccgt ctcctcagcc tccaccaagg
gcccatcggt cttccccctg 480 gcaccctcct ccaagagcac ctctgggggc
acagcggccc tgggctgcct ggtcaaggac 540 tacttccccg aaccggtgac
ggtgtcgtgg aactcaggcg ccctgaccag cggcgtgcac 600 accttcccgg
ctgtcctaca gtcctcagga ctctactccc tcagcagcgt ggtgaccgtg 660
ccctccagca gcttgggcac ccagacctac atctgcaacg tgaatcacaa gcccagcaac
720 accaaggtcg acaagaaagt tgagcccaaa tcttcataat aacccgggag
cttgcatgca 780 aattctattt caaggagaca gtcataatga aatacctatt
gcctacggca gccgctggat 840 tgttattact cgctgcccaa ccagcgatgg
ccgacatcga gctcacccag tctccagcct 900 ccctttctgc gtctgtggga
gaaactgtca ccatcacatg tcgagcaagt gggaatattc 960 acaattattt
agcatggtat cagcagaaac agggaaaatc tcctcagctc ctggtctatt 1020
atacaacaac cttagcagat ggtgtgccat caaggttcag tggcagtgga tcaggaacac
1080 aatattctct caagatcaac agcctgcagc ctgaagattt tgggagttat
tactgtcaac 1140 atttttggag tactcctcgg acgttcggtg gaggcaccaa
gctcgagatc aaacggactg 1200 tggctgcacc atctgtcttc atcttcccgc
catctgatga gcagttgaaa tctggaactg 1260 cctctgttgt gtgcctgctg
aataacttct atcccagaga ggccaaagta cagtggaagg 1320 tggataacgc
cctccaatcg ggtaactccc aggagagtgt cacagagcag gacagcaagg 1380
acagcaccta cagcctcagc agcaccctga cgctgagcaa agcagactac gagaaacaca
1440 aagtctacgc ctgcgaagtc acccatcagg gcctgagctc gcccgtcaca
aagagcttca 1500 accgcggaga gtcatagtaa gaattc 1526 190 249 PRT
Artificial Sequence scFv form of the anti-oxazalone antibody NQ11
190 Gln Val Gln Leu Gln Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly
1 5 10 15 Ser Leu Arg Leu Ser Cys Ala Thr Ser Gly Phe Thr Phe Ser
Asn Tyr 20 25 30 Tyr Met Gly Trp Val Arg Gln Pro Pro Gly Lys Ala
Leu Glu Trp Leu 35 40 45 Gly Ser Val Arg Asn Lys Val Asn Gly Tyr
Thr Thr Glu Tyr Ser Ala 50 55 60 Ser Val Lys Gly Arg Phe Thr Ile
Ser Arg Asp Asn Phe Gln Ser Ile 65 70 75 80 Leu Tyr Leu Gln Ile Asn
Thr Leu Arg Thr Glu Asp Ser Ala Thr Tyr 85 90 95 Tyr Cys Ala Arg
Gly Tyr Asp Tyr Gly Ala Trp Phe Ala Tyr Trp Gly 100 105 110 Gln Gly
Thr Leu Val Thr Val Ser Ser Gly Gly Gly Gly Ser Gly Gly 115 120 125
Gly Gly Ser Gly Gly Gly Gly Ser Asp Ile Glu Leu Thr Gln Thr Pro 130
135 140 Leu Ser Leu Pro Val Ser Leu Gly Asp Gln Ala Ser Ile Ser Cys
Arg 145 150 155 160 Ser Ser Gln Ser Ile Val His Ser Asn Gly Asn Thr
Tyr Leu Glu Trp 165 170 175 Tyr Leu Gln Lys Pro Gly Gln Ser Pro Lys
Leu Leu Ile Tyr Lys Val 180 185 190 Ser Asn Arg Phe Ser Gly Val Pro
Asp Arg Phe Ser Gly Ser Gly Ser 195 200 205 Gly Thr Asp Phe Thr Leu
Lys Ile Ser Arg Val Glu Ala Glu Asp Leu 210 215 220 Gly Val Tyr Tyr
Cys Phe Gln Gly Ser His Val Pro Tyr Thr Phe Gly 225 230 235 240 Gly
Gly Thr Lys Leu Glu Ile Lys Arg 245 191 747 DNA Artificial Sequence
nucleotide sequence encoding scFv form of the anti-oxazalone
antibody NQ11 191 caggtgcagc tgcaggagtc aggaggaggc ttggtacagc
ctgggggttc tctgagactc 60 tcctgtgcaa cttctgggtt caccttcagt
aattactaca tgggctgggt ccgccagcct 120 ccaggaaagg cacttgagtg
gttgggttct gttagaaaca aagttaatgg ttacacaaca 180 gagtacagtg
catctgtgaa ggggcggttc accatctcca gagataattt ccaaagcatc 240
ctctatcttc aaataaacac cctgagaact gaggacagtg ccacttatta ctgtgcaaga
300 ggctatgatt acggggcctg gtttgcttac tggggccaag ggaccctggt
caccgtctcc 360 tcaggtggag gcggttcagg cggaggtggc tctggcggtg
gcggatcgga catcgagctc 420 acccaaactc cactctccct gcctgtcagt
cttggagatc aagcctccat ctcttgcaga 480 tctagtcaga gcattgtaca
tagtaatgga aacacctatt tagaatggta cctgcagaaa 540 ccaggccagt
ctccaaagct cctgatctac aaagtttcca accgattttc tggggtccca 600
gacaggttca gtggcagtgg atcggggaca gatttcacac tcaagatcag cagagtggag
660 gctgaggatc tgggagttta ttactgcttt caaggttcac atgttccgta
cacgttcgga 720 ggggggacca agctcgagat caaacgg 747 192 8 PRT
Artificial Sequence amino terminus of phoAla 166 192 Arg Thr Pro
Glu Met Pro Val Leu 1 5 193 48 DNA Artificial Sequence 5' insertion
site of phoAla 166 in frame to geneIII 193 tctcacagtg cacaaactgt
tgaacggaca ccagaaatgc ctgttctg 48 194 7 PRT Artificial Sequence
carboxy terminus of phoAla 166 194 Lys Ala Ala Leu Gly Leu Lys 1 5
195 45 DNA Artificial Sequence 3' insertion site of phoAla 166 in
frame to geneIII 195 aaagccgctc tggggctgaa agcggccgca gaaactgttg
aaagt 45 196 6 PRT Artificial Sequence amino terminus of scFv PCR
product 196 Gln Val Gln Leu Gln Glu 1 5 197 6 PRT Artificial
Sequence carboxy terminus of scFv PCR product 197 Lys Leu Glu Ile
Lys Arg 1 5 198 33 DNA Artificial Sequence 5' end of scFv PCR
product 198 tttaatgagg atccacaggt gcagctgcaa gag 33 199 27 DNA
Artificial Sequence 3' end of scFv PCR product 199 aagcttgaga
tcaaacggga tccattc 27 200 15 DNA Artificial Sequence site in
geneIII for introduction of BamHI site via olgio G3 Bamlink 200
gagggtggtg gctct 15 201 15 DNA Artificial Sequence site in geneIII
for introduction of BamHI site via olgio G3 Bamlink 201 gagggtggcg
gctct 15 202 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 202 gagggtggcg
gctct 15 203 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 203 gagggtggcg
gcact 15 204 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 204 gagggcggcg
gctct 15 205 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 205 gagggtggtg
gttct 15 206 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 206 gagggcggcg
gctct 15 207 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 207 gagggcggcg
gctct 15 208 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 208 gagggcggcg
