U.S. patent application number 10/680067 was filed with the patent office on 2005-08-11 for bioreactive allosteric polynucleotides.
This patent application is currently assigned to Yale University. Invention is credited to Breaker, Ronald R..
Application Number | 20050176017 10/680067 |
Document ID | / |
Family ID | 26710009 |
Filed Date | 2005-08-11 |
United States Patent
Application |
20050176017 |
Kind Code |
A1 |
Breaker, Ronald R. |
August 11, 2005 |
Bioreactive allosteric polynucleotides
Abstract
Polynucleotides having allosteric properties that modify a
function or configuration of the polynucleotide with a chemical
effector and/or physical signal are employed primarily as
biosensors and/or enzymes for diagnostic and catalytic purposes. In
some preferred embodiments, the polynucleotides are DNA enzymes
that are used in solution/suspension or attached to a solid support
as biosensors to detect the presence or absence of a compound, its
concentration, or physical change in a sample by observation of
self-catalysis. Chemical effectors include organic compounds such
as amino acids, amino acid derivatives, peptides, nucleosides,
nucleotides, steroids, and mixtures of these with each other and
with metal ions, cellular metabolites or blood components obtained
from biological samples, steroids, pharmaceuticals, pesticides,
herbicides, food toxins, and the like. Physical signals include
radiation, temperature changes, and combinations thereof.
Inventors: |
Breaker, Ronald R.;
(Guilford, CT) |
Correspondence
Address: |
MINTZ, LEVIN, COHN, FERRIS, GLOVSKY
AND POPEO, P.C.
ONE FINANCIAL CENTER
BOSTON
MA
02111
US
|
Assignee: |
Yale University
New Haven
CT
|
Family ID: |
26710009 |
Appl. No.: |
10/680067 |
Filed: |
October 6, 2003 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10680067 |
Oct 6, 2003 |
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09849069 |
May 4, 2001 |
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6630306 |
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09849069 |
May 4, 2001 |
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09331809 |
Jun 18, 1999 |
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09331809 |
Jun 18, 1999 |
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PCT/US97/24158 |
Dec 18, 1997 |
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60033684 |
Dec 19, 1996 |
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60055039 |
Aug 8, 1997 |
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Current U.S.
Class: |
435/6.11 ;
435/183; 435/320.1; 435/325; 435/6.12; 435/69.1; 536/23.2 |
Current CPC
Class: |
C12N 15/101 20130101;
C12N 2310/121 20130101; C12Q 1/6811 20130101; C12N 2310/12
20130101; C12Q 1/6825 20130101; C12Q 2521/337 20130101; C12Q
2521/337 20130101; C12Q 2525/205 20130101; C12Q 2525/205 20130101;
C12Q 1/6825 20130101; C12N 2310/322 20130101; C12Q 1/6825 20130101;
C12N 15/113 20130101; C07K 2319/00 20130101; C12N 2310/111
20130101; C12Q 1/6811 20130101; C12Q 2521/337 20130101 |
Class at
Publication: |
435/006 ;
435/069.1; 435/183; 435/320.1; 435/325; 536/023.2 |
International
Class: |
C12Q 001/68; C12N
009/00; C07H 021/04 |
Goverment Interests
[0002] The invention was made with partial government support under
NIH grant GM59343. The government has certain rights in the
invention.
Claims
1-20. (canceled)
21. A polynucleotide of mixed RNA and DNA nucleotide composition
comprising an allosteric site and an enzyme domain spatially
distinct from said allosteric site, wherein reversible interaction
of a chemical effector with the allosteric site on the
polynucleotide reversibly alters the cleavage function or
configuration of the polynucleotide, wherein the chemical effector
is a metal ion or small molecule having a molecular weight of 300
Daltons or less.
22. The polynucleotide of mixed RNA and DNA nucleotide composition
of claim 21, wherein the cleavage function or configuration of the
polynucleotide is altered in less than 60 minutes after interaction
with the chemical effector.
23. A polynucleotide of mixed RNA and DNA nucleotide composition
comprising an allosteric site and an enzyme domain spatially
distinct from said allosteric site, wherein the rate of catalysis
of the enzyme domain is reversibly modulated by interaction with a
chemical effector, wherein the chemical effector is a metal ion or
small molecule having a molecular weight of 300 Daltons or
less.
24. The polynucleotide of mixed RNA and DNA nucleotide composition
of claim 23, wherein an observable change in the rate of catalysis
of the enzyme domain occurs 6 minutes or less after interaction
with the chemical effector.
25. The polynucleotide of mixed RNA and DNA composition of claim
24, wherein the observable change in the rate of catalysis of the
enzyme domain occurs in 1 minute or less.
26. The polynucleotide of mixed RNA and DNA composition of claim
23, wherein the rate of catalysis of the enzyme is measured by
observing enzyme self-cleavage or substrate cleavage.
27. The polynucleotide of mixed RNA and DNA nucleotide composition
according to claims 21 or 23, wherein the chemical effector is a
small molecule selected from the group consisting of amino acids,
amino acid derivatives, peptides, nucleosides, nucleotides, and
steroids.
28. The polynucleotide of mixed RNA and DNA nucleotide composition
according to claims 21 or 23, wherein said composition comprises
modified nucleotides.
29. A biosensor comprising the polynucleotides of mixed RNA and DNA
nucleotide composition according to claims 21 or 23.
30. The biosensor of claim 29, wherein the polynucleotide of mixed
RNA and DNA composition is attached to a solid support.
31. A method for detecting the presence or absence of a compound or
its concentration in a sample, comprising the step of: contacting
the sample with a polynucleotide of mixed RNA and DNA composition,
said polynucleotide comprising an allosteric site and an enzyme
domain spatially distinct from said allosteric site, wherein
reversible interaction of the compound with the allosteric site on
the polynucleotide alters the cleavage function or configuration of
the polynucleotide relative to that of a control sample, wherein
the chemical effector is a metal ion or small molecule having a
molecular weight of 300 Daltons or less; and further wherein an
alteration in function or configuration of the polynucleotide
indicates the presence or absence of a compound or its
concentration in the sample.
32. The method of claim 31, wherein the presence or absence of a
compound or its concentration is detected by observation of an
alteration in the cleavage function of the polynucleotide.
33. The method of claim 31, wherein the chemical effector is a
small molecule selected from the group consisting of amino acids,
acid derivatives, peptides, nucleosides, nucleotides, and
steroids.
34. A polynucleotide of mixed RNA and DNA composition, said
polynucleotide comprising an allosteric site and an enzyme domain
spatially distinct from said allosteric site, having three stem
components, stem I, stem II and stem III, wherein stem I and stem
III are polynucleotide sequences which together form the enzyme
domain and stem II is a polynucleotide sequence which forms the
allosteric site, wherein interaction of a chemical effector with
the allosteric site reversibly alters the cleavage function or
configuration of the polynucleotide, further wherein the chemical
effector is a metal ion or a small molecule having a molecular
weight of 300 Daltons or less.
35. The polynucleotide according to claim 34, wherein the cleavage
function or configuration of the polynucleotide is altered in less
than 60 minutes after interaction with the chemical effector.
36. A polynucleotide of mixed RNA and DNA composition, said
polynucleotide comprising an allosteric site and an enzyme domain
spatially distinct from said allosteric site, having three stem
components, stem I, stem II and stem III, wherein stem I and stem
III are polynucleotide sequences which together form the enzyme
domain and stem II is a polynucleotide sequence which forms the
allosteric site, wherein interaction of a chemical effector with
the allosteric site reversibly modulates the rate of catalysis of
the polynucleotide, further wherein the chemical effector is a
metal ion or a small molecule having a molecular weight of 300
Daltons or less.
37. The polynucleotide of claim 36, wherein an observable change in
the rate of catalysis of the polynucleotide occurs in 6 minutes or
less after interaction with the chemical effector.
38. The polynucleotide of claim 37, wherein the observable change
occurs one minute or less after interaction with the chemical
effector.
39. The polynucleotide of claim 36, wherein the chemical effector
is a small molecule selected from the group consisting of amino
acids, amino acid derivatives, peptides, nucleosides, nucleotides,
and steroids.
40. A biosensor comprising the polynucleotide according to claims
34 or 36.
41. A method for detecting the presence or absence of a compound or
its concentration in a sample comprising contacting the sample with
a polynucleotide according to claims 34 or 36, whereby reversible
interaction of the compound with the allosteric site alters the
cleavage function or configuration of the polynucleotide relative
to that of a control sample, and observing said alteration in the
cleavage function or configuration of the polynucleotide, wherein
the compound is a chemical effector that is a metal ion or small
molecule having a molecular weight of 300 Daltons or less and
further wherein an alteration in function or configuration of the
polynucleotide indicates the presence or absence of a compound or
its concentration in the sample.
42. The method of claim 41, wherein the presence or absence of a
compound or its concentration is detected by observation of an
alteration in the cleavage function of the polynucleotide.
43. The method of claim 42, wherein the compound is a chemical
effector that is selected from the group consisting of amino acids,
amino acid derivatives, peptides, nucleosides, nucleotides, and
steroids.
44. A polynucleotide of claim 36, wherein the rate of catalysis of
the enzyme is measured by observing enzyme self cleavage or
substrate cleavage.
45. A biosensor of claim 40, wherein the polynucleotide is attached
to a solid support.
Description
CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This application is a continuation-in-part of co-pending
U.S. application Ser. No. 09/331,809, filed Jun. 18, 1999 as a
national phase entry of PCT/US97/24158, filed internationally Dec.
18, 1997 and claiming priority benefit of U.S. Provisional
application Ser. No. 60/033,684, filed Dec. 19, 1996 and Ser. No.
60/055,039, filed Aug. 8, 1997.
BACKGROUND OF THE INVENTION
[0003] 1. Field of the Invention
[0004] This invention relates primarily to functional DNA
polynucleotides that exhibit allosteric properties, and to
catalytic RNA and DNA polynucleotides that have catalytic
properties with rates that can be controlled by a chemical
effector, a physical signal, or combinations thereof. Bioreactive
allosteric polynucleotides of the invention are useful in a variety
of applications, particularly as biosensors.
[0005] Biosensors are widely used in medicine, veterinary medicine,
industry, and environmental science, especially for diagnostic
purposes. Biosensors are typically composed of a biological
compound (sensor material) that is coupled to a transducer, in
order to produce a quantitative readout of the agent or conditions
under analysis. Usually, the biological component of the biosensor
is a macromolecule, often subject to a conformational change upon
recognition and binding of its corresponding ligand. In nature,
this effect may immediately initiate a signal process (e.g., ion
channel function in nerve cells). Included in the group of
`affinity sensors` are lectins, antibodies, receptors, and
oligonucleotides. In biosensors, ligand binding to the affinity
sensor is detected by optoelectronic devices, potentiometric
electrodes, field effect transistors (FETs), or the like.
[0006] Alternatively, the specificity and catalytic power of
proteins have been harnessed to create biosensors that operate via
enzyme function. Likewise, proteins have been used as immobilized
catalysts for various industrial applications. The catalytic
activity of purified enzymes or even whole organelles,
microorganisms or tissues can be monitored by potentiometric or
amperometric electrodes, FETs, or thermistors. The majority of
biosensors that are commercially available are based on enzymes, of
which the oxidoreductases and lyases are of great interest. It is
nearly exclusively the reactants of the reactions catalyzed by
these enzymes for which transducers are available. These
transducers include potentiometric electrodes, FETs, pH- and
O.sub.2-sensitive probes, and amperometric electrodes for
H.sub.2O.sub.2 and redox mediators. For example, the
oxidoreductases, a group of enzymes that catalyze the transfer of
redox equivalents, can be monitored by detectors that are sensitive
to H.sub.2O.sub.2 or O.sub.2 concentrations.
[0007] Enzymes are well-suited for application in sensing devices.
The binding constants for many enzymes and receptors can be
extremely low (e.g., avidin; K.sub.d=10.sup.15 M) and the catalytic
rates are on the order of a few thousand per second, but can reach
600,000 sec.sup.-1 (carboanhydrase) (45). Enzymes can be monitored
as biosensors via their ability to convert substrate to product,
and also be the ability of certain analytes to act as inhibitors of
catalytic function.
[0008] Organic chemistry and biochemistry have reached a state of
proficiency where new molecules can be made to simulate the
function of protein receptors and enzymes. Macrocyclic rings,
polymers for imprinting, and self-assembling monolayers are now
being intensively investigated for their potential application in
biosensors. In addition, the immune system of animals can be
harnessed to create new ligand-binding proteins that can act as
artificial biorecognition systems. Antibodies that have been made
to bind transition-state analogues can also catalyze chemical
reactions, thereby functioning as novel `artificial enzymes` (36).
The latter examples are an important route to the creation of
biosensors that can be used to detect non-natural compounds, or
that function under non-physiologic conditions.
[0009] 2. Description of Related Art
[0010] In nature, RNA not only serves as components of the
information transfer process, but also performs tasks that are
typically accomplished by proteins, including molecular recognition
and catalysis. A seemingly endless variety of aptamers, and even
DNA aptamers can be created in vitro that bind various ligands with
great affinity and specificity (17). Nucleic acids likely have an
extensive and as yet untapped ability adopt specific conformations
that can bind ligands and also to catalyze chemical transformations
(16). The engineering of new RNA and DNA receptors and catalysts is
primarily achieved via in vitro selection, a method by which
trillions of different oligonucleotide sequences are screened for
molecules that display the desired function. This method consists
of repeated rounds of selection and amplification in a manner that
simulates Darwinian evolution, but with molecules and not with
living organisms (4). One drawback to the use of existing enzymes
as biosensors is that one is limited to developing a sensor based
on the properties of existing enzymes or receptors. A significant
advantage can be gained if one could `tailor-make` the sensor for a
particular application. It would be desirable to employ nucleic
acids to create entirely new biosensors that have properties and
specificities that span beyond the range of capabilities of current
biosensors.
[0011] In vitro selection has been the main vehicle for new
ribozyme discoveries in recent years. The catalytic repertoire of
ribozymes includes RNA and DNA phosphoester hydrolysis and
transesterification, RNA ligation, RNA phosphorylation, alkylation,
amide and ester bond formation, and amide cleavage reactions.
Recent evidence has shown that biocatalysis is not solely the realm
of RNA and proteins. DNA has been shown to form catalytic
structures that efficiently cleave RNA (5,7), that ligate DNA (10),
and that catalyze the metallation of porphyrin rings (24). As
described herein, self-cleaving DNAs have been isolated from a
random-sequence pool of molecules that operate via a redox
mechanism, making possible the use of an artificial DNA enzyme in
place of oxidoreductase enzymes in biosensors. In addition, these
DNA enzymes or `deoxyribozymes` are considerably more stable that
either RNA or protein enzymes--an attractive feature for the sensor
component of a biosensor device.
BRIEF SUMMARY OF THE INVENTION
[0012] It is an object of the invention to provide examples of RNA
and DNA sensing elements for use in biosensors, including
polynucleotides attached to a solid support. Both RNA and DNA can
be designed to bind a variety of ligands with considerable
specificity and affinity. In addition, both RNA and DNA can be made
to catalyze chemical transformations under user-defined conditions.
