U.S. patent application number 10/309690 was filed with the patent office on 2003-07-24 for method for sequencing and characterizing polymeric biomolecules using aptamers and a method for producing aptamers.
This patent application is currently assigned to Praelux Incorporated. Invention is credited to Kwagh, Jae-Gyu, Macklin, John J., Mitsis, Paul G., Ulmer, Kevin M..
Application Number | 20030138831 10/309690 |
Document ID | / |
Family ID | 22470069 |
Filed Date | 2003-07-24 |
United States Patent
Application |
20030138831 |
Kind Code |
A1 |
Kwagh, Jae-Gyu ; et
al. |
July 24, 2003 |
Method for sequencing and characterizing polymeric biomolecules
using aptamers and a method for producing aptamers
Abstract
The present invention relates to methods for sequencing a
polymeric biomolecule and methods for structurally characterizing
the same comprising using aptamers. In a preferred embodiment of
this invention, these methods relate to using the single polymeric
biomolecule. The invention also relates to a method for selecting
aptamers useful for sequencing nucleic acids and aptamers generated
by the method. The invention also provides aptamers that recognize
and bind to AMP, dAMP, GMP, dGMP, CMP and dCMP.
Inventors: |
Kwagh, Jae-Gyu; (Fairless
Hills, PA) ; Macklin, John J.; (Wenonah, NJ) ;
Mitsis, Paul G.; (Trenton, NJ) ; Ulmer, Kevin M.;
(Cohasset, MA) |
Correspondence
Address: |
FISH & NEAVE
1251 AVENUE OF THE AMERICAS
50TH FLOOR
NEW YORK
NY
10020-1105
US
|
Assignee: |
Praelux Incorporated
Lawrenceville
NJ
|
Family ID: |
22470069 |
Appl. No.: |
10/309690 |
Filed: |
December 3, 2002 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10309690 |
Dec 3, 2002 |
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09578634 |
May 25, 2000 |
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6515120 |
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60135863 |
May 25, 1999 |
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Current U.S.
Class: |
435/6.12 ;
435/6.1; 435/7.1 |
Current CPC
Class: |
C12Q 1/6869 20130101;
C12Q 1/6811 20130101; C12Q 1/6869 20130101; C12Q 2525/205
20130101 |
Class at
Publication: |
435/6 ;
435/7.1 |
International
Class: |
C12Q 001/68; G01N
033/53 |
Claims
We claim:
1. A method for sequencing a polymeric biomolecule comprising the
steps of separating a terminal monomer from the polymeric
biomolecule and detecting the separated terminal monomer using an
aptamer.
2. A method for structurally characterizing a polymeric biomolecule
comprising the step of contacting the polymeric biomolecule with an
aptamer that specifically detects a monomer of the polymeric
biomolecule.
3. The method according to claim 1, wherein a single polymeric
biomolecule is sequenced.
4. The method according to claim 1 or 2, wherein the polymeric
biomolecule is selected from the group consisting of a
polynucleotide, a polysaccharide or a polypeptide.
5. The method according to claim 1 or 2, wherein the aptamer is a
single-stranded DNA molecule.
6. The method according to claim 1, wherein the detection step is
carried out at a low temperature.
7. The method according to claim 2, wherein the step of contacting
the polymeric biomolecule with the monomer is carried out a low
temperature.
8. The method according to claim 2, wherein the low temperature is
approximately a temperature between less than 10.degree. C. to
above freezing point.
9. The method according to claim 1, wherein the sequencing is
automated.
10. The method according to claim 1 or 2, wherein a label is
attached to the aptamer.
11. The method according to claim 1 or 2, wherein the method
further comprises the contacting the aptamer with a second factor
which is labeled.
12. The method according to claim 10 or 11, wherein the label is an
optically detectable species.
13. The method according to claim 1, wherein the polymeric
biomolecule is a deoxyribose nucleic acid and the separation step
comprises the use of an exonuclease.