gttct 15 209 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 209 gagggcggcg
gctct 15 210 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 210 gagggcggcg
gttct 15 211 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 211 gagggcggcg
gctct 15 212 15 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 212 gagggtggcg
gatcc 15 213 11 DNA Artificial Sequence site in geneIII for
introduction of BamHI site via olgio G3 Bamlink 213 gagggtggcg g 11
214 114 PRT Artificial Sequence VH of scFv from mouse immunized
with 2-phenyl-5-oxazolone 214 Gln Val Gln Leu Gln Gln Ser Gly Ala
Glu Leu Ala Arg Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys Lys
Ala Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30 Thr Met His Trp Val
Lys Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile
Asn Pro Ser Ser Gly Tyr Thr Asn Tyr Asn Gln Lys Phe 50 55 60 Lys
Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser Thr Ala Tyr 65 70
75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr Tyr
Cys 85 90 95 Ala Asn Arg Tyr Gly Ala Tyr Trp Gly Gln Gly Thr Thr
Val Thr Val 100 105 110 Ser Ser 215 114 PRT Artificial Sequence VH
of scFv from mouse immunized with 2-phenyl-5-oxazolone 215 Gln Val
Gln Leu Gln Gln Ser Gly Ala Glu Leu Ala Lys Pro Gly Ala 1 5 10 15
Ser Val Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Arg Asp 20
25 30 Trp Met His Trp Leu Lys Gln Arg Pro Gly Gln Gly Leu Glu Trp
Ile 35 40 45 Gly Tyr Ile Asn Pro Ser Thr Gly Tyr Thr Glu Tyr Asn
Gln Lys Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser
Ser Ser Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu
Asp Ser Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asn Tyr Gly Leu Tyr
Trp Gly Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 216 115 PRT
Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 216 Gln Val Gln Leu Gln Gln Ser Gly Pro Glu
Leu Val Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys Lys Ala
Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30 Val Met His Trp Val Lys
Gln Lys Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile Asn
Pro Tyr Asn Asp Gly Thr Lys Tyr Asn Glu Lys Phe 50 55 60 Lys Asp
Lys Ala Thr Leu Thr Ser Asp Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80
Met Glu Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr Tyr Cys 85
90 95 Ala Ile Tyr Arg Ser Phe Pro Tyr Trp Gly Gln Gly Thr Thr Val
Thr 100 105 110 Val Ser Ser 115 217 116 PRT Artificial Sequence VH
of scFv from mouse immunized with 2-phenyl-5-oxazolone 217 Gln Val
Gln Leu Gln Gln Ser Gly Pro Glu Leu Val Lys Pro Gly Ala 1 5 10 15
Ser Val Lys Ile Ser Cys Lys Ala Ser Gly Tyr Ser Phe Thr Gly Tyr 20
25 30 Phe Met Asn Trp Val Lys Gln Ser His Gly Lys Ser Leu Glu Trp
Ile 35 40 45 Gly Arg Ile Asn Pro Tyr Asn Gly Asp Thr Phe Tyr Asn
Gln Lys Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Val Asp Lys Ser
Ser Ser Thr Ala His 65 70 75 80 Met Glu Leu Leu Ser Leu Thr Ser Glu
Asp Ser Ala Val Tyr Tyr Cys 85 90 95 Val Gly Ile Thr Thr Arg Phe
Ala Tyr Trp Gly Gln Gly Thr Thr Val 100 105 110 Thr Val Ser Ser 115
218 113 PRT Artificial Sequence VH of scFv from mouse immunized
with 2-phenyl-5-oxazolone 218 Gln Val Gln Leu Gln Glu Ser Gly Pro
Gly Leu Val Ala Pro Ser Gln 1 5 10 15 Ser Leu Ser Ile Thr Cys Thr
Val Ser Gly Phe Ser Leu Thr Ser Tyr 20 25 30 Gly Val His Trp Val
Arg Gln Pro Pro Gly Lys Gly Leu Glu Trp Leu 35 40 45 Gly Val Ile
Trp Ala Gly Gly Ser Thr Asn Tyr Asn Ser Ala Leu Met 50 55 60 Ser
Arg Leu Ser Ile Ser Lys Asp Asn Ser Lys Ser Gln Val Phe Leu 65 70
75 80 Lys Met Asn Ser Leu Gln Thr Asp Asp Thr Ala Met Tyr Tyr Cys
Ala 85 90 95 Arg Asp Arg Gly Asp Tyr Trp Gly Gln Gly Thr Thr Val
Thr Val Ser 100 105 110 Ser 219 114 PRT Artificial Sequence VH of
scFv from mouse immunized with 2-phenyl-5-oxazolone 219 Gln Val Lys
Leu Gln Gln Ser Gly Pro Glu Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser
Val Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25
30 Leu Met His Trp Val Lys Gln Arg Pro Gly Gln Gly Leu Lys Trp Ile
35 40 45 Gly Tyr Ile Asn Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln
Lys Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser
Ser Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp
Ser Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp
Gly Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 220 114 PRT
Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 220 Gln Val Gln Leu Gln Gln Ser Gly Ala Glu
Leu Val Arg Pro Gly Ala 1 5 10 15 Ser Val Lys Leu Ser Cys Lys Ala
Ser Gly Tyr Thr Phe Thr Arg Tyr 20 25 30 Leu Met His Trp Val Lys
Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile Asn
Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln Lys Phe 50 55 60 Lys Asp
Glu Ala Thr Leu Thr Ala Asp Lys Ser Ser Asn Thr Ala Tyr 65 70 75 80
Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr Tyr Cys 85
90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp Gly Gln Gly Thr Thr Val Thr
Val 100 105 110 Ser Ser 221 114 PRT Artificial Sequence VH of scFv
from mouse immunized with 2-phenyl-5-oxazolone 221 Gln Val Gln Leu
Gln Gln Ser Gly Pro Glu Leu His Lys Pro Gly Ala 1 5 10 15 Ser Val
Lys Ile Ser Cys Lys Ala Ser Gly Tyr Ser Phe Ser Arg Asn
20 25 30 Tyr Met His Trp Val Lys Gln Ser His Gly Lys Ser Leu Glu
Trp Ile 35 40 45 Gly Tyr Ile Ala Pro Phe Asn Gly Gly Thr Thr Tyr