A combination of rational design and combinatorial methods has been
used to create prototype biosensors based on RNA and DNA.
[0013] These and other objects of the invention are accomplished by
the present invention, which provides purified functional DNA
polynucleotides that exhibit allosteric properties that modify a
function or configuration of the polynucleotide with a chemical
effector, a physical signal, or combinations thereof. The invention
further provides purified functional polynucleotides having
catalytic properties with rates that can be controlled by a
chemical effector, a physical signal, or combinations thereof. Some
embodiments are enzymes exhibiting allosteric properties that
modify the rate of catalysis of the enzyme. In addition, the
invention encompasses biosensors comprising bioreactive allosteric
polynucleotides described herein.
[0014] Examples of chemical effectors include, but are not limited
to, organic compounds such as amino acids, amino acid derivatives,
peptides, nucleosides, nucleosides, nucleotides, steroids, and
mixtures of organic compounds and metal ions. In some embodiments,
the effectors are microbial or cellular metabolites or components
of bodily fluids such as blood and urine obtained from biological
samples. In other embodiments, the effectors are pharmaceuticals,
pesticides, herbicides, and food toxins. Physical signals include,
but are not limited to, radiation and temperature changes.
[0015] The invention also provides methods for determining the
presence or absence of compounds, or compound concentrations in
biological, industrial, and environmental samples, and physical
changes in such samples using bioreactive allosteric
polynucleotides of the invention and biosensors incorporating
them.
DESCRIPTION OF THE FIGURES
[0016] FIG. 1 is a schematic diagram of an example of a biosensor
of the invention. In this embodiment, a self-cleaving DNA is
immobilized on a solid matrix that is mounted in a plastic
`spin-column`. The self-cleaving DNA remains inactive, unless it
encounters a specific effector molecule that causes allosteric
induction. Test sample is added to the porous matrix, allowed to
incubate, then the solution is collected at the bottom of the tube
via centrifugation. Since catalytic activity is a function of the
presence (in concentration) of the effector, the concentration of
released DNA fragments will report the presence and quantity of
effector.
[0017] FIG. 2 illustrates a sequence and secondary-structure model
for a self-cleaving DNA of the invention (SEQ ID NO: 1). The
bracket indicates the main region of DNA cleavage.
[0018] FIG. 3 sketches an example of (A) an immobilized DNA
biocatalyst of the invention and (B) a simple reactor assembly.
[0019] FIG. 4 shows a demonstration of catalytic function by
immobilized DNA enzymes. 5' .sup.32P-labeled RNA substrate was
applied to a streptavidin column (AffiniTip Strep 20, Genosys
Biotechnologies) that was derivatized with 5'-biotinyl DNA enzyme.
The DNA enzyme was immobilized to give an effective concentration
of .about.1 .mu.M. Substrate (0.5 .mu.M was applied to the column
in repetitive 20 .mu.L aliquots, allowed to react for 10 min., then
recovered for analysis by polyacrylamide gel electrophoresis.
Fraction of substrate cleaved was plotted as a function of volume
eluted.
[0020] FIG. 5 illustrates hammerhead ribozyme constructs described
in Example 1 below. H1 (SEQ ID NO: 2) is identical to the ribozyme
`HH15` that was originally characterized by Fedor and Uhlenbeck
(12). H2 (SEQ ID NO: 3) carries an additional G-C base pair in stem
I and is flanked on each end by accessory sequences that are
designed as short hairpins to reduce the occurance of inactive
structures. H3 (SEQ ID NO: 4) is an integrated hammerhead ribozyme
that includes an RNA domain corresponding to a truncated version of
an ATP- and adenosine-specific aptamer (35). H4 and H5 are modified
versions of H3 that include an aptamer-domain mutation and a 3
base-pair extension of stem II, respectively. Arrowheads indicate
the site of ribozyme-mediated cleavage.
[0021] FIG. 6 shows evidence of ATP- and adenosine-mediated
inhibition of a hammerhead ribozyme described in Example 1. (A)
Hammerhead constructs H1, H2 and H3 (400 nM) were incubated with
trace amounts of (5'-.sup.32P)-labeled substrate (S) in the absence
(-) or presence (+) of 1 mM ATP for 30 min. (B) The specificity of
the effector molecule was examined by incubating H3 and S for 45
min as described in Example 1 without (-) or with 1 mM of various
nucleotides as indicated. Similarly, constructs H4 and H5 were
examined for activity in the presence of 1 mM ATP. Reaction
products were separated by a denaturing (8 M urea) 20%
polyacrylamide gel and visualized by autoradiography. E, S and P
identify enzyme, substrate and product bands, respectively.
[0022] FIG. 7 plots kinetic analysis results of the catalytic
inhibition of H3 by ATP described in Example 1. (A) Plot of H3
ribozyme activity (400 mM) in the presence of 10 .mu.M (open
circles) and 1 mM (filled circles) ATP. Dashed line represents the
average initial slope obtained in the absence of ATP or in the
presence of as much as 1 mM dATP. (B) Plot of H3 ribozyme activity
(k.sub.obs) in the presence of various concentrations of dATP (open
circles) and ATP (filled circles). Also plotted on the y axis are
k.sub.obs values for H1, H2 and H3 (open squares, filled squares
and open circles, respectively) with no added effector
molecules.
[0023] FIG. 8 (A) depicts integrated constructs for allosteric
induction by ATP (H6, SEQ ID NO: 5 and H7, SEQ ID NO: 6) and
allosteric inhibition by theophilline (H8) described in Example 1.
H7 replaces the central U-A pair with a G.U mismatch and is
designed to further reduce hammerhead catalysis. H8 is analogous to
H3 except that the ATP-aptamer domain is replaced by the
theophylline aptamer corresponding to `mTCT8-4' that was described
by Jenison, et al. (21). Arrowhead indicates the site of
ribozyme-mediated cleavage. (B) Induction of ribozyme catalysis
during the course of a ribozyme reaction was examined by incubating
H6 in the absence (open circles) and presence (open squares) of 1
mM ATP, and when ATP is added (filled circles), to a final
concentration of 1 mM during an ongoing ribozyme reaction. Arrow
indicates the time of ATP addition.
[0024] FIG. 9 shows in vitro selection of self-cleaving DNAs
described in Example 2. In a a, (I) a pool of 5'-biotinylated DNAs
is immobilized on a streptavidin matrix, washed to remove unbound
DNAs, then (II) eluted under the desired reaction conditions to
separate self-cleaving DNAs from those that are inactive. (III)
Selected DNAs are amplified by the polymerase chain reaction (PCR)
and (IV) the selection round is completed by immobilizing the
resulting double-stranded DNAs on new matrix followed by removal of
the nonbiotinylated strand by chemical denaturation. (V) The pool
is prepared for further analysis by PCR amplification with
non-biotinylated primers. Encircled B indicates 5' biotin. In b,
the construct used for the initial round of selection contains a
domain of 50 random-sequence nucleotides (N.sub.50) flanked by 38
and 14 nucleotides of defined sequence. DNAs used in subsequent
rounds carry an additional 26 nucleotides, as defined by primer 1
(SEQ ID NO: 7; primer 2 is SEQ ID NO: 8). Precursors that cleave
within the overlined region retain sufficient 5' primer binding
site for amplification and are expected to be favored during
selection. In c, self-cleavage activity of the initial DNA pool
(G0) and the pool isolated after seven rounds (G7) of selection. 5'
.sup.32P-labeled precursor DNA (Pre) was incubated in the presence
(+) or absence (-) of 10 .mu.M each of Cu.sup.2+ and ascorbate, or
in the absence of Cu.sup.2+ or ascorbate (--Cu.sup.2+ and -asc,
respectively) for various times as indicated. M is 5'
.sup.32P-labeled primer 3 and Clv identifies cleavage products.
[0025] FIG. 10 shows sequence analysis and catalytic activity of
individual G8 DNAs described in Example 2 (SEQ ID NOs: 9-31). In a,
alignment of 34 sequences reveal the presence of two major classes
of molecules that are characterized by sets of common sequences
(boxed nucleotides). DNAs that were encountered more than once are
identified by noting the number of occurrences in parentheses. In
b, self-cleavage activity of 5 nM 5' .sup.32P-labeled precursor DNA
from G8 DNA and from individuals CA1, CA2 and CA3 in the absence
(-) or presence (+) of Cu.sup.2+ and ascorbate (10 .mu.M each) are
shown.
[0026] FIG. 11 depicts cleavage site analysis of CA3 (lane 2), an
optimized variant (variant 1, FIG. 13b) of CA3 (lane 3) and CA1
(lane 4) described in Example 2. DNA size markers (lane 1) are 5'
.sup.32P-labeled DNAs of 10-13 nucleotides as indicated. The
nucleotide sequence of these markers correspond to the 5' terminal
constant region of the precursor.
[0027] FIG. 12 (a) shows an artificial phylogeny of CA1 (SEQ ID NO:
30) variants described in Example 2. The numbered sequence is
wild-type CA1, and nucleotides of variants that differ from this
sequence are aligned below. A dash indicates a deleted nucleotide.
(b) Partial secondary-structure model for a variant of CA1
(arrowhead, SEQ ID NO: 32). Numbered nucleotides are derived from
the region that was randomized in the starting pool. Asterisk
indicates the primary cleavage site and the bar defines the region
that undergoes detectable cleavage. Not detailed are nucleotides
within the 3' primer binding site that are also required for
catalytic activity.
[0028] FIG. 13 shows a Cu.sup.2+-dependent self-cleaving DNA
described in Example 2. (a) Cleavage assay of G8 DNA, CA1 (SEQ ID
NO: 30), CA3 (SEQ ID NO: 31) and the optimized population of CA3
variants was isolated after mutagenesis followed by five additional
rounds of selection. (b) Sequence alignment of individual CA3
variants that have been optimized for catalytic function with
Cu.sup.2+. The numbered sequence is wild-type CA3, and nucleotides
of variants that differ from this sequence are aligned below. A
dash indicates a deleted nucleotide. Arrowheads identify CA3
variants 1-3 as denoted. Asterisk and bar indicate the major and
minor Clv 2 cleavage sites, respectively.
[0029] FIG. 14 shows the sequence and predicted secondary
structures of minimized self-cleaving DNAs described in Example 3.
(A) Sequence and secondary structure of a synthetic 69-nucleotide
self-cleaving DNA that was isolated by in vitro selection (SEQ ID
NO: 33). Numbers identify nucleotides that correspond to the
50-nucleotide random-sequence domain that was included in the
original DNA pool (note that 19 bases of this domain have been
deleted). The conserved nucleotides (11-31, boxed) are similar to
those previously used to define this class of deoxyribozymes
(Example 2). (B) A 46-nucleotide truncated version of class II DNAs
that retains full activity (SEQ ID NO: 34). I and II designate
stem-loop structures of the 46 mer that are predicted by the
structural folding program `DNA mfold` (18, 19), and that were
confirmed by subsequent mutational analysis (FIG. 15). The
conserved core of the deoxyribozyme spans nucleotides 27-46 and the
major site of DNA cleavage is designated by the arrowhead.
Encircled nucleotides can be removed to create a bimolecular
complex where nucleotides 1-18 constitute the `substrate`
subdomain, and nucleotides 22-46 constitute the `catalyst`
subdomain.
[0030] FIG. 15 shows a confirmation of stems I and II by mutational
analysis described in Example 3. (A) Trace amounts of 5'
.sup.32P-labeled substrate DNAs (s1-s3) were incubated with 5 .mu.M
complementary or non-complementary catalyst DNAs (c1-c3) in
reaction buffer A containing 10 .mu.M CuCl.sub.2 at 23.degree. C.
for 15 min. Reaction products were separated by denaturing 20%
polyacrylamide gel electrophoresis (PAGE) and imaged by
autoradiography. Bracket identifies the position of the substrate
cleavage products. (B) Self-cleavage activity of the original 46
mer sequence compared to the activity of variant DNAs with base
substitutions in stem II. Individual 46 mer variants (100 .mu.M 5'
.sup.32P-labeled precursor DNA) were incubated for the times
indicated under reaction conditions as described above. Clv1 and
Clv2 identify 5'-cleavage fragments produced upon precursor DNA
(Pre) scission at the primary and secondary sites, respectively.
Mutated positions are defined using the numbering system given in
FIG. 14.
[0031] FIG. 16 identifies a triplex interaction between substrate
and catalyst DNAs described in Example 3. A revised structural
representation portrays a triple-helix interaction (dots) between
the four base pairs of stem II and four consecutive pyrimidine
residues near the 5' end of the substrate DNA. c4 and s4 represent
sequence variants of c3 (SEQ ID NO: 36) and s3 (SEQ ID NO: 35) that
retain base pairing within stem II, and that use an alternate
sequence of base triples. DNA cleavage assays were conducted as
described in FIG. 15A. Bracket identifies the position of the
substrate cleavage products.
[0032] FIG. 17 shows targeted cleavage of DNA substrates using
deoxyribozymes with engineered duplex and triplex recognition
elements. (A) A 101-nucleotide DNA incorporating three different
deoxyribozyme cleavage sites was prepared by automated chemical
synthesis (SEQ ID NO: 37). Each cleavage site consists of an
identical leader sequence (shaded boxes) followed by a stem I
recognition element of unique sequence. The specific base
complementation between the synthetic catalyst DNAs c1, c3 and c7
are also depicted. The catalytic core sequences and the leader
sequence/stem II interactions for each site are identical (inset).
Asterisks indicate G-T wobble pairs that allow cross reaction
between c1 and the target for c3. Dots indicate base triple
interactions. (B) Cleavage of the 101 mer DNA by c1, c3, and c7 was
examined by incubating trace amounts of 5' .sup.32P-labeled
substrate in reaction buffer containing 30 .mu.M CuCl.sub.2 at
23.degree. C. for 20 min., either in the absence (-) or presence of
5 .mu.M catalyst DNA as indicated. Reaction products were separated
by denaturing 10% PAGE and visualized by autoradiography. (C)
Similarly, a 100-nucleotide DNA was prepared that contained three
identical stem I pairing regions (shaded boxes) preceded by eight
successive pyrimidine nucleotides of unique sequence (SEQ ID NO:
38). Three synthetic deoxyribozymes (c9, c10, c11) that carry
identical stem I paring elements (inset) and extended stem II
subdomains of unique sequence, were designed to target the three
cleavage sites exclusively through DNA triplex interactions. (D)
Cleavage of 100 mer DNA by c9, c10, and c11 was established as
described in (B) above. Miscleavage is detected for each
triplex-guided deoxyribozyme upon extended exposure during
autoradiography (e.g., c11), indicating that weak-forming triplex
interactions allow some DNA-cleavage activity to occur.