14. The method according to claim 1, wherein the polymeric
biomolecule is a polysaccharide and the separation step comprises
the use of a mixture of exoglycosidases.
15. The method according to claim 1, wherein the polymeric
biomolecule is a polypeptide and the separation step comprises the
use of a carboxy exopeptidase.
16. The method according to claim 1, wherein the separated terminal
monomer is deposited onto a surface.
17. The method according to claim 16, wherein the surface is
passivated against non-specific adsorption of the recognition
molecules.
18. The method according to claim 16, wherein the surface is
patterned into regions of differing hydrophilicity to restrict area
onto which the terminal monomer is deposited.
19. A method for producing an aptamer for recognizing a target
monomer comprising the steps of (1) separating the aptamer from a
mixture of aptamers by subjecting the mixture of aptamers to an
affinity system comprising the target monomer at low temperature,
(2) amplifying the aptamer that bound to the affinity system, and
(3) repeating the separation and amplification steps until the
aptamer having the desired affinity and selectivity for the target
monomer is obtained.
20. The method according to claim 19, wherein the low temperature
is approximately a temperature between less than 10.degree. C. to
above freezing point.
21. The method according to claim 19 and 20, wherein the target
monomer is a ribonucleotide or deoxyribonucleotide.
22. A method for producing an aptamer for recognizing a target
nucleotide or a target nucleoside comprising the steps of
separating the aptamer from a mixture of aptamers using an affinity
system, wherein the affinity system comprises the target nucleotide
attached to a solid support through the 5'-carbon of the sugar ring
of the target nucleotide and amplifying the aptamers bound to the
target by polymerase chain reaction (PCR).
23. The method according to claim 22, wherein the aptamers are
amplified using primers that are labeled.
24. The method according to claim 22, wherein the aptamers are
labeled with fluorescent dye.
25. The method according to claim 22, wherein the target nucleotide
is attached to the solid support through the Hoogsteen on the 5'
carbon on the sugar ring.
26. The method according to claim 22, wherein the separation step
is conducted at a low temperature.
27. The method according to claim 26, wherein the low temperature
is approximately a temperature between less than 10.degree. C. to
above freezing point.
28. An aptamer produced according to the method of claim 19 or
22.
29. A single-stranded nucleic acid molecule comprising a DNA
sequence 5'-CGGRGGAGGNACGGRGGAG-3' (SEQ ID NO: 1), wherein R is G
or A and N is any one of G, A, T or C.
30. The single-stranded nucleic acid molecule according to claim
29, comprising a DNA sequence selected from the group consisting of
SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO:
10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ
ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO:
20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ
ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO:
29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 34, SEQ
ID NO: 35 and SEQ ID NO: 36.
31. A single-stranded nucleic acid molecule comprising a DNA
sequence 5'-GGGAGGGTN.sub.1N.sub.2N.sub.3GGN.sub.4G-3' (SEQ ID NO:
2), wherein N.sub.1, N.sub.2, N.sub.3, and N.sub.4 is any monomer
selected from the group consisting of A, C, G and T.
32. The single-stranded nucleic acid molecule according to claim
31, comprising a DNA sequence selected from the group consisting of
SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID
NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 67; SEQ ID NO: 75
and SEQ ID NO: 76.
33. The single-stranded nucleic acid molecule according to claim
31, wherein N.sub.4 is T or C.
34. A single-stranded nucleic acid molecule comprising a DNA
sequence 5'-GGT N.sub.1N.sub.2N.sub.3GGN.sub.4G-3' (SEQ ID NO: 3)
wherein N.sub.1, N.sub.2, N.sub.3, and N.sub.4 is any monomer
selected from the group consisting of A, C, G and T.
35. The single-stranded nucleic acid molecule according to claim
34, comprising a DNA sequence selected from the group consisting of
SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72; SEQ ID NO: 73 and SEQ
ID NO: 74.