Asn Gln Lys Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Val Asp Arg
Ser Ser Ser Thr Ala Tyr 65 70 75 80 Met His Leu Ser Ser Leu Thr Ser
Glu Asp Ser Ala Val Tyr Tyr Cys 85 90 95 Ala Thr Asp Tyr Gly Arg
Asp Trp Gly Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 222 114
PRT Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 222 Gln Val Lys Leu Gln Gln Ser Gly Pro Glu
Leu Ala Arg Pro Gly Val 1 5 10 15 Ser Val Lys Met Ser Cys Lys Ala
Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30 Ala Met His Trp Val Lys
Gln Ser Gln Ser Lys Ser Leu Glu Trp Ile 35 40 45 Gly Val Ile Ser
Thr Tyr Asn Gly Asn Thr Asn Tyr Asn Gln Lys Phe 50 55 60 Lys Gly
Lys Ala Thr Met Thr Val Asp Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80
Met Glu Leu Ala Arg Leu Thr Ser Glu Asp Ser Ala Ile Tyr Tyr Cys 85
90 95 Ala Arg Asp Tyr Gly Asp Tyr Trp Gly Gln Gly Thr Thr Val Thr
Val 100 105 110 Ser Ser 223 114 PRT Artificial Sequence VH of scFv
from mouse immunized with 2-phenyl-5-oxazolone 223 Gln Val Lys Leu
Gln Gln Ser Gly Ala Glu Leu Ala Arg Pro Gly Ala 1 5 10 15 Ser Val
Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Arg Tyr 20 25 30
Thr Met His Trp Val Lys Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35
40 45 Gly Tyr Ile Asn Pro Ser Ser Gly Tyr Thr Asn Tyr Asn Gln Lys
Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser
Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser
Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asp Arg Gly Ala Tyr Trp Gly
Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 224 114 PRT
Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 224 Gln Val Lys Leu Gln Gln Ser Gly Ala Glu
Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys Lys Ala
Ser Gly Tyr Thr Phe Thr Arg Asp 20 25 30 Trp Met His Trp Val Lys
Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile Asn
Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln Lys Phe 50 55 60 Lys Asp
Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80
Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr Tyr Cys 85
90 95 Ala Arg Asn Tyr Gly Leu Tyr Trp Gly Gln Gly Thr Thr Val Thr
Val 100 105 110 Ser Ser 225 114 PRT Artificial Sequence VH of scFv
from mouse immunized with 2-phenyl-5-oxazolone 225 Gln Val Gln Leu
Gln Gln Ser Gly Leu Glu Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val
Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Asn Tyr 20 25 30
Leu Met His Trp Val Lys Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35
40 45 Gly Tyr Ile Asn Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln Lys
Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser
Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser
Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp Gly
Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 226 114 PRT
Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 226 Gln Val Lys Leu Gln Gln Ser Gly Ala Glu
Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys Lys Ala
Ser Gly Tyr Thr Phe Thr Asn Tyr 20 25 30 Trp Met His Trp Val Lys
Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile Asn
Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln Lys Phe 50 55 60 Lys Asp
Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80
Met Gln Leu Ser Ser Leu Thr Ser Asp Asp Ser Ala Val Tyr Tyr Cys 85
90 95 Ala Arg Asp Tyr Gly Tyr Phe Trp Gly Gln Gly Thr Thr Val Thr
Val 100 105 110 Ser Ser 227 114 PRT Artificial Sequence VH of scFv
from mouse immunized with 2-phenyl-5-oxazolone 227 Gln Val Gln Leu
Gln Gln Ser Gly Ala Glu Leu Val Lys Pro Gly Ala 1 5 10 15 Ser Val
Lys Leu Ser Cys Lys Thr Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30
Thr Met His Trp Val Lys Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35
40 45 Gly Tyr Ile Asn Pro Ser Ser Gly Tyr Thr Asn Tyr Asn Gln Lys
Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser
Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser
Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp Gly
Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 228 114 PRT
Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 228 Gln Val Gln Leu Gln Gln Ser Gly Ala Glu
Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys Glu Ala
Ser Gly Tyr Thr Phe Thr Ser His 20 25 30 Leu Met His Trp Val Lys
Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile Asn
Pro Arg Thr Gly Tyr Thr Glu Tyr Asn Gln Lys Phe 50 55 60 Lys Asp
Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80
Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr Tyr Cys 85
90 95 Ala Arg Asp Tyr Gly Ala Tyr Trp Gly Gln Gly Thr Thr Val Thr
Val 100 105 110 Ser Ser 229 114 PRT Artificial Sequence VH of scFv
from mouse immunized with 2-phenyl-5-oxazolone 229 Gln Val Lys Leu
Gln Gln Ser Gly Ala Glu Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val
Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30
Trp Met His Trp Val Lys Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35
40 45 Gly Tyr Ile Asn Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln Lys
Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser
Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser
Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp Gly
Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 230 114 PRT
Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 230 Gln Val Lys Leu Gln Gln Ser Gly Ala Glu
Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys Lys Ala
Thr Gly Tyr Thr Phe Thr Ser Tyr 20 25 30 Leu Met His Trp Val Lys
Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile Asn
Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln Lys Phe 50 55 60 Lys Asp
Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80
Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr Tyr Cys 85
90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp Gly Gln Gly Thr Thr Val Thr
Val 100 105 110 Ser Ser 231 114 PRT Artificial Sequence VH of scFv
from mouse immunized with 2-phenyl-5-oxazolone 231 Gln Val Gln Leu
Gln Gln Ser Gly Ala Glu Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val
Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30
Val Met His Trp Val Lys Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35
40 45 Gly Tyr Ile Asn Pro Ser Ser Gly Tyr Thr Asn Tyr Asn Gln Lys
Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser
Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser
Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asn Tyr Gly Ile Tyr Trp Gly
Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 232 114 PRT
Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 232 Gln Val Gln Leu Gln Gln Ser Gly Ala Glu
Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys Lys Ala
Ser Gly Tyr Thr Phe Thr Thr Phe 20 25 30 Leu Met His Trp Leu Lys
Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile Asn
Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln Lys Phe 50 55 60 Lys Asp
Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80
Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr Tyr Cys 85
90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp Gly Gln Gly Thr Thr Val Thr
Val 100 105 110 Ser Ser 233 114 PRT Artificial Sequence VH of scFv
from mouse immunized with 2-phenyl-5-oxazolone 233 Gln Val Lys Leu
Gln Gln Ser Gly Ala Glu Leu Ala Arg Pro Gly Ala 1 5 10 15 Ser Val
Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30
Thr Met His Trp Val Lys Gln Arg Pro Gly Gln Gly Leu Gly Trp Ile 35
40 45 Gly Tyr Ile Asn Pro Ser Ser Gly Tyr Thr Asn Tyr Asn Gln Lys
Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser
Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser
Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp Gly
Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 234 114 PRT
Artificial Sequence VH of scFv from mouse immunized with
2-phenyl-5-oxazolone 234 Gln Val Lys Leu Gln Gln Ser Gly Ala Glu
Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys Lys Ala
Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30 Thr Met His Trp Val Lys
Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35 40 45 Gly Tyr Ile Asn
Pro Thr Thr Gly Tyr Thr Glu Tyr Asn Gln Lys Phe 50 55 60 Lys Asp
Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80
Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr Tyr Cys 85
90 95 Ala Arg Asp Tyr Gly Tyr Tyr Trp Gly Gln Gly Thr Thr Val Thr
Val 100 105 110 Ser Ser 235 114 PRT Artificial Sequence VH of scFv
from mouse immunized with 2-phenyl-5-oxazolone 235 Gln Val Lys Leu
Gln Gln Ser Gly Ala Glu Leu Ala Lys Pro Gly Ala 1 5 10 15 Ser Val
Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Arg Asp 20 25 30
Trp Met His Trp Leu Lys Gln Arg Pro Gly Gln Gly Leu Glu Trp Ile 35
40 45 Gly Tyr Ile Asn Pro Ser Thr Gly Tyr Thr Glu Tyr Asn Gln Lys
Phe 50 55 60 Lys Asp Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser
Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser
Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Asn Tyr Gly Tyr Tyr Trp Gly
Gln Gly Thr Thr Val Thr Val 100 105 110 Ser Ser 236 109 PRT
Artificial Sequence VL of scFv from mouse immunized with
2-phenyl-5-oxazolone 236 Asp Ile Glu Leu Thr Gln Ser Pro Ser Ser
Leu Ser Ala Ser Leu Gly 1 5 10 15 Glu Arg Val Ser Leu Thr Cys Arg
Ala Ser Gln Glu Ile Ser Ser Gly 20 25 30 Tyr Leu Ser Trp Leu Gln
Gln Lys Pro Asp Gly Ser Ile Lys Arg Leu 35 40 45 Ile Tyr Ala Ala
Ser Thr Leu Glu Ser Gly Val Pro Lys Arg Phe Ser 50 55 60 Gly Ser
Arg Ser Gly Ser Asp Tyr Ser Leu Thr Ile Ser Ser Leu Glu 65 70 75 80
Ser Glu Asp Phe Ala Asp Tyr Tyr Cys Leu Gln Tyr Ala Ser Tyr Pro 85
90 95 Thr Phe Gly Ala Gly Thr Lys Leu Glu Ile Lys Arg Ala 100 105
237 110 PRT Artificial Sequence VL of scFv from mouse immunized
with 2-phenyl-5-oxazolone 237 Asp Ile Glu Leu Thr Gln Ser Pro Ala
Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val Thr Met Thr Cys
Arg Ala Ser Ser Ser Val Ser Ser Ser 20 25 30 Tyr Leu His Trp Tyr
Gln Gln Lys Pro Gly Ala Ser Pro Lys Val Trp 35 40 45 Ile Tyr Ser
Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg Phe Ser 50 55 60 Gly
Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Ser Val Glu 65 70
75 80 Ala Glu Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Tyr Ser Gly Tyr
Pro 85 90 95 Leu Thr Phe Gly Ala Gly Thr Lys Leu Glu Ile Lys Arg
Ala 100 105 110 238 110 PRT Artificial Sequence VL of scFv from
mouse immunized with 2-phenyl-5-oxazolone 238 Asp Ile Glu Leu Thr
Gln Ser Pro Thr Thr Met Ala Ala Ser Pro Gly 1 5 10 15 Glu Lys Ile
Thr Ile Thr Cys Ser Ala Ser Ser Ser Ile Ser Ser Asn 20 25 30 Tyr