[0033] FIG. 18 illustrates the in vitro selection of
histidine-dependent deoxyribozymes described in Example 4. (a) A
pool of 4.times.10.sup.13 biotin-modified DNAs was immobilized on a
streptavidin-derivatized column matrix. Each DNA carries a single
embedded RNA linkage (rA) and a 40-nucleotide random-sequence
domain that is flanked by regions that are complementary to
nucleotides that reside both 5' and 3' of the target phosphodiester
(pairing elements i and ii; SEQ ID NOs: 39 and 40). These
pre-engineered substrate-binding interactions are expected to
increase the probability of isolating active catalysts (7). DNAs
that catalyze the cleavage of the RNA linkage upon incubation with
a solution buffered with histidine were released from the matrix,
were amplified by the polymerase chain reaction (PCR), and the
amplification products again were immobilized to complete the
selection cycle (14-16). (b) Four classes of deoxyribozymes were
determined by sequence comparison (SEQ ID NOs 41 to 44). Variants
within each group differed by no more that two mutations from the
sequences shown. Catalytic assays active (+) when either HEPES or
histidine buffers are used, while class II DNAs not active (-) when
histidine is absent. Arrowhead identifies the site of cleavage and
numbers correspond to the original 40-nucleotide random-sequence
domain.
[0034] FIG. 19 shows sequences and secondary structures of variant
deoxyribozymes discussed in Example 4. (a) Individual DNAs isolated
after reselection of mutagenized pools based on the class II
deoxyribozyme (II) (SEQ ID NO: 45) or the HD2 deoxyribozyme (HD2
pool, SEQ ID NO: 46). Depicted are the nucleotide sequences for the
mutagenized core of the parent DNAs and the nucleotide changes for
each variant deoxyribozyme examined after reselection.
Deoxyribozymes HD1 (SEQ ID NO: 47) and HD2 (SEQ ID NO: 48) were
recovered from DNA pools generated after five rounds of reselection
with 50 or 5 mM histidine, respectively. (b) Each deoxyribozyme was
reorganized to create a bimolecular complex, whereby separate
substrate molecules are recognized by two regions of base
complementation (stems I and II) with the enzyme domain.
Deoxyribozyme nucleotides are numbered consecutively from the 5'
terminus.
[0035] FIG. 20 shows cofactor recognition by a deoxyribozyme
described in Example 4. (a) Catalytic activity of HD1 with
L-histidine, D-histidine, and various dipeptides that received (+)
or did not receive (-) pretreatment with hydrochloric acid. HD1 (10
.mu.M) was incubated in the presence of trace amounts of 5'
.sup.32P-labeled substrate oligonucleotide (FIG. 19b) and were
incubated at 23.degree. C. for 2.5 hr with 50 mM L-histidine,
D-histidine, or various dipeptides as indicated. Reaction products
were analyzed by denaturing (8 M urea) polyacrylamide gel
electrophoresis (PAGE) and imaged by autoradiography. S and P
identify substrate and product (5'-cleavage fragment) bands,
respectively. (b) Chemical structures of L-histidine and the
analogues used to probe deoxyribozyme cofactor specificity. (c)
Representative deoxyribozyme assays for HD1 (E1) catalytic activity
with selected amino acids and histidine analogues. Reactions and
analyses were conducted as described in a.
[0036] FIG. 21 are graphs showing the involvement of histidine in
deoxyribozyme function described in Example 4. (a)
Concentration-dependent induction of deoxyribozyme function by
histidine. Open and shaded arrowheads indicate the concentration of
histidine that was maintained during the selection of HD1 and HD2,
respectively. (b) Dependence of deoxyribozyme function on pH. Data
represented in the main plot was produced using 1 mM histidine
while data given in the inset was obtained using 5 mM histidine.
Data depicted with filled, open, and shaded circles was collected
using MES-, Tris-, and CAPS-buffered solutions, respectively.
DETAILED DESCRIPTION OF THE INVENTION
[0037] Natural ribozymes and artificial ribozymes and
deoxyribozymes that have been isolated by in vitro selection are
not known to operate as allosteric ribozymes. This invention is
based upon the finding that small-molecule effectors can bind to
ribozyme and deoxyribozyme domains and modulate catalytic rate. As
will be discussed more fully below, in the practice of the
invention, an effector molecule or effect binds or affects an
allosteric site that is spatially distinct from that of the enzyme
or reporter domain. Allosteric polynucleotides of the invention can
thus rapidly interconvert from an "off" state to an "on" state, or
vice versa, reversibly, on a time scale that is relevant for their
use as biosensors and bioswitches. For example, using rational
design strategies, a `hammerhead` self-cleaving ribozyme described
herein was coupled to different aptamer domains to produce
ribozymes whose rates can be specifically controlled by adenosine
and it's 5'-phosphorylated derivatives. A number of other
allosteric ribozymes have been created that are sensitive to a
variety of other effectors, including drug compounds, biological
metabolites, and toxic metals. It is possible to construct, using a
mix of in vitro selection and rational design strategies, novel
biosensors that rely on nucleic acid sensor elements. To achieve
this, unique RNA or DNA sequences can be appended to ribozymes or
deoxyribozymes, thereby creating new enzymes having catalytic rates
that can be influenced by specific chemical effectors (e.g.,
molecules of diagnostic interest), physical signals, and
combinations thereof.
[0038] About 50 years ago, it was observed with some polypeptide
enzymes that catalytic plots of reaction velocity, V, versus
substrate concentration [S], displayed sigmoidal plots, rather than
hyperbolic plots predicted by the simple enzyme+substrate model of
enzymatic action described by Michaelis-Menten in 1913. In 1965,
Monod, et al., explained these findings by suggesting that
enzymatic reaction rates were altered by regulatory domains (3a).
In this classical model of "allostery", enzymatic activity by
"allosteric enzymes" is modulated by reversible binding to
compounds, termed "effectors", at specific sites other than the
enzyme's substrate binding sites, which, accordingly, are called
"allosteric" sites. At constant enzyme and substrate
concentrations, binding of a negative "effector" reduces the
reaction rate ("allosteric inhibition"), and binding of a positive
"effector" increases the rate ("allosteric activation"). Allosteric
inhibition may be achieved a number of ways, including reducing the
binding affinity of the enzyme for its substrate (often reported as
increases in Michaelis-Menton parameter K.sub.m) and/or by
increasing the time required for each catalytic turnover (often
reported as a decrease in V.sub.max). Conversely, allosteric
activation may occur either by reduction in K.sub.m or by an
increase in V.sub.max, or both.
[0039] Decades later it was found that polynucleotides could also
catalyze chemical reactions, and in 1995, Porta and Lizardi
described what they called the first "allosteric" ribozyme (32a).
This was a hammerhead, self-cleaving ribozyme that could be
rendered active by incubating it with a 35-nucleotide antisense DNA
oligomer for several hours. Notwithstanding the terminology used in
the paper, this was not a true allosteric effect. Antisense
interactions such as that described between the oligonucleotide and
the ribozyme are typically comprised of strong base pairing
contacts that have slow kinetic interchange between bound and
unbound states. There was no allosteric interconversion (from an
"off" state to an "on" state, or vice versa) disclosed upon
addition of the 35-mer to an ongoing reaction mixture. Instead,
Porta and Lizardi described a ribozyme construct which had a
folding pathway that could be dictated by the 35-mer, but not
allosterically switched from active to inactive forms immediately
upon addition or depletion of a small effector molecule to or from
the reaction mixture. Hence, their need for long preincubation and
incubation times, and a large oligonucleotide that could
kinetically and thermodynamically lock the ribozyme into an active
configuration.
[0040] In contrast, in the practice of the invention, purified
functional DNA and/or polynucleotides that exhibit true allosteric
properties that modify a function or configuration of the
polynucleotide with a chemical effector, a physical signal, or
combinations thereof, are constructed. The function of
polynucleotides of the invention is not necessarily controlled by
base pairing to an oligonucleotide, but, instead, by binding of a
small molecule effector to an allosteric binding site, or
interaction of a physical signal with an allosteric site, spatially
distinct from the enzyme domain, such that the function of the
polynucleotide is allosterically modulated. In some embodiments,
the polynucleotide is an enzyme exhibiting allosteric properties
that modify the rate of catalysis of the enzyme. The invention
further provides functional RNA or DNA polynucleotides having
catalytic properties with rates that can be positively and/or
negatively controlled by a chemical effector, a physical signal, or
combinations thereof. For example, where enzyme polynucleotides of
the invention exhibit a reaction rate that is enhanced or inhibited
by reversible binding to a chemical effector at an allosteric
binding site spatially distinct from the substrate binding or
self-cleaving site. In some embodiments, the polynucleotides
contain from about 100 or fewer bases; others are much larger.
[0041] Allosteric polynucleotides of the invention are comprised of
any natural, recombinant, or synthetic RNA, DNA and mixtures of RNA
and DNA. As used herein, the terms "DNA" and "RNA" specifically
include sequences that have RNA and/or DNA analogues. Analogues
include chemically modified bases and unusual natural bases.
Further encompassed by the invention are polynucleotides modified
during or after preparation of the domains and constructs using
standard means. DNA and/or RNA starting materials for the domains,
and constructs and complexes containing them, may be isolated from
whole organisms, tissues or tissue cultures; constructed from
nucleotides and oligonucleotides using standard means; obtained
commercially; selected from random and enriched in vitro or in vivo
sequence pools; and combinations thereof.
[0042] Any element, ion, and/or molecule can be used as chemical
effectors for interaction with the bioreactive allosteric
polynucleotides of the invention. It is an advantage of the
invention that the rational design strategies used to construct the
polynucleotides (discussed more fully below) can be adapted to a
great variety of effectors. A vast number of ligand-responsive
ribozymes with dynamic structural characteristics can be generated
in a massively parallel fashion (23b). Examples include, but are
not limited to, organic compounds and mixtures of organic compounds
and metal ions. Chemical effectors may be amino acids, amino acid
derivatives, peptides (including peptide hormones), polypeptides,
nucleosides, nucleotides, steroids, sugars or other carbohydrates,
pharmaceuticals, and mixtures of any of these. Many are small;
hence, peptides having 9 or fewer amino acid substitutents and
disaccharides and trisaccharides are typical polypeptide and
carbohydrate effectors. Illustrated hereafter are theophylline, ATP
and modified ATP; 3-methylxanthine, cGMP, cCMP, cAMP, FMN, cobalt,
cadmium, nickel, zinc, and manganese have also been shown to be
effectors that modulate the reaction rates of polynucleotides of
the invention (see, for example, various effectors described in
21a, 23a, 23b, 36a, 39a, 39b, 39c, and 39e). In many preferred
embodiments, small molecule effectors, typically having a molecular
weight of about 300 or less, are employed, including metal ions,
amino acids, amino acid derivatives, nucleosides, nucleotides,
simple sugars, and steroids. Effectors can be much larger in other
embodiments; larger molecule effectors can have molecular weights
ranging in the tens or thousands Da, and sometimes even larger;
protein effectors, for example, can range up to 500,000, and
sometimes several million, Da. In some embodiments, the chemical
effectors are microbial or cellular metabolites or other biological
samples. Components found in liquid biological samples such blood,
serum, urine, semen, tears, and biopsy homogenates taken from
patients for medical or veterinary diagnostic or therapeutic
purposes are particularly preferred chemical effectors in some
embodiments (36a). In industrial and environmental applications,
the effectors are pesticides, herbicides, food toxins, product
ingredients, reactants, and contaminants, drugs, and the like.
Allosteric polynucleotides of the invention can be used to detect
the presence or absence of compounds, as well as their
concentration (36a).
[0043] Bioreactive polynucleotides of the invention exhibit
allosteric properties that modify polymer function or configuration
with a physical signal or a combination of a physical signal and a
chemical effector in alternate embodiments. Physical signals
include, but are not limited to, radiation (23a), temperature
changes, movement, physical conformational changes in samples, and
combinations thereof. Physical signals include, but are not limited
to, tags, beacons, and the like allosteric reporters that respond
to UV, IR, and/or visible light (23b, 44b). The effects are
reversible. Chemical effectors binding to allosteric ribozymes
and/or deoxyribozymes of the invention, for example, can enhance or
inhibit the catalytic rate, or do both. It is an advantage of the
invention that, because the molecules are truely allosteric, any
type of allosteric interconversion is possible. Hence, a sample of
allosteric polynucleotide enzymes can be fully active, partially
active, or fully inactive. In other words, acting as a switch, they
can be all "on" or all "off", or exhibit any level of activity
between "on" or "off". (For a further discussion of switches, see
Soukup and Breaker, 39c). Morever, because they are truly
allosteric, the observable response time to an effector molecule or
effect is immediate. The kinetics of allosteric polynucleotides are
similar to what is observed with allosteric polypeptides.
Illustrated hereafter are polynucleotides that react in less than
60 minutes, preferably inless than 6 minutes, and most preferably,
in less than about a minute. (See, for example, FIGS. 7 and 8.)
Most preferred allosteric polynucleotides respond to effectors
within seconds.
[0044] Many embodiments employ bioreactive allosteric
polynucleotides of the invention as biosensors in solution or
suspension or attached to a solid support such as that illustrated
in FIG. 1. Alone or as a component of a biosensor, the
polynucleotides are used to detect the presence or absence of a
compound or its concentration and/or a physical signal by contact
with the polynucleotide. In a typical practice of these methods, a
sample is incubated with the polynucleotide or biosensor comprising
the polynucleotide as a sensing element for a time under conditions
sufficient to observe a modification or configuration of the
polynucleotide caused by the allosteric interaction. These are
monitored using any method known to those skilled in the art, such
as measurement and/or observation of polynucleotide self-cleavage;
binding of a radioactive, fluorescent, or chromophoric tag; binding
of a monoclonal or fusion phage antibody; or change in component
concentration, spectrophotometric, or electrical properties. It is
an advantage of the invention that current biosensor technology
employing potentiometric electrodes, FETs, various probes, redox
mediators, and the like can be adapted for use in conjunction with
the new polynucleotide biosensors of the invention for measurement
of changes in polynucleotide function or configuration.
[0045] The initial studies described in the Examples that follow
have involved the creation and characterization of novel RNA- and
DNA-cleaving enzymes that function with specific cofactors, or that
can be regulated by specific small-molecule chemical effectors,
physical signals, or combinations thereof. It is clear that
additional molecules with similar sensor and biocatalytic
properties can be created by similar means, thereby expanding the
applications of such molecules. The creation and characterization
of a prototype biosensor for ATP is given herein. One construct
(H3) in particular shows ATP concentration-dependent catalytic
activity, indicating that this ribozyme could be adapted for use in
reporting the concentration of this ligand in test solutions.
Specifically, H3 RNA actively self-cleaves in concentrations of ATP
that are below 1 micromolar, but is maximally inhibited (170-fold
rate reduction) in the presence of 1 millimolar ATP (FIG. 3b). The
catalytic rate of the ribozyme in concentrations of ATP that range
between these two extremes is reflective of the ATP concentration,
and can be used to determine unknown concentration values. It is
important to note that the receptor portion of this allosteric
ribozyme is completely artificial (created via in vitro selection)
(35), and could be exchanged for other artificial or natural
receptor domains that are specific for other ligands.
[0046] New and highly-specific receptors can be made via in vitro
selection or `SELEX` (4,5) using simple chromatographic and nucleic
acid amplification techniques (4, and illustrated in the Examples).