36. A single-stranded nucleic acid molecule comprising a DNA
sequence 5'-TGGGN.sub.1TGGGN.sub.2N.sub.3TGGGN.sub.4AGGGT-3' (SEQ
ID NO: 4 or SEQ ID NO: 90), wherein N.sub.1, N.sub.2, and N.sub.4
is any monomer selected from the group consisting of A, C, G and T
and N.sub.3 is no momomer or any monomer selected from the group
consisting of A, C, G and T.
37. The single-stranded nucleic acid molecule according to claim
36, comprising a DNA sequence selected from the group consisting of
SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 42; SEQ ID
NO: 44, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 54,
SEQ ID NO: 55, SEQ ID NO: 56 and SEQ ID NO: 57.
38. A single-stranded nucleic acid molecule comprising a DNA
sequence selected from the group consisting of SEQ ID NO: 17, SEQ
ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45; SEQ ID NO:
48; SEQ ID NO: 50, SEQ ID NO: 51, SEQ IS NO: 52, SEQ ID NO: 53, SEQ
ID NO: 58, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 69.
39. The nucleic acid molecule according to claims 29-38 that is not
more than 120 nucleotides in length.
40. The nucleic acid molecule according to claim 39 that is not
more than 50 nucleotides in length.
41. The nucleic acid molecule according to claim 29, wherein
upstream of the DNA sequence is a 5' flanking region comprising the
DNA sequence 5'-CCTACT-3' and downstream of the DNA sequence is a
3' flanking region comprising the DNA sequence 5'-AGTAGG-3'.
42. The nucleic acid molecule according to claim 29, wherein
upstream of the DNA sequence is a 5' flanking region comprising the
DNA sequence 5'-AGATG-3' and downstream of the DNA sequence is a 3'
flanking region comprising the DNA sequence 5'-CATCG-3'.
44. The nucleic acid molecule according to claim 42, wherein the 5'
flanking region is 5'-GCCTCATGTCGAACCTACTGGA-3' (SEQ ID NO: 77) and
the 3' flanking region is 5'-GGAAGTAGGTGAGGGAG-3' (SEQ ID NO:
78).
45. The nucleic acid molecule according to claim 31, wherein
upstream of the DNA sequence is a 5' flanking region comprising the
DNA sequence 5'-TCATGTCGAAGGGGCGTATGGGCTTTG-3' (SEQ ID NO: 79) and
downstream of the DNA sequence is a 3' flanking region comprising
the DNA sequence 5'-ACATGT-3'.
46. The nucleic acid molecule according to claim 31, wherein
upstream of the DNA sequence is a 5' flanking region comprising the
DNA sequence TGATCCGCGGCAGTGC-3' (SEQ ID NO: 80) and downstream of
the DNA sequence is a 3' flanking region comprising the DNA
sequence 5'-TGCTTGGAGCAATGGCGATGA- CGGATC-3' (SEQ ID NO: 81).
47. The nucleic acid molecule according to claim 36, wherein
upstream of the DNA sequence is a 5' flanking region comprising the
DNA sequence 5'-AGTGACACCAC-3' (SEQ ID NO: 82) and downstream of
the DNA sequence is a 3' flanking region comprising the DNA
sequence 5'-TGTGGAATCAC-3' (SEQ ID NO: 83).
48. The nucleic acid molecule according to claim 36, wherein
upstream of the DNA sequence is a 5' flanking region comprising the
DNA sequence 5'-AGATCGCCATAAG-3' (SEQ ID NO: 84) and downstream of
the DNA sequence is a 3' flanking region comprising the DNA
sequence 5'-GGAGCAATGGCGAT-3' (SEQ ID NO: 85).
49. The nucleic acid molecule according to claims 29, 31, 34 and
36, wherein one or more of the phosphodiester linkages between the
nucleotides have been replaced with a linkage that increases the
stability of the nucleic acid molecule.