Leu His Trp Tyr Gln Gln Lys Pro Gly Phe Ser Pro Lys Leu Leu 35 40
45 Ile Tyr Arg Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg Phe Ser
50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Gly Thr
Met Glu 65 70 75 80 Ala Glu Asp Val Ala Thr Tyr Tyr Cys Gln Gln Gly
Ser Thr Ile Pro 85 90 95 Leu Thr Phe Gly Ala Gly Thr Lys Leu Glu
Ile Lys Arg Ala 100 105 110 239 110 PRT Artificial Sequence VL of
scFv from mouse immunized with 2-phenyl-5-oxazolone 239 Asp Ile Glu
Leu Thr Gln Ser Pro Thr Thr Met Ala Ala Ser Pro Gly 1 5 10 15 Glu
Lys Ile Thr Ile Thr Cys Ser Ala Ser Ser Ser Ile Ser Ser Asn 20 25
30 Tyr Leu His Trp Phe Gln Gln Lys Pro Gly Phe Ser Pro Lys Leu Leu
35 40 45 Ile Ser Arg Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg
Phe Ser 50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile
Gly Thr Met Glu 65 70 75 80 Ala Glu Asp Val Ala Thr Tyr Tyr Cys Gln
Gln Gly Ser Thr Ile Pro 85 90 95 Phe Thr Phe Gly Ser Gly Thr Lys
Leu Glu Ile Lys Arg Ala 100 105 110 240 108 PRT Artificial Sequence
VL of scFv from mouse immunized with 2-phenyl-5-oxazolone 240 Asp
Ile Glu Leu Thr Gln Ser Pro Ala Ile Met Ser Ala Ser Pro Gly 1 5 10
15 Glu Lys Val Thr Ile Thr Cys Ser Ala Ser Ser Ser Val Asn Tyr Met
20 25 30 His Trp Phe Gln Gln Lys Pro Gly Thr Ser Pro Lys Leu Trp
Ile Tyr 35 40 45 Arg Thr Ser Asn Leu Ala Ser Gly Val Pro Thr Arg
Phe Ser Gly Ser 50 55 60 Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile
Ser Arg Met Glu Ala Glu 65 70 75
80 Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Arg Ser Ser Tyr Pro Pro Thr
85 90 95 Phe Gly Ser Gly Thr Lys Leu Glu Ile Lys Arg Ala 100 105
241 108 PRT Artificial Sequence VL of scFv from mouse immunized
with 2-phenyl-5-oxazolone 241 Asp Ile Glu Leu Thr Gln Ser Pro Ala
Ile Met Ser Ala Phe Pro Gly 1 5 10 15 Glu Lys Val Thr Met Thr Cys
Ser Ala Ser Ser Ser Val Ser Tyr Met 20 25 30 His Trp Tyr Gln Gln
Lys Ser Gly Thr Ser Pro Lys Arg Trp Ile Tyr 35 40 45 Asp Thr Ser
Lys Leu Ala Ser Gly Val Pro Ala Arg Phe Ser Gly Ser 50 55 60 Gly
Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Ser Met Glu Ala Glu 65 70
75 80 Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Phe Ser Ser Asn Pro Leu
Thr 85 90 95 Phe Gly Ala Gly Thr Lys Leu Glu Leu Lys Arg Ala 100
105 242 108 PRT Artificial Sequence VL of scFv from mouse immunized
with 2-phenyl-5-oxazolone 242 Asp Ile Glu Leu Thr Gln Ser Pro Ala
Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val Thr Met Thr Cys
Ser Ala Ser Ser Ser Ile Asn Tyr Met 20 25 30 His Trp Tyr Gln Gln
Lys Pro Gly Ala Ser Pro Lys Arg Trp Ile Tyr 35 40 45 Asp Thr Ser
Lys Leu Ala Ser Gly Val Pro Ala Arg Phe Ser Gly Ser 50 55 60 Gly
Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Ser Met Glu Ala Glu 65 70
75 80 Asp Ala Ala Thr Tyr Tyr Cys His Gln Arg Ser Ser Tyr Pro Trp
Thr 85 90 95 Phe Gly Gly Gly Thr Lys Leu Glu Ile Lys Arg Ala 100
105 243 108 PRT Artificial Sequence VL of scFv from mouse immunized
with 2-phenyl-5-oxazolone 243 Asp Ile Glu Leu Thr Gln Ser Pro Ala
Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val Thr Met Thr Cys
Ser Ala Ser Ser Ser Val Ser Tyr Met 20 25 30 His Trp Tyr Gln Gln
Lys Ser Gly Thr Ser Pro Lys Arg Trp Ile Tyr 35 40 45 Asp Thr Ser
Lys Leu Ala Ser Gly Val Pro Ala Arg Phe Ser Gly Ser 50 55 60 Gly
Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Ser Met Glu Ala Glu 65 70
75 80 Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Trp Ser Ser Asn Pro Leu
Thr 85 90 95 Phe Gly Ala Gly Thr Lys Leu Glu Ile Lys Arg Ala 100
105 244 108 PRT Artificial Sequence VL of scFv from mouse immunized
with 2-phenyl-5-oxazolone 244 Asp Ile Glu Leu Thr Gln Ser Pro Ala
Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val Thr Ile Thr Cys
Ser Ala Ser Ser Ser Val Ser Tyr Ile 20 25 30 His Trp Pro Gln Gln
Lys Pro Gly Thr Ser Pro Lys Leu Trp Ile Tyr 35 40 45 Ser Thr Ser
Asn Leu Ala Ser Gly Val Pro Ala Arg Phe Ser Gly Ser 50 55 60 Gly
Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Arg Met Glu Ala Glu 65 70
75 80 Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Tyr His Ser Tyr Pro Leu
Thr 85 90 95 Phe Gly Ala Gly Thr Lys Leu Glu Ile Lys Arg Ala 100
105 245 110 PRT Artificial Sequence VL of scFv from mouse immunized
with 2-phenyl-5-oxazolone 245 Asp Ile Glu Leu Thr Gln Ser Pro Thr
Thr Met Ala Ala Ser Pro Gly 1 5 10 15 Glu Lys Ile Thr Ile Thr Cys
Ser Ala Ser Ser Ser Ile Ser Ser Asn 20 25 30 Tyr Leu His Trp Phe
Gln Gln Lys Pro Gly Phe Ser Pro Lys Leu Leu 35 40 45 Ile Tyr Arg
Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg Phe Ser 50 55 60 Gly
Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Gly Thr Met Glu 65 70
75 80 Ala Glu Asp Val Ala Thr Tyr Tyr Cys Gln Gln Gly Ser Ser Ile
Pro 85 90 95 Leu Thr Phe Gly Gly Gly Thr Lys Leu Glu Ile Lys Arg
Ala 100 105 110 246 110 PRT Artificial Sequence VL of scFv from
mouse immunized with 2-phenyl-5-oxazolone 246 Asp Ile Glu Leu Thr
Gln Ser Pro Thr Thr Met Ala Ala Ser Pro Gly 1 5 10 15 Glu Met Ile
Thr Ile Thr Cys Ser Ala Ser Ser Ser Ile Ser Ser Asn 20 25 30 Tyr
Leu His Trp Tyr Gln Gln Lys Pro Gly Phe Ser Pro Lys Leu Leu 35 40
45 Ile Tyr Arg Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg Phe Ser
50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Gly Ala
Met Glu 65 70 75 80 Ala Glu Asp Val Ala Thr Tyr Tyr Cys Gln Gln Gly