RNA and DNA `aptamers` produced in this way can act as efficient
and selective receptors for small organic compounds, metal ions,
and even large proteins. In a dramatic display of RNA receptor
function, a series of RNA aptamers for theophilline have been
isolated (35) that show .about.10,000-fold discrimination against
caffeine, which differs from theophilline by a single methyl
group.
[0047] One can isolate new classes of aptamers that are specific
for innumerable compounds to create novel biosensors or even
controllable therapeutic ribozymes for use in medical diagnostics,
environmental analysis, etc. In the examples that follow, simple
design strategies have been used to create conjoined
aptamer-ribozyme complexes who's rates can be controlled by small
effector molecules. Preliminary studies have already shown that
theophilline-dependent ribozymes can be created through rational
design. Theophilline, for example, is an important drug for the
treatment of asthma and it's therapeutic effect is highly dependent
on concentration. A biosensor for theophilline concentration would
be of significant value. Further examination of this allosteric
ribozyme and of other model ribozymes will help to lay the
biochemical and structural foundations for the design of additional
sensor molecules based on RNA and DNA.
[0048] It is an advantage of the invention that the discovery that
DNA can function as an enzyme (5) has made practical the
engineering of enzymes that are chemically more stable than either
RNA or proteins. The half-life for the hydrolytic breakdown of a
DNA phosphoester is 200 million years, making DNA the most stable
of the three major biopolymers. These features of DNA, coupled with
the fact that DNA also can be made to bind various ligand with
great specificity and affinity, make this polymer an attractive
medium for the creation of new industrial enzymes and as sensor
elements for diagnostics. Also, modified DNAs can be made that are
resistant to degradation by natural nucleases, making DNA analogues
an attractive format for use in biological solutions. As
illustrated hereafter, it has been found that DNA can be made to
self-cleave in a metal ion-dependent fashion. The creation of these
DNAs that catalyze their own cleavage in the presence of copper can
now be used as a sensitive reporter of free copper concentration in
solution. Another example given below is a polynucleotide reactive
to histidine. Further engineering of such catalysts will yield
allosteric DNA enzymes that can be used to detect a wide variety of
ligands, or that report other reaction conditions such as the
concentration of salts, pH, temperature, etc. In addition, these
DNAs may be conducive to monitoring via amperometric H.sub.2O.sub.2
probes or by spectrophotometric analysis of the redox state of
copper. Clearly, the diversity of signal read-out for both RNA and
DNA sensors can be expanded.
[0049] Another feature of the invention is that use of
polynucleotides as biosensors offer advantages over protein-based
enzymes in a number of commercial and industrial processes.
Problems such as protein stability, supply, substrate specificity
and inflexible reaction conditions all limit the practical
implementation of natural biocatalysts. As outlined above, however,
DNA can be engineered to operate as a catalyst under defined
reactions conditions. Moreover, catalysts made from DNA are
expected to be much more stable and can be easily made by automated
oligonucleotide synthesis. In addition, DNA catalysts are already
selected for their ability to function on a solid support and are
expected to retain their activity when immobilized.
[0050] The invention further encompasses the use of bioreactive
allosteric polynucleotides attached to a solid support for use in
catalytic processes. Immobilizing novel DNA enzymes will provide a
new form of enzyme-coated surfaces for the efficient catalysis of
chemical transformations in a continuous-flow reactor under both
physiological and non-physiological conditions. The isolation of
new DNA enzymes can be each tailor-made to efficiently catalyze
specific chemical transformations under user-defined reaction
conditions. The function of catalytic DNAs to create enzyme-coated
surfaces that can be used in various catalytic processes is
described herein and illustrated in FIG. 4. Due to the high
stability of the DNA phosphodiester bond, such surfaces are
expected to remain active for much longer than similar surfaces
that are be coated with protein- or RNA-based enzymes.
[0051] A variety of different chromatographic resins and coupling
methods can be employed to immobilize DNA enzymes. For example, a
simple non-covalent method that takes advantage of the strong
binding affinity of streptavidin for biotin to carry out a model
experiment is illustrated in FIG. 3. In other embodiments, DNA
enzymes can be coupled to the column supports via covalent links to
the matrix, thereby creating a longer-lived catalytic support.
Various parameters of the system including temperature, reaction
conditions, substrate and cofactor concentration, and flow rate can
be adjusted to give optimal product yields. In fact, these
parameters can be preset based on the kinetic characteristic that
are displayed by the immobilized DNA enzyme. However, in practice,
product formation will be monitored and the chromatographic
parameters will be adjusted accordingly to optimize the system.
[0052] A prototype system for the large-scale processing of RNA
substrates using an immobilized DNA enzyme is described herein.
Product yields have been determined by analysis of .sup.32P-labeled
substrate and product molecules by polyacrylamide gel
electrophoresis of eluant samples. Multiple turn-over of
immobilized enzyme during tests of the reactive chromatographic
surface has been observed (FIG. 4). The in vitro selection and
engineering of new tailor-made DNA biocatalysts will produce
catalytic surfaces for practical use and of unprecedented stability
and catalytic versatility.
EXAMPLES
[0053] The following examples are presented to further illustrate
and explain the present invention and should not be taken as
limiting in any regard.
Example 1
[0054] As mentioned above, natural ribozymes (8) and ribozymes that
have been isolated by in vitro selection are not known to operate
as allosteric enzymes (6). This example illustrates allosteric
ribozymes.
[0055] Using simple rational design concepts, aptamer domains with
hammerhead self-cleaving ribozymes (13) were joined in a modular
fashion, to create a series of catalytic RNAs that are amenable to
both positive and negative allosteric control by small-molecule
effectors. Initial efforts were focused on the 40-nucleotide
ATP-binding aptamer, termed `ATP-40-1', that was described by
Sassanfar and Szostak (35). This motif shows a specific affinity
for adenosine 5' triphosphate (ATP; K.sub.D .about.10 .mu.M) and
adenosine, but has no detected affinity for a variety of ATP
analogues including 2'-deoxyadenosine 5' triphosphate (dATP) or the
remaining three natural ribonucleoside triphosphates. The aptamer
also undergoes a significant conformational change upon ligand
binding, as determined by chemical probing studies. These
characteristics were exploited to create a conjoined
aptamer-ribozyme molecule that could be subject to ATP-dependent
allosteric control.
[0056] The initial integrated design, H3, incorporates several key
features into an otherwise unaltered bimolecular hammerhead
ribozyme that is embodied by H1 (FIG. 5). Each ribozyme and
conjoined aptamer-ribozyme was prepared by in vitro transcription
from a double-stranded DNA template that was produced by the
polymerase chain reaction using the corresponding antisense DNA
template and the primers 5'GAATTCTAATACGACTCACTATAGGCGAAAGCCGGGCGA
(SEQ ID NO: 49) and 5'GAGCTCTCGCTACCGT (SEQ ID NO: 50). The former
primer encodes the promoter for T7 RNA polymerase. 50-.mu.l
transcription reactions were performed by incubating of 30 pmoles
template DNA in the presence of 50 mM Tris-HCl (pH 7.5 at
23.degree. C.), 15 mM MgCl.sub.2, 5 mM dithiothreitol, 2 mM
spermidine, 2 mM of each NTP, 20 .mu.Ci (.alpha.-.sup.32P)-UTP and
600 units T7 RNA polymerase for 2 hr at 37.degree. C. RNA products
were separated by polyacrylamide gel electrophoresis (PAGE),
visualized by autoradiography and the ribozymes were recovered from
excised gel slices by crush-soaking in 10 mM Tris-HCl (pH 7.5 at
23.degree. C.), 200 mM NaCl and 1 mM EDTA and quantified by liquid
scintillation counting. The RNA substrate was prepared (Keck
Biotechnology Resource Laboratory, Yale University) by standard
solid-phase methods and the 2'-TBDMS group was removed by 24-hr
treatment with triethylamine trihydrofluoride (15 .mu.l per
AU.sub.260 crude RNA). Substrate RNA was purified by PAGE, isolated
by crush-soaking, (5'-.sup.32P)-labeled with T4 polynucleotide
kinase and (.gamma.-.sup.32P)-ATP, and repurified by PAGE. Even
after exhaustive incubation with H1, approximately 45% of the RNA
remains uncleaved. The kinetic calculations have been adjusted
accordingly.
[0057] Superficially, sequences at the 5' and 3' termini were
appended to make the constructs amenable to amplification by
reverse transcription-polymerase chain reaction methods for future
studies. Surveyed independently as H2 (FIG. 5), these changes
causes a 6-fold reduction in k.sub.obs compared to H1 (rates are
summarized in Table 1). In addition to the 5'-and 3'-terinal
flanking sequences, H3 includes a modified hammerhead stem II that
carries the ATP aptamer. The decision to locate the aptamer here
was made primarily because changes in stem II can have large
effects on the catalytic rates of hammerhead ribozymes (28). In the
absence of ATP, this alteration causes an additional two-fold
reduction in rate compared to H1.
[0058] The RNA-cleavage activity of H3 is significantly reduced
when incubated with 1 mM ATP (FIG. 6A). In contrast, ATP has no
effect on the cleavage activity of H1 or H2. Moreover, inhibition
is observed in the presence of adenosine, but not with dATP or the
other ribonucleoside triphosphates (FIG. 2B). This inhibition is
highly specific and is consistent with the observed binding
specificity of the aptamer (35).
1TABLE 1 Catalytic rates of various ribozyme constructs. Constructs
denoted with * and .dagger., contain either a functional ATP
aptamer or a defective ATP aptamer, respectively. k.sub.obs
(min.sup.-1) construct stem II none ATP dATP H1 1 0.58 -- -- H2 2
0.10 -- -- H3* 3 0.054 0.00031 0.053 H4.dagger. 4 0.042 0.061 --
H5* 5 0.075 0.13 -- H6* 6 0.022 0.12 0.027 H7* 7 0.0012 0.0098
0.0009
[0059] To investigate the mechanism of inhibition of H3 by ATP, two
additional integrated constructs (FIG. 5) were designed. H4 is
identical to H3, but carries a G to C point mutation that is
expected to eliminate ATP binding by the aptamer domain (35). As
expected, this mutation eliminates the inhibitory effect of ATP.
The allosteric effect may be due to the proximity of the aptamer
and hammerhead domains. Specifically, structural models of the
hammerhead indicate a parallel orientation for stems I and II (32).
In the uncomplexed state, the aptamer domain is likely to exist in
a single or a set of conformational state(s) that allow catalysis
to proceed unhindered. However, when complexed with ATP, this
domain undergoes a conformational change that presumably causes
steric interference between structures that are appended to stems I
and II. H5 carries an additional three base pairs in helix II, to
further separate the domains, and is not inhibited by ATP. This is
consistent with an allosteric inhibition mechanism that involves
conformational change and the mutually-exclusive formation of
aptamer and ribozyme domains.
[0060] The inhibitory effect of ATP with H3 has been confirmed and
quantitated by kinetic analysis. Ribozyme activity assays were
conducted with trace amounts of substrate and excess ribozyme
concentrations that significantly exceed K.sub.m. Replicate
k.sub.obs values obtained for H1 and H2 at 200, 400 and 800 nM
ribozyme concentration under identical assay conditions differed by
less that two fold, suggesting that for each construct, k.sub.obs
values approach V.sub.max. Reactions also contained 50 mM Tris-HCl
(pH 7.5 at 23.degree. C.) and 20 mM MgCl.sub.2, and were incubated
at 23.degree. C. with concentrations of effector molecules and
incubation times as noted for each experiments. Ribozyme and
substrate were preincubated separately for 10 min in reaction
buffer and also with effector molecules when present, and reactions
were initiated by combining preincubated mixtures. Assays with H8
were conducted in 50 mM HEPES (pH 7.3 at 23.degree. C.), 500 mM
NaCl and 10 mM MgCl.sub.2. Catalytic rates (k.sub.obs) were
obtained by plotting the fraction of substrate cleaved versus time
and establishing the slope of the curve that represents the initial
velocity of the reaction by a least-squares fit to the data.
Kinetic assays were analyzed by PAGE and were visualized and
analyzed on a Molecular Dynamics Phosphorimager. When shorter
effector-molecule preincubations are used, the catalytic burst was
more prominent and when encountered, a post-burst slope was used in
the calculations. Replicate experiments routinely gave k.sub.obs
values that differed by less than 50% and the values reported are
averages of two or more experiments. Equivalent rates were also
obtained for duplicate ribozyme and substrate preparations.
[0061] The H3 ribozyme displays different cleavage rates, after a
brief burst phase, with different concentrations of ATP (FIG. 7A),
with the curve closely predicting the K.sub.D of the aptamer for
its ligand. A plot of k.sub.obs versus ATP or dATP concentration
(FIG. 7B) demonstrates that H3 undergoes .about.170-fold reduction
in catalytic rate with increasing concentrations of ATP, but is not
inhibited by dATP.
[0062] Whether ATP could also be made to function as a positive
effector of ribozyme function was investigated by designing H6 and
subsequently H7 (FIG. 8A), both which were found to display
ATP-dependent allosteric induction. H6 is similar to H5, except
that four Watson/Crick base-pairs in stem II are replaced with
less-stable G.U mismatches. These changes are expected to
significantly weaken stem II and result in diminished ribozyme
activity. It was intended to exploit the fact that the G-C pair
that begins stem II within the aptamer domain is not paired in the
absence of ATP, but will form a stable pair when ATP is complexed
(35), thereby increasing the overall stability of the stem and
inducing catalytic activity. Indeed, a .about.5-fold reduction in
catalytic activity with H6 compared to H5 was found, yet ribozyme
function could be specifically and fully recovered with ATP. The
catalytic rate of H6 is also enhanced by ATP when added during the
course of the reaction (FIG. 8B).
[0063] As with allosteric effectors of proteins, there is no true
similarity between the effector molecule and the substrate of the
ribozyme. Substrate and effector occupy different binding sites,
yet conformational changes upon effector binding result in
functional changes in the neighboring catalytic domain. The
specificity of allosteric control of ribozymes can be exquisite,
and in this example the ribozyme activity is sensitive to the
difference of a single oxygen atom in the effector molecule.
[0064] With similar model studies, a palate of design options and
strategic approaches that can be used to create ribozymes with
controlled catalytic activity can be built. The principles used
here (secondary binding sites, conformational changes, steric
effects and structural stabilization) as well as others may be
generally applicable and can be used to design additional
allosteric ribozymes, or even allosteric deoxyribozymes (37). For
example, an allosteric hammerhead (H8, FIG. 8A) that includes the
theophylline aptamer described by Jenison, et al. (21) was
designed. This construct displays a modest 3-fold reduction in
ribozyme activity (k.sub.obs of 0.006 v. 0.002 min.sup.-1) when
theophylline is added to a final concentration of 100 .mu.M. In
addition, Sargueil, et al. (21) have suggested similar studies with
the `hairpin` self-cleaving ribozyme.