50. The nucleic acid molecule according to claim 29 that recognizes
and binds to a nucleotide selected from the group consisting of an
AMP or a dAMP.
51. The nucleic acid molecule according to claim 31 or 34 that
recognizes and binds to a nucleotide selected from the group
consisting of an CMP or a dCMP.
53. The nucleic acid molecule according to claim 36 that recognizes
and binds to a nucleotide selected from the group consisting of a
GMP or a dGMP.
54. The nucleic acid molecule according to claim 38, wherein the
DNA sequence is SEQ ID NO: 17 and wherein the nucleic acid molecule
recognizes and binds to a nucleotide selected from the group
consisting of an AMP or dAMP.
55. The nucleic acid molecule according to claim 38, wherein the
DNA sequence is selected from the group consisting of SEQ ID NO:
65, SEQ ID NO: 68 and SEQ ID NO: 69 and wherein the nucleic acid
molecule recognizes and binds to a nucleotide selected from the
group consisting of an CMP or dCMP.
56. The nucleic acid molecule according to claim 38, wherein the
DNA sequence is selected from the group consisting of SEQ ID NO:
40, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45; SEQ ID NO: 48; SEQ
ID NO: 50, SEQ ID NO: 51, SEQ IS NO: 52, SEQ ID NO: 53 and SEQ ID
NO: 58, and wherein the nucleic acid molecule recognizes and binds
to a nucleotide selected from the group consisting of an GMP or
dGMP.
57. The nucleic acid molecule according to any one of claims 48-56,
wherein equilibrium dissociation constant of the binding of the
nucleic acid molecule to the nucleotide is one hundred micromolar
to submicromolar.
58. The nucleic acid molecule according to claim 57, wherein the
equilibrium dissociation constant of the binding of the nucleic
acid molecule to the nucleotide is less than 3 .mu.M.
Description
[0001] This application claims benefit from U.S. Provisional
Application No. 60/135,863. The invention herein was made in part
with Government support from the Department of Health and Human
Services. Accordingly, the U.S. Government may have certain rights
in this invention.
TECHNICAL FIELD OF THE INVENTION
[0002] The present invention provides aptamers that recognize and
bind to guanosine (GMP), deoxyguanosine (dGMP), adenosine (AMP),
deoxyadenosine (dAMP), cytosine (CMP) and deoxycytosine (dCMP). The
present invention also relates to a method for sequencing a
polymeric biomolecule and a method for structurally characterizing
the same comprising the use of aptamers. In a preferred embodiment
of this invention, these methods relate to the sequencing or
characterization of a single polymeric biomolecule. The invention
also relates to a method for selecting aptamers useful for
sequencing nucleic acids.
BACKGROUND OF THE INVENTION
[0003] Knowing the primary structure and composition of polymeric
biomolecules, such as DNA, RNA, polysaccharides, lipids and
polypeptides, is important for scientific and medical research and
the development of medical treatments. For example, information
regarding the primary structure of certain polymeric biomolecules
is important for studying the genetic basis of certain diseases,
understanding role that polysaccharides play in cellular
recognition processes, determining the DNA sequence of a purified
protein and producing recombinant proteins for assays for screening
drugs. Thus, fast, accurate and efficient methods for determinating
the primary structure and composition of a polymeric biomolecule,
especially a biomolecule that is long and/or is in short supply,
are important for progress in research.