Ser Ser Ile Pro 85 90 95 Tyr Thr Phe Gly Ala Gly Thr Lys Leu Glu
Ile Lys Arg Ala 100 105 110 247 110 PRT Artificial Sequence VL of
scFv from mouse immunized with 2-phenyl-5-oxazolone 247 Asp Ile Glu
Leu Thr Gln Ser Pro Thr Thr Met Ala Ala Ser Pro Gly 1 5 10 15 Glu
Lys Ile Thr Ile Thr Cys Ser Ala Ser Ser Ser Ile Ser Ser Asn 20 25
30 Tyr Leu His Trp Tyr Gln Gln Lys Pro Gly Phe Ser Pro Lys Leu Leu
35 40 45 Ile Tyr Arg Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg
Phe Ser 50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile
Gly Thr Met Glu 65 70 75 80 Ala Glu Asp Val Ala Thr Tyr Tyr Cys Gln
Gln Gly Ser Ser Ile Pro 85 90 95 Tyr Thr Phe Gly Gly Gly Thr Lys
Leu Glu Ile Lys Arg Ala 100 105 110 248 110 PRT Artificial Sequence
VL of scFv from mouse immunized with 2-phenyl-5-oxazolone 248 Asp
Ile Glu Leu Thr Gln Ser Pro Thr Thr Met Ala Ala Ser Pro Gly 1 5 10
15 Glu Lys Ile Thr Ile Thr Cys Ser Ala Ser Ser Ser Ile Ser Ser Asn
20 25 30 His Leu His Trp Tyr Gln Gln Lys Pro Gly Phe Ser Pro Lys
Leu Leu 35 40 45 Ile Tyr Arg Thr Ser Asn Leu Ala Ser Gly Val Pro
Ala Arg Phe Ser 50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu
Thr Ile Gly Thr Met Glu 65 70 75 80 Ala Glu Asp Val Ala Thr Tyr Tyr
Cys Gln Gln Gly Ser Gly Ile Pro 85 90 95 Tyr Thr Phe Gly Gly Gly
Thr Lys Leu Glu Ile Lys Arg Ala 100 105 110 249 110 PRT Artificial
Sequence VL of scFv from mouse immunized with 2-phenyl-5-oxazolone
249 Asp Ile Glu Leu Thr Gln Ser Pro Thr Thr Met Ala Ala Ser Pro Gly
1 5 10 15 Glu Lys Ile Thr Ile Thr Cys Ser Ala Ser Ser Ser Ile Ser
Ser Asn 20 25 30 Tyr Leu His Trp Tyr Gln Gln Lys Pro Gly Phe Ser
Pro Lys Leu Leu 35 40 45 Ile Tyr Arg Thr Ser Asn Leu Ala Ser Gly
Val Pro Ala Arg Phe Ser 50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr
Ser Leu Thr Ile Gly Thr Met Glu 65 70 75 80 Ala Glu Asp Val Ala Thr
Tyr Tyr Cys Gln Gln Gly Ser Ser Ile Pro 85 90 95 Phe Thr Phe Gly
Gly Gly Thr Lys Leu Glu Ile Lys Arg Ala 100 105 110 250 110 PRT
Artificial Sequence VL of scFv from mouse immunized with
2-phenyl-5-oxazolone 250 Asp Ile Glu Leu Thr Gln Ser Pro Ala Ile
Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Ile Thr Ile Thr Cys Ser
Ala Ser Ser Ser Ile Ser Ser Asn 20 25 30 Tyr Leu His Trp Tyr Gln
Gln Lys Pro Gly Phe Ser Pro Lys Leu Leu 35 40 45 Ile Tyr Arg Thr
Ser Asn Leu Ala Ser Gly Val Pro Ala Arg Phe Ser 50 55 60 Gly Ser
Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Gly Thr Met Glu 65 70 75 80
Ala Glu Asp Val Ala Thr Tyr Tyr Cys Gln Gln Gly Ser Ser Ile Pro 85
90 95 Tyr Thr Phe Gly Gly Gly Thr Lys Leu Glu Ile Lys Arg Ala 100
105 110 251 108 PRT Artificial Sequence VL of scFv from mouse
immunized with 2-phenyl-5-oxazolone 251 Asp Ile Glu Leu Thr Gln Ser
Pro Ala Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val Thr Met
Thr Cys Ser Ala Ser Ser Ser Val Ser Tyr Met 20 25 30 His Trp Tyr
Gln Gln Lys Ser Gly Thr Ser Pro Lys Arg Trp Ile Tyr 35 40 45 Asp
Thr Ser Lys Leu Ala Ser Gly Val Pro Ala Arg Phe Ser Gly Ser 50 55
60 Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Ser Met Glu Ala Glu
65 70 75 80 Asp Val Ala Thr Tyr Tyr Cys Gln Gln Trp Ser Ser Asn Pro
Leu Thr 85 90 95 Phe Gly Ala Gly Thr Lys Leu Glu Ile Lys Arg Ala
100 105 252 108 PRT Artificial Sequence VL of scFv from mouse
immunized with 2-phenyl-5-oxazolone 252 Asp Ile Glu Leu Thr Gln Ser
Pro Ala Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val Thr Leu
Thr Cys Ser Ala Ser Ser Ser Val Arg Tyr Val 20 25 30 Asn Trp Phe
Gln Gln Lys Ser Gly Thr Ser Pro Lys Arg Trp Ile Tyr 35 40 45 Asp
Thr Ser Lys Leu Ala Ser Gly Val Pro Ala Arg Phe Ser Gly Ser 50 55
60 Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Ser Met Glu Ala Glu
65 70 75 80 Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Trp Thr Ser Asn Pro
Pro Thr 85 90 95 Phe Gly Gly Gly Thr Lys Leu Glu Ile Lys Arg Ala
100 105 253 108 PRT Artificial Sequence VL of scFv from mouse
immunized with 2-phenyl-5-oxazolone 253 Asp Ile Glu Leu Thr Gln Ser
Pro Ala Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val Thr Met
Thr Cys Ser Ala Ser Ser Ser Val Ser Tyr Met 20 25 30 His Trp Tyr
Gln Gln Lys Ser Gly Thr Ser Pro Lys Arg Trp Ile Tyr 35 40 45 Asp
Thr Ser Lys Leu Ala Ser Gly Val Pro Ala Arg Phe Ser Gly Ser 50 55
60 Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Ser Met Glu Ala Glu
65 70 75 80 Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Trp Ser Thr Asn Ala
Leu Thr 85 90 95 Phe Gly Ala Gly Thr Lys Leu Glu Ile Lys Arg Ala
100 105 254 110 PRT Artificial Sequence VL of scFv from mouse
immunized with 2-phenyl-5-oxazolone 254 Asp Ile Glu Leu Thr Gln Ser
Pro Ala Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val Thr Met
Thr Cys Ser Ala Ser Ser Ser Val Thr Ser Asn 20 25 30 Tyr Leu Asn
Trp Tyr Gln Gln Lys Ser Gly Ala Ser Pro Lys Leu Trp 35 40 45 Val
Tyr Ser Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg Phe Ser 50 55
60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Ser Val Glu
65 70 75 80 Ala Glu Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Tyr Ser Gly
Tyr Pro 85 90 95 Leu Thr Phe Gly Ala Gly Thr Lys Leu Glu Ile Lys
Arg Ala 100 105 110 255 110 PRT Artificial Sequence VL of scFv from
mouse immunized with 2-phenyl-5-oxazolone 255 Asp Ile Glu Leu Thr