Example 2
[0065] The isolation by in vitro selection of two distinct classes
of self-cleaving DNAs from a pool of random-sequence
oligonucleotides are reported in this example. Individual catalysts
from `class I` require both Cu.sup.2+ and ascorbate to mediate
oxidative self-cleavage. Individual catalysts from class II were
found to operate with copper as the sole cofactor. Further
optimization of a class II individual by in vitro selection yielded
new catalytic DNAs that facilitate Cu.sup.2+-dependent
self-cleavage with rate a enhancement that exceed 1 million fold
relative to the uncatalyzed rate of DNA cleavage.
[0066] DNA is more susceptible to scission via
depurination/.beta.-elimina- tion or via oxidative mechanisms than
by hydrolysis (27). To begin a comprehensive search for artificial
DNA-cleaving DNA enzymes, DNAs that facilitate self-cleavage by a
redox-dependent mechanism were screened for. Cleavage of DNA by
chelates of redox-active metals (e.g., Fe.sup.3+, Cu.sup.2+) in the
presence of a reducing agent is expected to be a more facile
alternative to DNA phosphoester hydrolysis due to the reactivity of
hydroxyl radicals that are produced by reduction of H.sub.2O.sub.2
(i.e., Fenton reaction). Moreover, a variety of natural and
artificial `chemical nucleases` rely on similar cleavage mechanisms
(38-39).
[0067] Beginning with a pool of .about.2.times.10.sup.13
random-sequence DNAs (FIG. 13b), eight rounds of selection were
carried out (5, 10) (see materials and methods section, below) for
DNAs that self-cleave in the presence of CuCl.sub.2 and ascorbate.
The DNA pool that was isolated after seven rounds (G7 DNA) displays
robust self-cleavage activity that requires both Cu.sup.2+ and
ascorbate (FIG. 13c). Trace amounts of non-specific DNA cleavage
can be detected with Cu.sup.2+ and ascorbate concentrations of 100
.mu.M or above, but no cleavage of random-sequence (G0) DNA was
detected under the final selection conditions (10 .mu.M of each
cofactor). In contrast, incubation of G7 DNA yields a number of
distinct DNA cleavage products, suggesting that the pool contains
multiple classes of DNAs that promote self-cleavage at unique
sites.
[0068] Sequence analysis of individual DNAs from G8 reveals a
diverse set of catalysts that were divided into two groups (FIG.
10a) based on sequence similarities. Cleavage assays from three
representative DNAs (CA1, CA2 and CA3) confirm that two distinct
classes of catalysts have been isolated (FIG. 10b). It was expected
that the cleavage sites for the selected catalysts would reside
exclusively within the first 23 nucleotides of the original
construct (FIG. 13b). Cleavage in this region would result in
release of the molecule from the solid matrix, yet the cleaved
molecules would retain enough of the original primer-binding site
to allow amplification by PCR. Cleavage elsewhere in a molecule
would release a DNA fragment that has lost the 5'-terminal
primer-binding site, and would be incapable of significant
amplification during PCR. Surprisingly, although CA1 promotes DNA
cleavage within this expected region, CA2 and CA3 each cleave at a
primary region (Clv 1) near the 5' terminus as expected, and at a
distal region (Clv 2) that resides within the domain that was
randomized in the original DNA pool. The Clv 1/Clv 2 product ratio
of CA3 is approximately 2:1.
[0069] The distribution of cleavage products between the two sites
in CA3 is expected to result in a significant disadvantage during
the selection process. About 35% of CA3-like molecules cleave
within the center of the molecule (and hence are probably not
amplified), while only about 65% cleave at the expected site and
can be perpetuated in the next round of selection via amplification
by PCR. In contrast, 100% of the catalysts that cleave exclusively
in the primer-binding region can be amplified, giving individuals
from class I an apparent selective advantage. However, CA3-like
catalysts were found to persist in additional rounds of in vitro
selection and actually come to dominate the population by
generation 13. The success of these catalysts can be understood, in
part, by examining the catalytic rates of CA1 and CA3. The cleavage
rate (k.sub.obs) of 0.018 min.sup.-1 was obtained for CA1 under the
final selection conditions, while cleavage at Clv 1 of CA3 occurs
with a k.sub.obs of 0.14 min.sup.-1. Despite a high frequency of
miscleavage, class II catalysts more rapidly cleave at the correct
site, giving CA3-like catalysts a distinct selective advantage over
catalysts from class I.
[0070] Cleavage sites for both classes have been further localized
by gel-mobility analysis of the 5' .sup.32P-labeled self-cleavage
products (FIG. 11). CA1 produces a major cleavage product with a
gel mobility that corresponds to a 9-nucleotide fragment, and also
yields a series of minor products that correspond to DNAs of 3 to 8
nucleotides. The cleavage site heterogeneity observed for CA1 is
consistent with an oxidative cleavage mechanism that involves a
diffusible hydroxyl radical. Typically, cleavage of nucleic acids
by an oxidative cleaving agent occurs over a range of nucleotides,
with a primary cleavage site flanked on each side by sites that are
cleaved with decreasing frequency. It has been suggested that the
frequency of DNA cleavage is proportional to the inverse of the
distance that separates the target phosphoester linkage and the
generation site of the hydroxyl radical (18). However, the
distribution of cleavage products formed by CA1 are indicative of a
unique active site that permits localized DNA cleavage to occur
only at nucleotides that immediately flank the 5' side of the major
cleavage site.
[0071] Similarly, Clv 1 of CA3 consists of a series products that
range in mobility from 9 to 14 nucleotides, with the major product
corresponding to a 12-nucleotide DNA (FIG. 11). The major product
formed upon DNA scission at Clv 2 corresponds to 70 nucleotides,
with minor products corresponding to DNAs of 66-69 nucleotides. The
most frequent site of cleavage at Clv 2 is located near position 34
(G) of the original random-sequence domain. Oxidative cleavage of
DNA can proceed by a variety of pathways, each that produce
distinct cleavage-product termini (22). Therefore, conformation of
these cleavage sites must now proceed by conducting a more detailed
analysis of the chemical structures of the reaction products.
[0072] To gain insight into the secondary structure of CA1, an
artificial phylogeny (2) of functional CA1 sequence variants for
comparative sequence analysis (47) were produced. The 50
nucleotides that corresponds to the original random-sequence domain
were mutagenized by preparing a synthetic DNA pool such that each
wild-type nucleotide occurs with a probability of 0.85 and each
remaining nucleotide occurs with a probability of 0.05. The
resulting pool was subjected to five additional rounds of selection
for activity in the presence of 10 .mu.M each of Cu.sup.2+ and
ascorbate. Sequence alignment of 39 resulting clones (FIG. 12a)
reveal two main regions (nucleotides 20-28 and 41-50) of
strictly-conserved sequence interspersed with regions that tolerate
variation. A total of 25 positions experienced two mutations or
less. Other positions show sequence covariation, indicating that
these nucleotides may make physical contact in the active
conformation of the deoxyribozyme. For example, A32 and G40
frequently mutate to C or T, respectively. This suggests a
preference for these bases to pair as C-G or A-T. Indeed, this
inferred pairing occurs in a region (nucleotides 28-44) that has
considerable base-pairing potential, consistent with the formation
of a hairpin structure.
[0073] Using sequence data and truncation analyses, a partial
secondary-structure model for CA1 was constructed (FIG. 12b). Both
the 5'- and 3'-terminal nucleotides show significant base-pairing
potential with the substrate domain of the molecule. The putative
hairpin domain described above (nucleotides 28-44) is flanked by
the conserved 3' terminus and by a highly-conserved region that is
composed mainly of G residues. It was found that removal of an
additional G-rich region that is located in the 3' primer binding
site abolishes the catalytic activity of CA1. Extended stretches of
G residues that form `G-quartet` structures (46) have been
identified in a number of other single-stranded DNAs (3,20,26,48).
The G-rich sequence in CA1 may also form a G-quartet, either
independently or with other stretches of G residues that occur
elsewhere in the primary structure of the catalyst.
[0074] CA1 has no detectable activity in the absence of ascorbate,
but surprisingly, both the G8 population DNA and CA3 display
significant cleavage when only Cu.sup.2+ is added (FIG. 13a). A
k.sub.obs=8.times.10.sup.-4 min.sup.-1 for Clv 1 was measured for
CA3 in the presence of 10 .mu.M Cu.sup.2+. In vitro selection was
employed to isolate CA3 variants with enhanced the Cu.sup.2+-dep
endent activity of CA3. CA3 was mutagenized (see above) and
subjected to five rounds of selection using 10 .mu.M Cu.sup.2+ as
the sole cofactor. Sequence alignment of 40 resulting clones (FIG.
13b) reveal a single region of highly-conserved sequence, spanning
nucleotides 15 to 50 of the original random-sequence domain. The
base identity of 27 nucleotides within this region were found to
vary in three or fewer individuals. The most notable exceptions to
this sequence conservation are a T deletion between nucleotides 39
and 45, and a T to G mutation that occurs at nucleotide 28. In a
related selection experiment, active variants of CA3 in which
nucleotides 1 through 20 of the original random-sequence domain
have been deleted were isolated.
[0075] The catalytic activity of the reselected CA3 pool improved
by nearly 100-fold, with variant DNAs 1, 2 and 3 (FIG. 13b)
displaying k.sub.obs values of 0.052 min.sup.-1, 0.033 min.sup.-1
and 0.043 min.sup.-1, respectively. The uncatalyzed rate of DNA
cleavage in the presence of Cu.sup.2+ was assessed by incubating 5'
.sup.32P-labeled DNA oligomer (primer 3) under identical
conditions. No Cu.sup.2+-dependent cleavage of DNA was detected,
even after a 2-week incubation at 23.degree. C. The overall rate
enhancement of the CA3 variants was estimated to be considerably
greater than 10.sup.6 fold compared to the uncatalyzed rate. Both
CA3 and variant 1 likely proceed via the same DNA cleavage
mechanism, as evident by their similar catalytic cleavage patterns
(FIG. 11). A synthetic 87-nucleotide version of variant 1 that
lacks the 3'-terminal primer-binding site remains active
(k.sub.obs=0.02 min.sup.-1 for Clv 1, 10 .mu.M Cu.sup.2+), while an
inhibitory effect is observed with 100 .mu.M Cu.sup.2+. In
addition, the self-cleavage activity of this truncated DNA has a pH
optimum of 7.5, with no specific monovalent cation requirement.
Sequential deletion of nucleotides from the 5' terminus of this DNA
results in a progressive reduction in catalytic activity, with a
4-nucleotide deletion resulting in nearly complete loss of
function.
[0076] The isolation of a variety of self-cleaving DNAs with
Cu.sup.2+/ascorbate-dependence is consistent with an earlier report
(23) of site-specific cleavage of a single-stranded DNA under
similar conditions. These results confirm that DNA is indeed
capable of forming a variety of structures that promote chemical
transformations. In addition, the catalytic rates for both classes
of self-cleaving DNAs compare favorably to those attained by other
deoxyribozymes and by natural and artificial ribozymes. The finding
that DNA is also able to perform self-cleavage with Cu.sup.2+ alone
is unexpected, since the mechanism for the oxidative cleavage of
DNA also requires a reducing agent such as ascorbate or a thiol
compound (38,39).
[0077] A number of chemical nucleases have been prepared by others
and examined for their potential as site-specific DNA-cleaving
agents. For example, 1,10-phenanthroline and similar agents bind
DNA, presumably via intercalation, and positions copper ions near
the ribose-phosphate backbone where formation of a reactive oxygen
derivative favors cleavage of the DNA chain (39). Alternatively,
metal-binding ligands have been attached to oligonucleotide probes,
in order to construct highly-specific DNA cleaving agents that
recognize DNA by triple-helix formation (26). The catalytic DNAs
described in this report likely replace the role of chemical
nucleases by forming their own metal-binding pockets so as to
promote region-specific self-cleavage. In fact, the addition of
1,10-phenanthroline to a catalytic assay of a synthetic class II
DNA actually inhibits catalytic function. The optimal Cu.sup.2+
concentration for the 87-nucleotide DNA is .about.10 .mu.M, with
catalytic activity dropping significantly at both 1 and 100 .mu.M
Cu.sup.2+. The inhibitory effect of 1,10-phenanthroline might be
due to the reduction in concentration of free Cu.sup.2+ upon
formation of Cu.sup.2+-phenanthrolin- e complexes.
[0078] While not wishing to be bound to any theory, several
different mechanisms for the oxidative cleavage of class II DNAs
seem possible. For example, the class II DNAs may simply scavenge
for trace amounts of copper and reducing agents that are present in
the reaction buffer. Alternatively, these DNA molecules might make
use of an internal chemical moiety as the initial electron donor.
In each example, the catalytic DNAs could still cleave by an
oxidative mechanism, but would at least appear to gain independence
from an external source of reducing agent. The importance of
H.sub.2O.sub.2 in oxidative processes can be examined with
catalase, an enzyme that efficiently promotes the dismutation of
H.sub.2O.sub.2 molecules to yield water and molecular oxygen. The
catalytic activity of a representative DNA from class II is
completely inhibited upon the addition of catalase, consistent with
the notion that H.sub.2O.sub.2 is a necessary intermediate in an
oxidative pathway for DNA cleavage. The catalytic rate of CA3
variants is greatly increased when incubated in the presence of
added H.sub.2O.sub.2. For example, the 87-nucleotide DNA can be
made to cleave quantitatively at Clv 1 (k.sub.obs=1.5 min.sup.-1)
in the presence of 10 .mu.M Cu.sup.2+ and 35 mM H.sub.2O.sub.2.
[0079] It has not been determined whether trace amounts of
H.sub.2O.sub.2 in water are used by the catalysts, or if the DNA
can produce H.sub.2O.sub.2 in the absence of a reducing agent. It
was found that preincubation of separate solutions of catalytic DNA
in reaction buffer (minus Cu.sup.2+) and of aqueous Cu.sup.2+,
followed by thermal denaturation of the catalase, results in full
self-cleavage activity upon mixing of the two solutions. We also
find that self-cleavage of the 87-nucleotide variant reaches a
combined maximum (Clv 1+Clv 2) of 70%, regardless of the
concentration of catalytic DNA present in the reaction. Similarly,
preincubation of a reaction mixture with excess unlabeled catalyst
(1 .mu.M) followed by the addition of a trace amount of identical
5' .sup.32P-labeled catalysts produces normal yields of labeled-DNA
cleavage products. Finally, addition of fresh reaction buffer to a
previously-incubated reaction mixture does not promote further DNA
cleavage, as might be expected if limiting amounts of reducing
agent were responsible for activity.
[0080] Certain constructs of the self-splicing ribozyme of
Tetrahymena have been shown to catalyze the cleavage of DNA via a
transesterification mechanism (19,33), and the ribozyme from RNase
P has been found to cleave DNA by hydrolysis (31). Such ribozymes
might also be made to serve as therapeutic DNA-cleaving agents,
analogous to the function of RNA-cleaving `catalytic antisense`
ribozymes (9). The secondary-structure model of CA1 (FIG. 12b)
includes stretches of predicted base pairing both 5' and 3' to the
primary cleavage site, suggesting that `substrate` and `enzyme`
domains can be separated. Likewise, preliminary analysis of class
II molecules reveals similar base complementation. It is expected
that both class I and class II DNAs can be engineered to create
catalytic DNAs that specifically cleave DNA substrates with
multiple turn-over kinetics.