[0004] DNA Sequencing
[0005] Approaches to sequencing DNA have varied widely. The
Maxam-Gilbert technique for sequencing (Maxam and Gilbert, 1977,
PNAS USA 74:560) involves four separate chemical cleavage reactions
using the same DNA molecules. The partial or total cleavage of the
DNAs, which are end-labeled, produce varying sized DNAs which are
run on a gel electrophoresis apparatus. The sequence of the DNA
molecule is determined from the migratory position of the bands in
the gel. The dideoxy method of sequencing (Sanger et al., 1977,
PNAS USA 74:5463) involves four enzymatic reactions using DNA
polymerase to synthesize fragments of varying lengths due to the
incorporation of a chain terminating dideoxy nucleotide into each
fragment. Typically, radioactively-labeled nucleotide(s) are
incorporated into the growing chains. Variations on the Sanger
method comprise the use of fluorescent dye-labeled primers or
nucleotide chain terminators. The reactions are then run on a gel
electrophoresis apparatus. The sequence of the DNA molecule is
determined from the migratory position of the cleaved bands in the
gel. Fluorescence emissions from the dyes are monitored. These
gel-based, ladder-like output methods are disadvantageous, in part,
because they (1) require substantial amounts of template DNA for
the reactions to occur, (2) produce a relatively small number of
resolvable, visual fragments per reaction, (3) require time for the
separation of the fragments and generation of the ladder, (4)
require resequencing and overlapping sequencing reactions to
determine the primary sequence of a long piece of DNA. A typical
DNA sequencing as described above may yield the sequence of 300-500
nucleotides of a desired nucleic acid.
[0006] Alternatively, sequencing methods involving the use of an
exonuclease to cleave off a terminal nucleotide of a single DNA
molecule have been described. Jett et al. (U.S. Pat. No. 4,962,037)
describes a method wherein a complementary strand of the DNA to be
sequenced is synthesized with nucleotides covalently bonded to a
fluorescent dye. Then, the labeled complementary strand of the
desired DNA is sequenced using exonuclease cleavage. In practice,
the exonuclease cleavage is hindered by the presence of dye on each
nucleotide. Ishikawa (U.S. Pat. No. 5,528,046) describes the use of
monoclonal antibodies against nucleotides A, G, T or C for
detecting nucleotides freed from the DNA being sequenced. The
monoclonal antibody in Ishikawa may be conjugated to a light
emitting reagent, particularly a luminescent enzyme, to facilitate
detection of the freed nucleotide. However, the use of monoclonal
antibodies is disadvantageous, inter alia, because the production
of monoclonal antibodies is labor intensive and requires
considerable animal and cell culture resources for production and
screening.
[0007] Thus, there is a need for alternative, sensitive methods for
rapidly and accurately obtaining the nucleic acid sequence
information. This is especially true for nucleic acid sequences
that are long (greater than 1000 bp) and/or in short supply (less
than nanomolar range).
[0008] 1.2 Protein Sequencing
[0009] Chemical protein sequencing has been and continues to be one
of the most popular methods for determining the primary structure
of proteins. See Stolowitz, "Chemical Protein Sequencing and Amino
Acid Analysis," Curr. Opin. Biotech. 4:9-13 (1993) and Hunkapiller,
M. W., "Contemporary Methodology for the Determination of the
Primary Structure of Proteins," Macromol. Seq. and Synthesis, Ed.
D. H. Schlesinger, pp.45-58, Alan R. Liss: New York, N.Y.
(1988).
[0010] Traditional chemical amino-terminal sequencing includes a
degradation step such as Edman degradation and a detection step.
Edman degradation typically includes a coupling step, a cleavage
step, and a conversion step. For example, in an Edman degradation,
the amino terminus of a target polypeptide is coupled to an
isothiocyanate reagent and then the derivatized N-terminal amino
acid is cleaved from the polypeptide with a strong organic acid.
The reagents of the Edman process may be delivered to the target
polypeptide in a vapor (gas-phase method) or in a liquid pulse
(pulsed-liquid method). The target polypeptide may be covalently
(e.g., with carbonyldiimidazole) or non-covalently (e.g., with
polybrene) attached to a solid support. Solid supports used in
protein sequencing include polyvinylidene difluoride (PVDF), glass
beads or polystyrene beads. The cleaved amino acid is typically
converted to a more stable phenylthiohydantoin (PTH) form by
treatment with an aqueous solution of strong organic acid. The PTH
amino acid may be detected, for example, by high pressure liquid
chromatography (HPLC) with UV absorbance detectors or by mass
spectrometry (Aebersold, R., et al., "Design, Synthesis, and
Characterization of a Protein Sequencing Reagent Yielding Amino
Acid Derivatives with Enhanced Detectability by Mass Spectrometry,"
Protein Science 1:494-503 (1992)).