Gln Ser Pro Ala Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu Lys Val
Thr Met Thr Cys Ser Ala Ser Ser Ser Val Ser Ser Asn 20 25 30 Tyr
Leu Asn Trp Tyr Gln Gln Lys Ser Gly Ala Ser Pro Lys Leu Trp 35 40
45 Ile Tyr Ser Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg Phe Ser
50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile Ser Arg
Met Glu 65 70 75 80 Ala Glu Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Arg
Ser Ser Tyr Pro 85 90 95 Leu Thr Phe Gly Ala Gly Thr Lys Leu Glu
Ile Lys Arg Ala 100 105 110 256 110 PRT Artificial Sequence VL of
scFv from mouse immunized with 2-phenyl-5-oxazolone 256 Asp Ile Glu
Leu Thr Gln Ser Pro Ala Ile Met Ser Ala Ser Pro Gly 1 5 10 15 Glu
Lys Val Thr Met Thr Cys Ser Ala Ser Ser Ser Val Ser Ser Asn 20 25
30 Tyr Leu His Trp Tyr Gln Gln Lys Ser Gly Ala Ser Pro Lys Leu Trp
35 40 45 Ile Tyr Ser Thr Ser Asn Leu Ala Ser Gly Val Pro Ala Arg
Phe Ser 50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu Thr Ile
Ser Ser Val Glu 65 70 75 80 Ala Glu Asp Ala Ala Thr Tyr Tyr Cys Gln
Gln Tyr Ser Gly Tyr Pro 85 90 95 Leu Thr Phe Gly Ala Gly Thr Lys
Leu Glu Ile Lys Arg Ala 100 105 110 257 110 PRT Artificial Sequence
VL of scFv from mouse immunized with 2-phenyl-5-oxazolone 257 Asp
Ile Glu Leu Thr Gln Ser Pro Ala Ile Met Ser Ala Ser Pro Gly 1 5 10
15 Glu Lys Val Thr Met Thr Cys Ser Ala Ser Ser Ser Val Ser Ser Asn
20 25 30 Tyr Leu His Trp Phe Gln Gln Lys Ser Gly Ala Ser Pro Lys
Leu Trp 35 40 45 Ile Tyr Ser Thr Ser Asn Leu Pro Ser Gly Val Pro
Ala Arg Phe Ser 50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu
Thr Ile Ser Ser Val Glu 65 70 75 80 Ala Glu Asp Ala Ala Thr Tyr Tyr
Cys Gln Gln Tyr Ser Gly Tyr Pro 85 90 95 Leu Thr Phe Gly Gly Gly
Thr Lys Leu Glu Ile Lys Arg Ala 100 105 110 258 110 PRT Artificial
Sequence VL of scFv from mouse immunized with 2-phenyl-5-oxazolone
258 Asp Ile Glu Leu Thr Gln Ser Pro Thr Thr Met Ala Ala Ser Pro Gly
1 5 10 15 Glu Lys Ile Thr Ile Thr Cys Ser Ala Ser Ser Ser Ile Ser
Ser Asn 20 25 30 Tyr Leu His Trp Tyr Gln Gln Lys Pro Gly Phe Ser
Pro Lys Leu Leu 35 40 45 Ile Tyr Arg Thr Ser Asn Leu Ala Ser Gly
Val Pro Ala Arg Phe Ser 50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr
Ser Leu Thr Ile Gly Thr Met Glu 65 70 75 80 Ala Glu Asp Val Ala Thr
Tyr Tyr Cys Gln Gln Gly Ser Ser Ile Pro 85 90 95 Leu Thr Phe Gly
Ala Gly Thr Lys Leu Glu Ile Lys Arg Ala 100 105 110 259 41 PRT
Artificial Sequence residues encoded by insertion site and
surrounding sequence in pHEN1 259 Leu Leu Ala Ala Gln Pro Ala Met
Ala Gln Val Gln Leu Gln Val Asp 1 5 10 15 Leu Glu Ile Lys Arg Ala
Ala Ala Glu Gln Lys Leu Ile Ser Glu Glu 20 25 30 Asp Leu Asn Gly
Ala Ala Thr Val Glu 35 40 260 126 DNA Artificial Sequence insertion
site and surrounding sequence in pHEN1 260 ttactcgcgg cccagccggc
catggcccag gtgcagctgc aggtcgacct cgagatcaaa 60 cgggcggccg
cagaacaaaa actcatctca gaagaggatc tgaatggggc cgcatagact 120 gttgaa
126 261 734 PRT Artificial Sequence scFvB18 261 Pro His Glu Thr Tyr
Arg Ser Glu Arg His Ile Ser Ser Glu Arg Ala 1 5 10 15 Leu Ala Gly
Leu Asn Val Ala Leu Gly Leu Asn Leu Glu Gly Leu Asn 20 25 30 Gly
Leu Asn Ser Glu Arg Gly Leu Tyr Ala Leu Ala Gly Leu Leu Glu 35 40
45 Val Ala Leu Leu Tyr Ser Pro Arg Gly Leu Tyr Ala Leu Ala Ser Glu
50 55 60 Arg Val Ala Leu Leu Tyr Ser Leu Glu Ser Glu Arg Cys Tyr
Ser Leu 65 70 75 80 Tyr Ser Ala Leu Ala Ser Glu Arg Gly Leu Tyr Thr
Tyr Arg Thr His
85 90 95 Arg Pro His Glu Thr His Arg Ser Glu Arg Thr Tyr Arg Thr
Arg Pro 100 105 110 Met Glu Thr His Ile Ser Thr Arg Pro Val Ala Leu
Leu Tyr Ser Gly 115 120 125 Leu Asn Ala Arg Gly Pro Arg Gly Leu Tyr
Ala Arg Gly Gly Leu Tyr 130 135 140 Leu Glu Gly Leu Thr Arg Pro Ile
Leu Glu Gly Leu Tyr Ala Arg Gly 145 150 155 160 Ile Leu Glu Ala Ser
Pro Pro Arg Ala Ser Asn Ser Glu Arg Gly Leu 165 170 175 Tyr Gly Leu
Tyr Thr His Arg Leu Tyr Ser Thr Tyr Arg Ala Ser Asn 180 185 190 Gly
Leu Leu Tyr Ser Pro His Glu Leu Tyr Ser Ser Glu Arg Leu Tyr 195 200
205 Ser Ala Leu Ala Thr His Arg Leu Glu Thr His Arg Val Ala Leu Ala
210 215 220 Ser Pro Leu Tyr Ser Pro Arg Ser Glu Arg Ser Glu Arg Thr
His Arg 225 230 235 240 Ala Leu Ala Thr Tyr Arg Met Glu Thr Gly Leu
Asn Leu Glu Ser Glu 245 250 255 Arg Ser Glu Arg Leu Glu Thr His Arg
Ser Glu Arg Gly Leu Ala Ser 260 265 270 Pro Ser Glu Arg Ala Leu Ala
Val Ala Leu Thr Tyr Arg Thr Tyr Arg 275 280 285 Cys Tyr Ser Ala Leu
Ala Ala Arg Gly Thr Tyr Arg Ala Ser Pro Thr 290 295 300 Tyr Arg Gly
Leu Tyr Ser Glu Arg Ser Glu Arg Thr Tyr Arg Thr Tyr 305 310 315 320
Arg Pro His Glu Ala Ser Pro Thr Tyr Arg Thr Arg Pro Gly Leu Tyr 325
330 335 Gly Leu Asn Gly Leu Tyr Thr His Arg Thr His Arg Val Ala Leu
Thr 340 345 350 His Arg Val Ala Leu Ser Glu Arg Ser Glu Arg Gly Leu
Tyr Gly Leu 355 360 365 Tyr Gly Leu Tyr Gly Leu Tyr Ser Glu Arg Gly
Leu Tyr Gly Leu Tyr 370 375 380 Gly Leu Tyr Gly Leu Tyr Ser Glu Arg
Gly Leu Tyr Gly Leu Tyr Gly 385 390 395 400 Leu Tyr Gly Leu Tyr Ser
Glu Arg Gly Leu Asn Ala Leu Ala Val Ala 405 410 415 Leu Gly Leu Tyr
Thr His Arg Gly Leu Asn Gly Leu Ser Glu Arg Ala 420 425 430 Leu Ala
Leu Glu Thr His Arg Thr His Arg Ser Glu Arg Pro Arg Gly 435 440 445
Leu Tyr Gly Leu Thr His Arg Val Ala Leu Thr His Arg Leu Glu Thr 450
455 460 His Arg Cys Tyr Ser Ala Arg Gly Ser Glu Arg Ser Glu Arg Thr
His 465 470 475 480 Arg Gly Leu Tyr Ala Leu Ala Val Ala Leu Thr His