[0081] In summary, two distinct classes of DNAs that promote their
own cleavage have been isolated. One class requires copper and
catalyzes the oxidative cleavage of DNA with a rate in excess of 1
million fold. Extensive regions of both classes of self-cleaving
DNAs are important for the formation of catalytic structures, as
implicated by sequence conservation found with selected
individuals. These results support the view that DNA, despite the
absence of ribose 2'-hydroxyl groups, has considerable potential to
adopt higher-ordered structures with functions that are similar to
ribozymes.
Materials and Methods
[0082] Oligonucleotides
[0083] All synthetic DNAs were prepared by automated chemical
synthesis (Keck Biotechnology Resource Laboratory, Yale
University). The starting pool is composed of DNAs that carry a
5'-terminal biotin moiety and a central domain of 50
random-sequence nucleotides. Primer 3 is an analogue of primer 1
(FIG. 13b) that contains a 3'-terminal ribonucleoside. Primer 4 is
the nonbiotinylated version of primer 2 (FIG. 13b). Primer 5 is the
5'-biotinylated form of primer 1.
[0084] In vitro Selection
[0085] A total of 40 pmoles of pool DNA in 40 .mu.l buffer A (50 mM
HEPES, pH 7.0 at 23.degree. C., 0.5 M NaCl, 0.5 M KCl) was loaded
on two streptavidin-matrix columns (Affinitip Strep20, Genosys
Biotechnologies) and incubated for .about.5 min. Unbound DNAs were
subsequently removed from each column by pre-elution with 500 .mu.l
of buffer A, then by 500 .mu.l 0.2 N NaOH, and the resulting
matrix-bound DNAs were equilibrated with 500 .mu.l buffer A.
Catalytic DNAs were eluted with three successive 20-.mu.l aliquots
of buffer B (buffer A, 100 .mu.M CuCl.sub.2, 100 .mu.M ascorbate)
for rounds 1-3, or buffer C (buffer A, 10 .mu.M CuCl.sub.2, 10
.mu.M ascorbate) for rounds 4-8. Eluate from each column was
combined with 120 .mu.l 4 mM EDTA and 40 pmoles each of primers 1
and 2. Selected DNAs and added primers were recovered by
precipitation with ethanol and amplified by PCR a 200 .mu.l
reaction containing 0.05 U .mu.l-1 Taq polymerase, 50 mM KCl, 1.5
mM MgCl.sub.2, 10 mM Tris-HCl (pH 8.3 at 23.degree. C.), 0.01%
gelatin, and 0.2 mM each dNTP for 25 cycles of 10 sec at 92.degree.
C., 10 sec at 50 .degree. C. and 30 sec at 72.degree. C. The
5'-terminal region of each cleaved DNA, including the biotin
moiety, was reintroduced at this stage. Subsequent rounds were
performed by immobilizing 20 pmoles of pool DNA on a single
streptavidin column and selected DNAs were amplified in a 100 .mu.l
reaction for 10 to 20 temperature cycles. Steps II-IV (FIG. 13)
were repeated until the population displayed the desired catalytic
activity, at which time the pool was PCR amplified with primers 1
and 3, cloned (Original TA Cloning Kit, Invitrogen) and sequenced
(Sequenase 2.0 DNA Sequencing Kit, U. S. Biochemicals).
Reselections with CA1 and CA3 were initiated with 20 pmoles
synthetic DNA. This is expected to offer near comprehensive
representation of all sequence variants with seven or fewer
mutations relative to wild type.
[0086] Catalytic Assays
[0087] 5'-.sup.32P-labeled precursor DNA was prepared by
PCR-amplifying double-stranded DNA populations or plasmid DNA using
5'-.sup.32P-labeled primer 4 and either primer 5 or primer 3. The
antisense strand is removed either by binding the biotinylated
strand to a streptavidin matrix (primer 5) or by alkaline cleavage
of the RNA phosphodiester-containing strand, followed by PAGE
purification (primer 3). DNA self-cleavage assays (.about.5 nM 5'
.sup.32P-labeled precursor DNA) were conducted at 23.degree. C. in
buffer A, with cofactors added as detailed for each experiment. For
both in vitro selection and for assays, reaction buffers that
contained ascorbate were prepared just prior to use. Self-cleavage
assays conducted with catalase (bovine liver, Sigma) contained 50
mM HEPES (pH 7.0 at 23.degree. C.), 50 mM NaCI, 10 .mu.M
CuCl.sub.2, and 0.5 U/.mu.l catalase, and were incubated at room
temperature for 20 min. Catalase activity was destroyed by heating
at 90.degree. C. for 5 min. Products were separated by denaturing
(8 M urea) polyacrylamide gel electrophoresis (PAGE) using a 10%
gel and visualized by autoradiography or visualized and quantitated
by PhosphorImager (Molecular Dynamics).
[0088] Cleavage Product Analysis
[0089] Primary cleavage sites for CA1 and CA3 were identified by
incubating 5' .sup.32P-labeled precursor DNA in buffer C and
assessing the gel mobility of the 5'-terminal cleavage fragments by
analysis using a denaturing 20% PAGE as compared to a series of 5'
.sup.32P-labeled synthetic DNAs that correspond in sequence to the
5' terminus of the precursor DNAs. Products resulting from sission
at Clv 2 were analyzed by denaturing 6% PAGE.
[0090] Kinetic Analysis
[0091] Catalytic rates were obtained by plotting the fraction of
precursor DNA cleaved versus time and establishing the slope of the
curve that represents the initial velocity of the reaction as
determined by a least-squares fit to the data. Kinetic assays were
conducted in buffer C or in buffer A plus 10 .mu.M CuCl.sub.2 as
indicated for each experiment. Rates obtained from replicate
experiments differed by less than two fold and the values reported
are averages of at least two analyses.
Example 3
[0092] This example describes a DNA structure that can cleave
single-stranded DNA substrates in the presence of ionic copper.
This deoxyribozyme can self-cleave, or it can operate as a
bimolecular complex that simultaneously makes use of duplex and
triplex interactions to bind and cleave separate DNA substrates.
DNA strand scission proceeds with a k.sub.obs of 0.2 min.sup.-1, a
rate that is .about.10.sup.12-fold faster than the uncatalyzed rate
of DNA phosphoester hydrolysis. The duplex and triplex recognition
domains can be altered, making possible the targeted cleavage of
single-stranded DNAs with different nucleotide sequences. Several
small synthetic DNAs were made to function as simple `restriction
enzymes` for the site-specific cleavage of single-stranded DNA.
[0093] A Minimal Cu.sup.2+-Dependent Self-cleaving DNA. In Example
2, a variety of self-cleaving DNAs were isolated by in vitro
selection from a pool of random-sequence DNAs. Most individual DNAs
that were isolated after eight rounds (G8) of selection conformed
to two distinct classes, based on similarities of nucleotide
sequence and DNA cleavage patterns. Although individual DNAs from
both class I and class II require Cu.sup.2+ and ascorbate for full
activity, the G8 DNA population displays weak self-cleavage
activity in the presence of Cu.sup.2+ alone. A representative class
II DNA termed CA3 was further optimized for ascorbate-independent
activity by applying in vitro selection to a DNA pool that was
composed of mutagenized CA3 individuals. The sequence data from
this artificial phylogeny of DNAs indicates that as many as 27
nucleotides, most of them located near the 3' terminus of the
molecule, are important for self-cleavage activity.
[0094] Beginning with the original G7 DNA population, an additional
six rounds of in vitro selection was carried out for DNAs that
self-cleave in the presence of 10 .mu.M Cu.sup.2+, without added
reducing agent. Analysis of the G13 population of DNAs revealed
robust self-cleavage activity, demonstrating that catalytic DNAs
can promote efficient cleavage of DNA using only a divalent metal
cofactor. The G13 population displays the same cleavage pattern
that was observed with individual class II DNAs, indicating that
class II-like DNAs dominate the final DNA pool.
[0095] A total of 27 individual DNAs from G13 were sequenced and,
without exception, each carried a 21-nucleotide sequence domain
that largely conformed to the consensus sequence that was used
previously to define class II self-cleaving DNAs. Although
individuals that have a strictly conserved core (spanning
nucleotides 11 to 31, FIG. 14A) dominate the G13 pool, two common
variations from this consensus sequence include a C to T mutation
at position 17 (6 of 28 individuals) or the presence of six
successive T's instead of five in the region spanning nucleotides
21 to 25 (4 of 27 individuals). However, significant differences in
nucleotide sequence were found to occur outside this conserved
domain, indicating that large portions of the class II
deoxyribozymes isolated may not be necessary for catalytic
activity. Indeed, three individual DNAs were found to have
undergone deletions of 16, 19, and 20 nucleotides within the
50-nucleotide domain that was randomized in the original starting
pool. The predicted secondary structure for the 19-nucleotide
deletion mutant (69 mer DNA, FIG. 14A), obtained by the Zucker `DNA
mfold` program (33,50; the DNA mfold server can be accessed on the
internet at www.ibc.wust1.edu/.about.zuker/dna/form1.cgi.),
indicates the presence of three base-paired regions; two involve
pairing between the original random-sequence domain and the
`substrate` domain, and one that involves putative base-pairing of
nucleotides that lie within the conserved-sequence region. A
synthetic DNA corresponding to the 69-mer depicted in FIG. 14A
undergoes Cu.sup.2+-dependent self-cleavage at two locations with a
combined catalytic rate of approximately 0.3 min.sup.-1 under the
conditions used for in vitro selection (see Materials and Methods
below for additional discussion on catalytic rates).
[0096] Whether the two pairing regions of the 69-mer that lie
within the variable-sequence region could be replaced by a smaller
stem-loop structure was tested by synthesizing a 46-mer DNA, in
which 26 nucleotides of this imperfect hairpin were replaced by the
trinucleotide loop GAA (FIG. 14B). As expected, the truncated `46
mer` DNA retains full catalytic activity, thereby confirming that
the deleted nucleotides are not essential for deoxyribozyme
function. This 46-nucleotide deoxyribozyme is predicted to adopt a
pistol-like secondary structure (FIG. 14B) composed of two
base-paired structural elements (stems I and II) flanked by regions
of single-stranded DNA. The primary site of DNA cleavage is located
at position 14 which resides within one of the putative stem
structures of the 46 mer. The catalyst also promotes DNA cleavage
within a region located apart from the main cleavage site (Example
2), as might be expected for a deoxyribozyme that makes use of an
oxidative cleavage mechanism (22).
[0097] Bimolecular Deoxyribozyme Complexes: Substrate Recognition
by Duplex and Triplex Formation. Separate `substrate` and
`catalyst` DNAs can be created from the 46 mer by eliminating the
connecting loop of stem I (FIG. 14B). Active bimolecular complexes
then can be reconstituted by combining independently prepared
substrate and catalyst DNAs. Both the unimolecular 46 mer and the
bimolecular complexes examined cleave with identical rates,
promoting primary-site cleavage with a k.sub.obs of approximately
0.2 min.sup.-1. The importance of stem I was confirmed (FIG. 15A)
by synthesizing different catalyst DNAs (c1, c2 and c3) and
assessing their ability to cleave different substrate molecules
(s1, s2 and s3). For example, c1 displays activity with its
corresponding substrate (s1), but not when the non-complementary
substrate DNAs s2 or s3 are substituted. Likewise, c2 and c3 only
cleave their corresponding substrate DNAs s2 and s3, respectively.
Extending stem I to create a more stable interaction was also found
to confer greater binding affinity between substrate and catalyst
oligonucleotides. These data indicate that base pairing
interactions that constitute stem I are an essential determinant
for catalyst/substrate recognition.
[0098] Stem II was examined by a similar approach using mutant
versions of the 46 mer self-cleaving DNA. A series of variant
deoxyribozymes with one or two mutations included in the putative
stem II structure were synthesized and assayed for catalytic
activity (FIG. 15B). Disruption of the original C35-G43 base pair
in stem II, either by mutation of C to G at position 35 or mutation
of G to C at position 43, results in a substantial loss of
activity. Cleavage activity is partially restored when these
mutations are combined in the same molecule to produce a G35-C43
base pair. These results are consistent with the stem-loop
structure modeled in FIG. 14. Additional support for the presence
of stem II was found upon sequence analysis of the deoxyribozymes
that are present in the original in vitro-selected pool of DNAs. A
single self-cleaving DNA was found with a core sequence that
differs significantly from that of the most frequently represented
deoxyribozyme. Nucleotides 38-40 of the more common 46 mer sequence
are replaced in the variant deoxyribozyme with the nucleotides
5'-CTGGGG. This alternative sequence extends stem II by a single
C-G base pair, consistent with the formation of the predicted
stem-loop structure.
[0099] Although the existence of stem II is supported by the data
derived from mutational analysis, the fact that total restoration
of deoxyribozyme activity was not achieved with restoration of base
complementation indicates that the identities of the base pairs in
this structural element are important for maximal catalytic
function. Moreover, it was found that mutation or deletion of
nucleotides 1-7 of the 46 mer result in a dramatic loss of DNA
cleavage activity. It was recognized that nucleotides 4-7 within
this essential region of the substrate form a polypyrimidine tract
that is complementary to the paired sequence of stem II for the
formation of a YR*Y DNA triple helix (14).
[0100] To examine the possibility of triplex formation in the
active structure of the deoxyribozyme, we modified both the base
pairing sequence of stem II (c4) and the sequence of the
polypyrimidine tract of the substrate (s4) to alter the
specificity, yet retain the potential for forming four contiguous
base triples (FIG. 16). The c4 variant DNA cleaves its
corresponding s4 DNA substrate, but shows no activity with a
substrate that carries the original polypyrimidine sequence. It was
found that even single mutations within stem II (e.g., FIG. 15B) or
single mutations within the poly-pyrimidine tract cause significant
reductions in catalytic activity. However, the introduction of six
mutations in a manner that is consistent with triplex formation
results in a variant (c4/s4) complex that displays full DNA
cleavage activity. This is the first example of a catalytic
polynucleotide, natural or artificial, that makes use of an
extended triple helix for the formation of its active structure
(43).
[0101] Targeted Cleavage of DNA `Restriction Sites` with
Deoxyribozymes. The results described above demonstrate that class
II deoxyribozymes identify substrate DNAs by simultaneously
utilizing two distinct recognition domains that are formed
separately by stems I and II. These structures might be further
exploited as recognition elements to engineer deoxyribozymes that
selectively cleave DNAs at different target sites. To demonstrate
this capability, a 101-nucleotide DNA that carries three identical
leader sequences, each followed by different stem I recognition
sequences was synthesized (FIG. 17A). Three catalyst DNAs (c1, c3
and c7) each were designed to be uniquely complementary to one of
the three target sites. When incubated separately with 101 mer
substrate, DNAs c3 and c7 cleave exclusively at their corresponding
target sites, while c1 cleaves at its intended site and also to a
lesser extent at the c3 cleavage site (FIG. 17B). The cross
reactivity observed with c1 can be explained by examining the
base-pairing potential of stem I. Of the six nucleotides in the c1
recognition sequence, four can form standard base pairs, while the
remaining two form G-T wobble pairs. The contribution of both
duplex and triplex recognition elements presumably allows for
detectable cleavage activity at this secondary location.