[0011] In an alternative chemical sequencing method, the
degradation step involves the thioacetylation of the amino-terminal
amino acid, which is detected by gas chromatography/mass
spectrometry (Stolowitz, ML et al., "Thioacetylation Method of
Protein Sequencing: Gas Chromatography/Ion Trap Mass Spectrometric
Detection of 5-acetoxy-2-Methylthiazoles," J. Protein Chem.
11:360-361 (1992)). In another chemical sequencing process, a
peptide ladder generated by Edman degradation is analyzed using
matrix-assisted, laser desorption, time-of-flight mass spectrometry
(Chait, et al., "Protein Ladder Sequencing," Science 262:89-92
(1993)).
[0012] Chemical cleavage of carboxy-terminal amino acids has been
achieved through a variety of methods (Inglis, A. S., "Chemical
Procedures for C-Terminal Sequencing of Peptides and Proteins,"
Analytical Biochemistry 195:183-196 (1991)). For example, the
carboxy-terminus of a polypeptide has been coupled to a thiocyanate
salt or thiocyanic acid (HSCN) to form a thiohydantoin or a
peptidyl isothiocyanate which may be cleaved to form a
thiohydantoin. The thiohydantoin-carboxy terminal amino acid can be
detected by its UV absorption. Other carboxy-terminal cleavage
reactions which do not involve the formation of a thiohydantoin can
be characterized by the formation of (1) an acyl urea; (2) an
O-peptidyl amino alcohol; (3) an N-peptidyl-2-oxazolidone; (4) an
oxazole; and (5) an azide which is converted into an isocyanate.
See, supra, Table 1 in Inglis.
[0013] Enzymatic digestion of terminal amino acids have been used
to sequence polypeptides. Some amino-terminal and carboxy-terminal
specific exopeptidases known in the art are carboxypeptidases (i.e.
Y, A, B, and P), aminopeptidase 1, LAP, proline aminodipeptidase,
leucine aminopeptidase, microsomal peptidase and cathepsin C.
Serine carboxypeptidases have proven to be useful in sequentially
cleaving residue by residue from the C-terminus of a protein or a
peptide. Carboxypeptidase Y (CPY), in particular, is an attractive
enzyme because it non-specifically cleaves all residues from the
C-terminus, including proline. See, e.g., Breddam et al. (1987)
Carlsburg Res. Commun. 52:55-63, U.S. Pat. No. 5,869,240
(Patterson); U.S. Pat. No. 5,792,664 (Chait et al.); and Tsugita et
al. (1992) "C-terminal Sequencing of Protein: A Novel Partial Acid
Hydrolysis and Analysis by Mass Spectrometry," Eur. J. Biochem.
206:691-696.
[0014] The methods described above require at a minimum
subfemtomole concentrations of polypeptide. They are also sensitive
to the purity of the polypeptide sample. For example, the presence
of a co-purifying protein contaminant during the sequencing of a
target polypeptide may give rise to sequencing errors. Further,
carryover of incomplete amino-terminal cleavage into the next cycle
results in a steadily increasing proportion of a population of
molecules being out of phase with the expected order of release.
Finally, recovery and detection of the cleaved amino acid can be
difficult under current methods.
[0015] Thus, there is a need for alternative, sensitive methods for
rapidly and accurately obtaining the primary amino acid sequence
information of polypeptides, especially for longer chain
polypeptides and/or for polypeptides that are in short supply.