Arg Thr His Arg 485 490 495 Ser Glu Arg Ala Ser Asn Thr Tyr Arg Ala
Leu Ala Ala Ser Asn Thr 500 505 510 Arg Pro Val Ala Leu Gly Leu Asn
Gly Leu Leu Tyr Ser Pro Arg Ala 515 520 525 Ser Pro His Ile Ser Leu
Glu Pro His Glu Thr His Arg Gly Leu Tyr 530 535 540 Leu Glu Ile Leu
Glu Gly Leu Tyr Gly Leu Tyr Thr His Arg Ala Ser 545 550 555 560 Asn
Ala Ser Asn Ala Arg Gly Ala Leu Ala Pro Arg Gly Leu Tyr Val 565 570
575 Ala Leu Pro Arg Ala Leu Ala Ala Arg Gly Pro His Glu Ser Glu Arg
580 585 590 Gly Leu Tyr Ser Glu Arg Leu Glu Ile Leu Glu Gly Leu Tyr
Ala Ser 595 600 605 Pro Leu Tyr Ser Ala Leu Ala Ala Leu Ala Leu Glu
Thr His Arg Ile 610 615 620 Leu Glu Thr His Arg Gly Leu Tyr Ala Leu
Ala Gly Leu Asn Thr His 625 630 635 640 Arg Gly Leu Ala Ser Pro Gly
Leu Ala Leu Ala Ile Leu Glu Thr Tyr 645 650 655 Arg Pro His Glu Cys
Tyr Ser Ala Leu Ala Leu Glu Thr Arg Pro Thr 660 665 670 Tyr Arg Ser
Glu Arg Ala Ser Asn His Ile Ser Thr Arg Pro Val Ala 675 680 685 Leu
Pro His Glu Gly Leu Tyr Gly Leu Tyr Gly Leu Tyr Thr His Arg 690 695
700 Leu Tyr Ser Leu Glu Thr His Arg Val Ala Leu Leu Glu Gly Leu Ile
705 710 715 720 Leu Glu Leu Tyr Ser Ala Arg Gly Ala Leu Ala Ala Leu
Ala 725 730 262 770 DNA Artificial Sequence scFvB18 262 ttctattctc
acagtgcaca ggtccagctg cagcagtctg gggctgagct tgtgaagcct 60
ggggcttcag tgaagctgtc ctgcaaggct tctggctaca ccttcaccag ctactggatg
120 cactgggtga agcagaggcc tggacgaggc cttgagtgga ttggaaggat
tgatcctaat 180 agtggtggta ctaagtacaa tgagaagttc aagagcaagg
ccacactgac tgtagacaaa 240 ccctccagca cagcctacat gcagctcagc
agcctgacat ctgaggactc tgcggtctat 300 tattgtgcaa gatacgacta
cggtagtagc tactactttg actactgggg ccaagggacc 360 acggtcaccg
tctcctcagg tggaggcggt tcaggcggag gtggctctgg cggtggcgga 420
tcccaggctg ttgggacaca ggaatctgca ctcaccacat cacctggtga aacagtcaca
480 ctcacttgtc gctcaagtac tggggctgtt acaactagta actatgccaa
ctgggtccaa 540 gaaaaaccag atcatttatt cactggtcta ataggtggta
ccaacaaccg agctccaggt 600 gttcctgcca gattctcagg ctccctgatt
ggagacaagg ctgccctcac catcacaggg 660 gcacagactg aggatgaggc
aatatatttc tgtgctctat ggtacagcaa ccattgggtg 720 ttcggtggag
gaaccaaact gactgtcctc gagatcaaac gggcggccgc 770 263 35 PRT
Artificial Sequence carboxy terminus of Hman CH1 and hinge from
pJM1-Fab D1.3 263 Lys Pro Ser Asn Thr Lys Val Asp Lys Lys Val Glu
Pro Lys Ser Ser 1 5 10 15 Thr Lys Thr His Thr Ser Gly Gly Glu Gln
Lys Leu Ile Ser Glu Glu 20 25 30 Asp Leu Asn 35 264 30 PRT
Artificial Sequence pelB leader and amino terminus of VK from
pJM1-Fab D1.3 264 Met Lys Tyr Leu Leu Pro Thr Ala Ala Ala Gly Leu
Leu Leu Pro Ala 1 5 10 15 Ala Gln Pro Ala Met Ala Asp Ile Glu Phe
Thr Gln Ser Pro 20 25 30 265 241 DNA Artificial Sequence linker
region of pJM1-Fab D1.3 265 aaccccagca acaccaaggt cgacaagaaa
gttgagccca aatcttcaac taagacgcac 60 acatcaggag gtgaacagaa
gctcatctca gaagaggatc tgaattaata agggagcttg 120 catgcaaatt
ctatttcaag gagacagtca taatgaaata cctattgcct acggcagccg 180
ctggattgtt attacctgct gcccaaccag cgatggccga catcgagttc acccagtctc
240 c 241 266 108 PRT Artificial Sequence light chain of D1.3 266
Asp Ile Gln Met Thr Gln Ser Pro Ala Ser Leu Ser Ala Ser Val Gly 1 5
10 15 Glu Thr Val Thr Ile Thr Cys Arg Ala Ser Gly Asn Ile His Asn
Tyr 20 25 30 Leu Ala Trp Tyr Gln Gln Lys Gln Gly Lys Ser Pro Gln
Leu Leu Val 35 40 45 Tyr Tyr Thr Thr Thr Leu Ala Asp Gly Val Pro
Ser Arg Phe Ser Gly 50 55 60 Ser Gly Ser Gly Thr Gln Tyr Ser Leu
Lys Ile Asn Ser Leu Gln Pro 65 70 75 80 Glu Asp Phe Gly Ser Tyr Tyr
Cys Gln His Phe Trp Ser Thr Pro Arg 85 90 95 Thr Phe Gly Gly Gly
Thr Lys Leu Glu Ile Lys Arg 100 105 267 108 PRT Artificial Sequence
light chain from clone M1F 267 Asp Ile Glu Leu Thr Gln Ser Pro Ser
Ser Leu Ser Ala Ser Leu Gly 1 5 10 15 Glu Arg Val Ser Leu Thr Cys
Arg Ala Ser Gln Asp Ile Gly Ser Ser 20 25 30 Leu Asn Trp Leu Gln
Gln Glu Pro Asp Gly Thr Ile Lys Arg Leu Ile 35 40 45 Tyr Ala Thr
Ser Ser Leu Asp Ser Gly Val Pro Lys Arg Phe Ser Gly 50 55 60 Ser
Arg Ser Gly Ser Asp Tyr Ser Leu Thr Ile Ser Ser Leu Glu Ser 65 70
75 80 Glu Asp Phe Val Asp Tyr Tyr Cys Leu Gln Tyr Ala Ser Ser Pro
Trp 85 90 95 Thr Phe Gly Gly Gly Thr Lys Leu Glu Leu Lys Arg 100
105 268 109 PRT Artificial Sequence light chain from M21 268 Asp
Ile Glu Leu Thr Gln Ser Pro Ala Leu Met Ala Ala Ser Pro Gly 1 5 10
15 Glu Lys Val Thr Ile Thr Cys Ser Val Ser Ser Ser Ile Ser Ser Ser
20 25 30 Asn Leu His Trp Tyr Gln Gln Lys Ser Glu Thr Ser Pro Lys
Pro Trp 35 40 45 Ile Tyr Gly Thr Ser Asn Leu Ala Ser Gly Val Pro
Val Arg Phe Ser 50 55 60 Gly Ser Gly Ser Gly Thr Ser Tyr Ser Leu
Thr Ile Ser Ser Met Glu 65 70 75 80 Ala Glu Asp Ala Ala Thr Tyr Tyr
Cys Gln Gln Trp Ser Ser Tyr Pro 85 90 95 Leu Thr Phe Gly Ala Gly
Thr Lys Leu Glu Ile Lys Arg 100 105 269 15 PRT Artificial Sequence
linker between VH-HuH2 and VK-HuK3 269 Gly Gly Gly Gly Ser Gly Gly
Gly Gly Ser Gly Gly Gly Gly Ser 1 5 10 15 270 15 PRT Artificial
Sequence linker between VH-HuH1 and VK-HuK4 270 Gly Gly Gly Gly Ser
Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser 1 5 10 15 271 15 PRT
Artificial Sequence linker between VH-HuH2 and VK-HuK4 271 Gly Gly
Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser 1 5 10 15 272
15 PRT Artificial Sequence linker between VH-HuH1 and VK-HuK3 272
Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser 1 5 10
15
* * * * *