[0102] The triplex interaction that is defined by the base-pairing
sequence of stem II can also be exploited to target specific DNA
substrates. We designed three new catalyst DNAs (c9, c10 and c11)
that carry identical stem I pairing subdomains, but that have
expanded and unique stem II subdomains (FIG. 17C). When incubated
separately with a 100-nucleotide DNA that carries three uniquely
complementary polypyrimidine tracts, each catalyst DNA cleaves its
corresponding target site with a rate that corresponds well with
that found for the original self-cleaving DNA. In this example,
substrate selectivity is determined almost entirely by triplex
formation, despite the presence of identical and extensive base
complementation (stem I) between catalyst and substrate
molecules.
[0103] Although DNA cleavage catalyzed by the deoxyribozyme is
focused within the substrate domain, substantial (.about.30%)
cleavage occurs within the conserved core of the catalyst strand.
This collateral damage causes inactivation of the deoxyribozyme
and, as a result, super-stoichiometric amounts of catalyst DNA are
needed to assure quantitative cleavage of DNA substrate. Cleavage
of the substrate subdomain proceeds more rapidly than does cleavage
within the catalytic core. In the presence of excess c1, s1 is
cleaved at a rate of approximately 0.2 min.sup.-1 (reaction buffer
containing 30 .mu.M CuCl.sub.2), reaching a plateau of 80% cleaved
after 20 min. In contrast, cleavage of c1 in the presence of excess
s1 proceeds more than 2-fold slower, consistent with our earlier
report that the ratio of self-cleavage localized in the substrate
domain to self-cleavage in the catalytic core gives a ratio of 2:1.
It was established that, barring inactivation by miscleavage, the
catalyst strand can undergo multiple turnover.
[0104] Cleaving Double-stranded DNA by Thermocycling. Class II
catalyst DNAs are not able to cleave target DNAs when they reside
within a duplex. The catalyst DNA, with its short recognition
sequence, presumably cannot displace the longer and more
tightly-bound complementary strand of the target in order to gain
access to the cleavage site. It was found that an effective means
for specific cleavage of one strand of an extended DNA duplex makes
use of repetitive cycles of thermal denaturation and reannealing.
For example, c3 remains inactive against a double-stranded DNA
target in the absence of thermal cycling, but efficiently cleaves
the same DNA substrate upon repeated heating and cooling cycles.
Cleavage of the radiolabeled target is quantitative after 6 thermal
cycles. DNA cleavage by class II DNAs occurs within the
base-pairing region corresponding to stem I, presumably when this
region is in double-helical form. This, coupled with the
observation of substrate recognition by triplex formation, suggests
that different DNA enzymes might be engineered to cleave duplex DNA
substrates without the need for thermal denaturation. Such
deoxyribozyme activity would be similar to that performed by a
number of triplex-forming oligonucleotides that have been
engineered to bind and cleave duplex DNA using a
chemically-tethered metal complex such as Fe-EDTA (24-27).
[0105] Conclusions. In its unimolecular arrangement, the class II
deoxyribozyme could be used to confer the capacity for
self-destruction to an otherwise stable DNA construct. In its
bimolecular form, the deoxyribozyme can act as an artificial
restriction enzyme for single-stranded DNA, whereas protein-based
nucleases that cleave non-duplex DNA do not demonstrate significant
sequence specificity. It is likely that Ymaximal discrimination by
class II catalysts between closely related target sequences can be
achieved through careful design of the duplex and triplex
recognition domains. This is expected to eliminate the cross
reactivity that was observed here. Although the role of most
nucleotides within the substrate domain are involved in substrate
recognition, the importance of each nucleotide within the leader
sequence has yet to be fully delineated. However, guided by the
basic rules of duplex and triplex formation, one w3can now engineer
highly-specific deoxyribozymes that can catalyze the cleavage of
single-stranded DNA at defined locations along a polynucleotide
chain.
Materials and Methods
[0106] Oligonucleotides
[0107] Synthetic DNAs were prepared by automated chemical synthesis
(Keck Biotechnology Resource Laboratory, Yale University), and were
purified by denaturing (8M urea) polyacrylamide gel electrophoresis
(PAGE) prior to use. Double-stranded 101 mer DNA was prepared by
the polymerase chain reaction (PCR) as described in Example 2 using
the primer DNAs 5' .sup.32P-GTCGACCTGCGAGCTCGA, (SEQ ID NO: 51)
5'GTAGATCGTAAAGCTTCG (SEQ ID NO: 52) and the 101 mer DNA oligomer
(FIG. 17A) as template.
[0108] In vitro Selection
[0109] Optimization of class II self-cleaving DNAs was achieved by
in vitro selection essentially as described In Example 2 using a
reaction mixture for DNA cleavage composed of 50 mM HEPES (pH 7.0
at 23.degree. C.), 0.5 M NaCl, 0.5 M KCl (buffer A), and that
included 10 .mu.M CUCl.sub.2. The selection process was initiated
with 20 pmoles G7 PCR DNA in which the 5' terminus of each catalyst
strand carried a biotin moiety, thereby allowing DNA from this and
subsequent generations to be immobilized on a
streptavidin-derivatized chromatographic matrix. Reaction time was
15 min. for immobilized DNA from G8-G10 and 12, 7 and 5 min. for
the G11-G13 DNA populations, respectively. Individual self-cleaving
DNAs from G13 were analyzed by cloning (Original TA Cloning Kit,
Invitrogen) and sequencing (Sequenase 2.0 DNA Sequencing Kit, U.S.
Biochemicals).
[0110] DNA Cleavage Assays
[0111] To assess the DNA cleavage activity of self-cleaving
molecules, radiolabeled precursor DNA was prepared by enzymatically
tagging the 5' terminus of synthetic DNAs in a reaction containing
25 mM CHES (pH 9.0 at 23.degree. C.), 5 mM MgCl.sub.2, 3 mM DTT, 1
.mu.M DNA, 1.2 .mu.M (.gamma.-.sup.32P)-ATP (.about.130 .mu.Ci),
and 1 U/.mu.L T4 polynucleotide kinase, which was incubated at
37.degree. C. for 1 hr. The resulting 5' .sup.32P-labeled DNA was
isolated by denaturing PAGE and recovered from the gel matrix by
crush-soaking in 10 mM Tris-HCl (pH 7.5 at 23.degree. C.), 0.2 M
NaCl, and 1 mM EDTA. The recovered DNA was concentrated by
precipitation with ethanol and resuspended in deionized water
(Milli-Q, Millipore). Self-cleavage assays using trace amounts of
radiolabeled precursor DNA (.about.100 pM) were conducted at
23.degree. C. in buffer A containing CuCl.sub.2 as indicated for
each experiment. Examinations of the DNA cleavage activity of
bimolecular complexes were conducted under similar conditions using
trace amounts of of 5' .sup.32P-labeled `substrate` DNA. Cleavage
products were separated by denaturing PAGE, imaged by
autoradiography or by PhosphorImager (Molecular Dynamics) and
product yields were determined by quantitation (ImageQuant) of the
corresponding precursor and product bands.
[0112] Kinetic Analyses
[0113] Catalytic rates were estimated by plotting the fraction of
precursor or substrate DNA cleaved versus time and establishing the
slope of the curve that represents the initial velocity of the
reaction as determined by a least-squares fit to the data. Upon
close examination, DNA cleavage in both the substrate and enzyme
domains displayed a brief lag phase that complicates the
determination of the initial cleavage rate. In order to avoid the
lag phase, the initial slope was calculated only using data
collected after the reaction had proceeded for 1 min. Rates
obtained from replicate experiments differed by less than 50% and
the values reported are averages of at least three analyses.
Example 4
[0114] The in vitro selection of a catalytic DNA that uses
histidine as the active component for an RNA cleavage reaction is
described in this example. An optimized deoxyribozyme only binds to
L-histidine or to several closely-related analogues and
subsequently catalyzes RNA phosphoester cleavage with a rate
enhancement of .about.10-million fold over the uncatalyzed rate.
While not wishing to be bound to any theory, the DNA-histidine
complex apparently performs a reaction that is analogous to the
first step of the catalytic mechanism of RNase A, in which the
imidazole group of histidine acts as a general base catalyst.
[0115] The class of deoxyribozymes that catalyze the cleavage of an
RNA phosphoester bond using the amino acid histidine as a cofactor
described herein is depicted in FIG. 18a. To assure that
metal-dependent deoxyribozymes were not recovered from the
random-sequence pool of DNAs, the divalent metal-chelating agent
ethylenedimainetetraacetic acid (EDTA) was included in a reaction
mixture that was buffered with 50 mM histidine (pH 7.5). After 11
rounds of selective amplification, the DNA pool displayed RNA
phosphoester-cleaving activity, both under in vitro selection
conditions, and in a reaction buffer containing HEPES (50 mM, pH
7.5) in place of histidine. Individual molecules cloned from the
final DNA pool were grouped into one of four sequence classes (FIG.
19b), and representative clones were tested for catalytic activity.
Only class II DNAs demonstrate complete dependence on histidine
while the remaining classes appear to operate independently of any
metal ion or small organic cofactor.
[0116] The catalytic rate for the original class II deoxyribozyme
was 1000-fold slower (k.sub.obs=1.5.times.10.sup.-3 min.sup.-1)
than most natural self-cleaving ribozymes (44). As a result,
further optimization of catalytic activity was sought in order to
provide an artificial phylogeny of variant catalysts for
comparative sequence analysis. A new DNA pool was prepared based on
the sequence of class II deoxyribozymes, such that the 39
nucleotides corresponding to the original random-sequence domain
were mutagenized with a degeneracy of 0.21 (6). Beginning with a
mutagenized pool that sampled all possible variant DNAs with seven
or fewer mutations relative to the original class II sequence,
parallel reselection was conducted using reaction solutions
buffered with either 50 mM histidine, or with 5 mM histidine and 50
mM HEPES. Individual DNAs isolated from the populations resulting
from five rounds of reselection are more active than the original
class II deoxyribozyme, and show specific patterns of conserved
sequences and mutation acquisition (FIG. 19a).
[0117] It was speculated that engineered pairing element i included
in the original DNA construct (FIG. 18a) was being utilized by
class II deoxyribozymes. In contrast, it was recognized that a
conserved-sequence domain near the 3' end of the core (FIG. 19a,
nucleotides 32-36) was identical to pairing element ii .
Considering these observations, individual deoxyribozymes HD1 and
HD2 were designed to operate as separate substrate and enzyme
domains (FIG. 19b). Specificity for the substrate oligonucleotide
is defined by the Watson/Crick base complementation between the
substrate and the two pairing arms of the enzyme domain. Class II
deoxyribozymes have an absolute requirement for histidine as show
by the activity of the bimolecular HD1 construct to `caged`
histidine delivered in the form of dipeptides, and to free amino
acids that were liberated from each dipeptide by acid hydrolysis
(FIG. 16a). In addition, HD1 accepts L-, but not D-histidine as a
cofactor. However, samples of D-histidine become active upon
treatment with HCl in accordance with the accelerated rate of
interconversion between the two isomeric forms in acidic conditions
(11).
[0118] A larger panel of histidine analogues were examined (Fogire
16b) in order to more carefully examine the chemical groups of
histidine that are important for catalytic activity and to rule out
the possibility that catalysis might be due to a contamination of a
metal ion cofactor. HD1 discriminates against a variety of
histidine analogues, but shows full activity with the methyl ester
of L-histidine (FIG. 16c). Both the 1-methyl- and
3-methyl-L-histidine analogues do not support HD1 activity,
indicating that the imidazole ring of histidine is important for
deoxyribozyme function. As expected, HD2 has a similar pattern of
cofactor discrimination (Table 2). Both catalysts show
stereospecific recognition of histidine, and make use of
interactions with the .alpha.-amino group, with both carboxyl
oxygens, and with the imidazole group in order to attain maximize
cofactor binding. Although a number of analogues cannot support
deoxyribozyme activity, no compounds function as competitive
inhibitors, indicating that their inactivity is due to the failure
to bind the deoxyribozyme.
2TABLE 2 Relative k.sub.obs values for HD2 in the presence of 25 mM
L-histidine and various analogues (k.sub.obs for L-histidine = 0.11
min.sup.-1). relative fold cofactor k.sub.obs discrimination
L-histidine 1 -- L-histidine methyl ester 0.93 1.1 L-histidine
benzyl ester 0.76 1.3 .alpha.-methyl-DL-histidine 0.041 24
histidinamide 0.025 40 glycyl-histidine 0.006 170 histidinol 0.003
330 3-methyl-L-histidine 0.002 500 D-histidine 0.001 1000
1-methyl-L-histidine <10.sup.-3 >1000
[0119] The rate constant for HD2-promoted catalysis (k.sub.obs of
0.2 min.sup.-1, 50 mM histidine) is similar to that of natural
self-cleaving ribozymes and corresponds to a rate enhancement of 10
million fold over the uncatalyzed reaction (k.sub.obs <10.sup.-8
min.sup.-1 under in vitro selection conditions). The dependence of
the rate constant on histidine concentration is characteristic of
the presence of a saturable binding site for histidine, although
neither HD2 nor HD1 reach saturation even at 100 mM concentration
of cofactor. The established specificity for particular cofactors,
however, indicates that both catalysts do indeed form a histidine
binding site. HD2 demonstrates greater activity with lower
histidine concentrations, perhaps reflecting a greater binding
affinity for histidine as would be expected due to its isolation
from a low-histidine selection regiment.
[0120] The pH-dependent activity profile for HD2 also implicates
histidine as an integral component of the catalytic process (FIG.
21b). The rate constant of HD2 is entirely independent of pH
between the values 7 and 9. However, the activity of this enzyme
drops precipitously at pH values that lie outside this optimum
range. Most revealing is the response of HD2 to low pH conditions.
The k.sub.obs values increase linearly with increasing pH between
pH 4.5 and 5.5, giving a slope of approximately 1. This result is
expected if the protonation state of a single functional group
determined the catalytic rate. Moreover, a rate constant that is
half the maximum value is obtained at pH 6, where this chemical
group will be half deprotonated. This value corresponds precisely
with the pK.sub.a for the imidazole group of free histidine. Taken
together, these results are consistent with a mechanism whereby the
imidazole group serves as a general base catalyst for the
deprotonation of the 2'-hydroxyl group, thereby activating the
oxygen for nucleophilic attack on the neighboring phosphorus
atom.
[0121] The loss of catalytic activity at higher pH values is not
expected to be due to the protonation state of histidine, unless
the pK.sub.a of the imidazole group of a putative second histidine
cofactor is dramatically shifted from its normal value. The
.beta.-amino group of histidine, which has a pK.sub.a of greater
than 9, conceivably could be involved in catalysis as well.