[0016] 1.3 Polysaccharide Sequencing
[0017] Polysaccharides play an important role in the regulation of
biological processes in every life form from bacteria to plants to
mammals. For example, carbohydrate moieties in glycoproteins are
have been shown to be involved in protein targeting, cell-cell
recognition, and antigen-antibody reaction (J. C. Paulson, Trends
Biochem. Sci., 14:272 (1989)).
[0018] Technologies for structurally characterizing target
polysaccharides include the use of enzymes, gel permeation
chromatography, high-performance anion exchange pulsed amperometric
detection, electrospray or laser desorption mass spectrometry,
capillary electrophoresis, hydrazinolysis, gas chromatography-mass
spectrometry (GCMS), fast-atom bombardment and liquid secondary ion
mass spectrometry and nuclear magnetic resonance (e.g., Geisow, M.,
"Shifting Gear in Carbohydrate Analysis," Bio/Technology
10:277-280). Methods for isolating and purifying polysaccharides
from proteins or lipids are known (e.g., Welply, J., (1989)
"Sequencing Methods for Carbohydrates and Their Biological
Applications," TIBTECH 7:5-10; Pazur, J., "Neutral
Polysaccharides," Carbohydrate Analysis: A Practical Approach, 2nd
Ed., Eds. M. F. Chaplain and J. F. Kennedy, Oxford University
Press, Inc.: New York, 1994).
[0019] Techniques for determining the sequence of target
polysaccharides include proton NMR, fast atom bombardment mass
spectroscopy, antibody or lectin-binding to the polypeptide to
confirm the presence of a particular oligonucleotide sequence, and
enzymatic digestion. Exoglycosidases commonly used for
oligosaccharide sequencing include mannosidases, hexosaminidases,
galactosidases, fucosidase, neuraminidases, and glucosidases (e.g.,
A. Kobata, Anal. Biochem., 100:1-14 (1979)).
[0020] One approach to carbohydrate sequencing is sequential
digestion of an oligosaccharide with an exoglycosidase of known
specificity (e.g., A. Kobata, in Biology of Carbohydrates, vol. 2.,
Eds. V. Ginsburg et al., John Wiley & Sons: New York (1984),
supra, A. Kobata, Anal Biochem., 100:1-14 (1979)). For example, a
tritiated polysaccharide would be digested with an exoglycosidase.
The cleavage reaction would be monitored by comparing the uncleaved
portion of the polysaccharide before and after exposure to the
enzyme using paper chromatography, gel electrophoresis, and gel
permeation chromatography. This technique is disadvantageous in
that it requires the repeated isolation and determination of the
oligosaccharide size before and after enzyme incubation.
Consequently, this method requires much starting material and time
and effort to isolate the uncleaved portion of oligossacharide.
[0021] Another method, the reagent array analysis method (RAAM),
has been used to sequence polysaccharides (e.g., Prime, S and T.
Merry, "Exoglysidase Sequencing of N-linked Glycans by the Reagent
Array Analysis Method (RAAM)," in Methods in Molecular Biology,
vol. 76: Glycoanalysis Protocols, Ed., E. F. Hounsell, Humana Press
Inc.:New Jersey (1998); C. T. Edge et al., PNAS USA 89:6338 (1992);
U.S. Pat. No. 5,100,778 (Dwek et al.)). This method involves the
digestion of an aliquot of target polypeptide with a defined
mixture of exoglycosidases such that the polypeptide in each
aliquot is digested up to a certain point. This is repeated with
other aliquots of the polypeptide and different, defined mixtures
of exoglycosidases. The uncleaved portion of the polypeptide in
each aliquot is analyzed to identify the sequence of the original
polysaccharide. Consequently, this method also requires much
starting material and time and effort to isolate the uncleaved
portion of the polysaccharide.
[0022] Thus, there is a need for alternative, sensitive methods for
rapidly and accurately obtaining the primary monosaccharide
sequence of polysaccharides, especially for longer chain
polysaccharides and/or for polysaccharides samples which are
limited in supply.