However, it is expected to find a loss of activity with pH values
in excess of 9 or less than 4.5 due to the significant level of
deprotonation of T and G residues or protonation of C and A
residues, respectively.
[0122] Histidine was chosen as a candidate cofactor because of the
potential for the imidazole side chain to function in both general
acid and general base catalysis near neutral pH. This property is
neither inherent to the four standard nucleotides of RNA nor to the
remaining natural amino acids. As a consequence, histidine is one
of the most-frequently used amino acids in the active sites of
protein enzymes. For example, two active-site histidines are
essential for the function of ribonuclease A from bovine pancreas,
where both of these capacities are used to accelerate RNA cleavage.
Although RNase A has long served as a model for the study of enzyme
action, the specific roles that each active-site reside play in the
catalytic process are still vigorously debated (31). The classical
view holds that the histidine at position 12 acts as a general base
for the deprotonation of the 2' hydroxyl, while the histidine at
position 119 acts as a general acid and protonates the 5' oxyanion
leaving group. Breslow and others (25,47) have proposed that the
role for histidine 119 instead may be to protonate the phosphorane
intermediate, thereby implicating general acid catalysis by the
imidazole group as a priority step during the catalytic process.
The data described herein indicate that the histidine cofactor for
class II deoxyribozymes is not involved in a protonation step, but
is functioning exclusively as a general base catalyst.
[0123] In comparison to proteins, the more repetitive nature of
monomeric units that make up nucleic acids limits both the
formation of fine structure in folded polynucleotides and the
chemical reactivity of RNA and DNA. The fact that a nucleic acid
enzyme can co-opt one of the favorite chemical units of
protein-based enzymes supports the notion that RNA could rally its
limited structure-forming potential and, using the catalytic tools
of modern protein enzymes, could produce and maintain a complex
metabolic state.
Materials and Methods
[0124] In vitro Selection and Reselection
[0125] In vitro selection was carried out essentially as described
previously (5,7,47). The initial DNA pool was prepared by PCR
amplification of the template
5'-CTAATACGACTCACTATAGGAAGAGATGGCGACATCTC
(N).sub.4GTGAGGTTGGTGTGGTTG (SEQ ID NOs: 53 and 54) (50 pmoles; N
an equal probability of occurrence of the four nucleotides) in a
500-.mu.L PCR reaction containing 400 pmoles of primer B2,
5'-biotin-GAATTCTAATACGA- CTCACTATrA (SEQ ID NO: 55), and 400
pmoles of primer 1, 5'-CAACCACACCAACCTCAC (SEQ ID NO: 56), with 4
thermocycles of 94.degree. C. (15 sec), 50.degree. C. (30 sec), and
72.degree. C. (30 sec). PCR reaction mixture was prepared as
described previously (16). Amplified DNA was precipitated with
ethanol, resuspended in binding buffer (50 mM HEPES (pH 7.5 at
23.degree. C.), 0.5 M NaCl, 0.5 M KCl, and 0.5 mM EDTA), and the
solution was passed through a streptavidin-derivatized affinity
matrix to generate inunobilized single-stranded DNA.sup.15. The
matrix displaying the pool DNA was repeatedly washed with binding
buffer (1.5 mL over 30 min), and subsequently eluted over the
course of 1 hr with three 20-.mu.L aliquots of reaction buffer in
which HEPES was replaced with 50 mM histidine (pH 7.5, 23.degree.
C.). In rounds 8-11, reaction time was reduced to 25-15 min to
favor those molecules that cleave more efficiently. Selected DNAs
were preciptitated with ethanol and amplified by PCR using primer 1
and primer 2, 5'-GAATTCTAATACGACTCACTATAGGAAGAGATGG- CGAC (SEQ ID
NO: 57), and the resulting PCR was reamplified as described above
to reintroduce the biotin and embedded ribonucleotide moieties.
[0126] Reselection of the class II deoxyribozyme was initiated with
a pool of 10.sup.13 DNAs, each carrying a 39-nucleotide core that
had been mutagenized with a degeneracy of 0.21 per position.
Similarly, HD2 reselection was conducted with an initial pool in
which 26 nucleotides was mutagenized to a degeneracy of 0.33 per
position. Individual from the final selected pools were analyzed by
cloning and sequencing. The DNA pools were prepared for this
process by PCR amplification using primer 2 in place of primer B2.
DNA populations and individual precursor DNAs were prepared for
assays as described previously (7).
[0127] Deoxyribozyme Catalysis Assays
[0128] All catalytic assays were conducted in the presence of 0.5 M
NaCl, 0.5 M KCl, 0.5 mM EDTA. Single turn-over assays contained a
trace amount (.about.50 nM) substrate oligonucleotide and an excess
(1-10 .mu.M) DNA catalyst as described for each assay. The cofactor
used was L-histidine unless otherwise stated. Reactions were
terminated by addition to an equal volume of a solution containing
95% formamide, 0.05% xylene cyanol, and 0.05% bromophenyl blue and
stored on ice prior to gel electrophoresis. Termination buffers
containing both urea and EDTA were incapable of completely
terminating deoxyribozyme activity.
[0129] Caged histidine experiments were conducted with intact
dipeptides or with a concentration of hydrolyzed dipeptide
products. Hydrolysis of dipeptides was achieved by incubating
solutions containing 100 mM dipeptide and 6 N HCl in a sealed tube
at 115.degree. C. for 23 hr. Samples were evaporated in vacuo,
coevaporated with deionized water, and the resuspended samples were
adjusted to neutral pH prior to use.
[0130] Catalytic rate constants (k.sub.obs) either were determined
by determining the initial velocity of the reaction (16) or by
plotting the natural log of the fraction substrate remaining over
time, where the negative slope of the line obtained over several
half lives represents k.sub.obs. The uncatalyzed rate was
determined by incubating a trace amount of 5' .sup.32P-labeled
substrate under reaction conditions in the absence of deoxyribozyme
at 23.degree. C. or at -20.degree. C. for 21 days. Comparative
analysis of RNA phosphoester cleavage indicates that the rate
constant for uncatalyzed RNA cleavage in the presence of histidine
does not exceed the speed of substrate degradation due to
radiolysis. It is expected that the maximum uncatalyzed rate for
cleavage of the embedded RNA linkage does not exceed 10.sup.-8
min.sup.-1. This value is .about.10-fold lower than the value
obtained in the presence of 1 mM Mg.sup.2+ (7).
[0131] The above description is for the purpose of teaching the
person of ordinary skill in the art how to practice the present
invention, and it is not intended to detail all those obvious
modifications and variations of it which will become apparent to
the skilled worker upon reading the description. It is intended,
however, that all such obvious modifications and variations be
included within the scope of the present invention, which is
defined by the following claims. The claims are intended to cover
the claimed components and steps in any sequence which is effective
to meet the objectives there intended, unless the context
specifically indicates the contrary.
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Sequence CWU 1
1
57 1 46 DNA artificial sequence self-cleaving DNA 1 gaattctaat
acgactcaaa gtgagtctgg gcctcttttt aagaac 46 2 34 RNA artificial
sequence H1 ribozyme 2 ggcgacccug augaggccga aaggccgaaa cggu 34 3
56 RNA artificial sequence H2 ribozyme 3 ggcgaaagcc gggcgacccu
gaugaggccg aaaggccgaa acgguagcga gagcuc 56 4 80 RNA artificial
sequence H3 ribozyme 4 ggcgaaagcc gggcgacccu gaugaguugg gaagaaacug
uggcacuucg 50 gugccagcaa cgaaacggua gcgagagcuc 80 5 89 RNA
artificial sequence H6 ribozyme 5 ggcgaaagcc gggcgacccu gaugaugagu
gugugggaag aaacuguggc 50 acuucggugc cagcguaugc gaaacgguag cgagagcuc
89 6 77 RNA artificial sequence H8 ribozyme 6 gaaagccggg cgacccugau
gaguugauac cagcacuucg gugcccuugg 50 cagcaacgaa acggguagcg agagcuc
77 7 35 DNA artificial sequence primer 1 7 gtttcgcatt ggactaagtc
ccaaccacac caacc 35 8 38 DNA artificial sequence primer 2 8
gaattctaat acgactcact ataggaagag atggcgac 38 9 49 DNA artificial
sequence G8 DNA 9 gcagccaagg gtaggagctg gaggatgaca ggcggggtga
taactagaa 49 10 49 DNA artificial sequence G8 DNA 10 ttatatagtc
gagtccattc gaggtaggcg ggaacggtac tggtagaag 49 11 52 DNA artificial
sequence G8 DNA 11 tctcacgtca ggagggtaga ctggtagcga taggcggcgg
ggtgtaacag aa 52 12 50 DNA artificial sequence G8 DNA 12 agagctgtgg
atctggagca aggaaatctcg gtaggcggg tttactagaa 50 13 48 DNA artificial
sequence G8 DNA 13 gccagaacct ccgtaggcgg aaatgagtaaa cattgtaga
agaggggg 48 14 45 DNA artificial sequence G8 DNA 14 gttagaacctc
gtaggcgga aatgagtaaac atgtagaag agggg 45 15 50 DNA artificial
sequence G8 DNA 15 gtttgaggga gacagatgtg gaaggcgggga gattgattc
tctagaaggt 50 16 40 DNA artificial sequence G8 DNA 16 aggtaggcgg
ggaatactaa cgctgttcagt attatagaa 40 17 48 DNA artificial sequence
G8 DNA 17 gtatggggta tatctgaagg cggaaatagct attgggctg ttgtagaa 48
18 50 DNA artificial sequence G8 DNA 18 agcaattcta ggataggcgg
gaaagtggaat atgcgtttc agttgtagaa 50 19 48 DNA artificial sequence
G8 DNA 19 attatggaag acagatgagg gcaggcgggaa tatacacat attaagaa 48
20 43 DNA artificial sequence G8 DNA 20 tgataggcgg ctaaccctgc
ttacgggttat ggttagtta gaa 43 21 43 DNA artificial sequence G8 DNA
21 tgataggcgg gctaacctgc cttcgggttat ggttagtta gaa 43 22 46 DNA
artificial sequence G8 DNA 22 gtatagtgat ctcgggtctc tgtctatgaag
aactgtagc cataat 46 23 44 DNA artificial sequence G8 DNA 23
gtatagtgat ctggggtctg tctatgaagaa ctgtagcca taat 44 24 50 DNA
artificial sequence G8 DNA 24 gtaagggtgt ctgggtctct tctggggaaga
actagagaa tgctgttggc 50 25 49 DNA artificial sequence G8 DNA 25
ctgagtgata taggtgtctg ggtctcttatg acgaatgta attaagaac 49 26 46 DNA
artificial sequence G8 DNA 26 tgtttagaag caggctctta cttatcttctg
ggcctcttt taagaa 46 27 47 DNA artificial sequence G8 DNA 27
tgtttagagg caggctctta atgcttctggg cctcttttt taagaac 47 28 49 DNA
artificial sequence G8 DNA 28 gtgagaagtt tcaattggac gtgagtctggg
tctctttgc gtgaagaac 49 29 39 DNA artificial sequence G8 DNA 29
tgtttagaac gaggctccta cttctggcctc ttttagac 39 30 50 DNA artificial
sequence C1 DNA 30 atagttaaga gcgcgtggta ggcgggaaca aatgtttacg
ttgtgtagaa 50 31 50 DNA artificial sequence C3 DNA 31 tgtttagaag
caggctctta cttatgcttc tgggcctctt ttttaagaac 50 32 87 DNA artificial
sequence C1 variant DNA 32 gaattctaat acgactcact ataggaagag
atggcgacat agttaagagc 50 tcggggtagg cgggaacaac gttcacgttg tgtagaa
87 33 69 DNA artificial sequence self-cleaving DNA 33 gaattctaat
acgactcact ataggaagag atggcgacct agattgagtc 50 tgggcctctt tttaagaac
69 34 46 DNA artificial sequence truncated class II DNA 34
gaattctaata cgactcaga atgagtctgg gcctcttttt aagaac 46 35 21 DNA
artificial sequence S3 DNA 35 gaattctaat acggcttacc g 21 36 28 DNA
artificial sequence C3 DNA 36 cggtaagcct gggcctcttt ttaagaac 28 37
65 DNA artificial sequence DNA with 3 cleavage sites 37 gtcgacctgc
gagctcgact catacgtcga tccctcatgt ggcttaccga 50 agctttacga tctac 65
38 58 DNA artificial sequence DNA with 3 cleavage sites 38
gtcgacctgcg agctttctc ttgctcttct ttgcttcttt ctaagcttta 50 cgatctac
58 39 44 DNA artificial sequence misc_RNA 20...22 portion 1 n is an
RNA A linkage 39 gaattctaat acgactcact nggaagagat ggcgacacac tctc
44 40 18 DNA artificial sequence portion 2 40 gtgaggttgg tgtggttg
18 41 39 DNA artificial sequence misc_RNA 20...22 class I DNA 41
gttgggtcac ggtatggggt cactcgacga aaatgccgg 39 42 39 DNA artificial
sequence class II DNA 42 aggattggtt ctgggtggggt aggagttag tgtgatccg
39 43 40 DNA artificial sequence class III DNA 43 cgggtcgagg
tggggaaaac aggcaaggct gttcaggatg 40 44 40 DNA artificial sequence
class IV DNA 44 aggattaagc cgaattccag cacactggcg gccgcttcac 40 45
38 DNA artificial sequence class II DNA 45 aggattggtt ctgggtgggt
aggaagttag tgtgagcc 38 46 31 DNA artificial sequence HD2 pool DNA
46 ttgatcgggg ctgtgcgggt aggaagtaat a 31 47 66 DNA artificial
sequence misc_RNA 9...11 HD1 n is an RNA A linkage 47 cgactcacat
nggaagagat gcatctcgca gttgggtctg gttgggtagg 50 aagttaatgt gagacg 66
48 65 DNA artificial sequence misc_RNA 11...13 HD2 n is an RNA A
linkage 48 cgactcacta tnggaagaga tgcatctctt gatcgggggc tgtgcgggta
50 ggaagtaata gtgag 65 49 39 DNA artificial sequence primer 49
gaattctaat acgactcacta taggcgaaag ccgggcga 39 50 16 DNA artificial
sequence primer 50 gagctctcg ctaccgt 16 51 18 DNA artificial
sequence primer 51 gtcgacctgc gagctcga 18 52 18 DNA artificial
sequence primer 52 gtagatcgta aagcttcg 18 53 38 DNA artificial
sequence template, part 1 53 ctaatacgac tcactatagg aagagatggc
gacatctc 38 54 18 DNA artificial sequence template, part 2 54
gtgaggttgg tgtggttg 18 55 23 DNA artificial sequence misc_RNA end
primer n is an RNA A 55 gaattctaat acgactcact atn 23 56 18 DNA
artificial sequence primer 56 caaccacacc aacctcac 18 57 38 DNA
artificial sequence primer 57 gaattctaat acgactcact ataggaagag
atggcgac 38
* * * * *
References