[0023] 1.4 Aptamers
[0024] Aptamers are small single stranded RNAs or DNAs
approximately 40-100 base pairs in length that form secondary and
tertiary structures which bind to other biological molecules. Some
aptamers having affinity to a specific protein, DNA, amino acid and
nucleotides have been described (e.g., K. Y. Wang, et al., "A DNA
Aptamer Which Binds to and Inhibits Thrombin Exhibits a New
Structural Motif for DNA," Biochemistry 32:1899-1904 (1993); Pitner
et al., U.S. Pat. No. 5,691,145; Gold, et al., "Diversity of
Oligonucleotide Function," Ann. Rev. Biochem. 64: 763-97 (1995);
Szostak et al., U.S. Pat. No. 5,631,146). High affinity and high
specificity binding aptamers have been derived from combinatorial
libraries (supra, Gold, et al.). Aptamers may have high affinities,
with equilibrium dissociation constants ranging from micromolar to
sub-nanomolar depending on the selection used. Aptamers may also
exhibit high selectivity, for example, showing a thousand fold
discrimination between 7-methylG and G (Haller, A. A., and Sarnow,
P., "In Vitro Selection of a 7-Methyl-Guanosine Binding RNA That
Inhibits Translation of Capped mRNA molecules, PNAS USA
94:8521-8526 (1997)) or between D and L-tryptophan (supra, Gold et
al.).
[0025] General methods for screening randomized oligonucleotides
for aptamer activity have been described. For example, Gold, et al.
(U.S. Pat. No. 5,270,163) describes the "SELEX" (Systematic
Evolution of Ligands by Exponential Enrichment) method. In Gold et
al., a candidate mixture of single stranded nucleic acid having
regions of randomized sequence is contacted with a target molecule.
Those nucleic acids having an increased affinity to the target are
partitioned from the remainder of the candidate mixture. The
partitioned nucleic acids are amplified to yield a ligand enriched
mixture. Szostak et al. (U.S. Pat. No. 5,631,146) describes a
method for producing a single stranded DNA molecule which binds
adenosine or an adenosine-5'-phosphate. In Szostak, aptamers with
affinity for adenosine or adenosine-5'-phosphate are partitioned
away from aptamers with less affinity using affinity column
chromatography. The ATP column of Szostak has ATP linked to the
agarose through the C8 carbon of the adenine base. The resulting
selected aptamers are unable to recognize portions of the adenine
base especially around the C8 region of the adenine base.
[0026] Aptamers with good specificity and affinity for adenosine
and the bases of other nucleotides are useful, inter alia, for DNA
and RNA sequencing according to the methods of this invention.
Thus, there exists a need for a method for obtaining an improved
selection of aptamers for sequencing and characterizing nucleic
acid molecules.
[0027] The methods of this invention satisfy several objectives.
They provide an alternative, highly sensitive and rapid method for
sequencing a polymeric biomolecule of extended length that does not
require labeling of the target polymeric biomolecule before
sequencing and avoids the repeated isolation and analysis of
uncleaved portions of a polymeric biomolecule of past sequencing
methods. They provide a method for sequencing or characterizing a
single polymeric biomolecule or an amount of polymeric biomolecule
below subfemtomolar range.
SUMMARY OF THE INVENTION
[0028] The invention provides methods for sequencing a polymeric
biomolecule comprising the steps of separating a terminal monomer
from the polymeric biomolecule and identifying the separated
terminal monomer using an aptamer. The separation step comprises
using a cleaving reagent to catalyze the hydrolysis of the terminal
monomer from the polymeric biomolecule. The polymeric biomolecule
may be attached to a solid support. In a preferred embodiment of
this invention, the cleaving agent is an enzyme such as an
exonuclease, an exogylcosidase or an exopeptidase. In a preferred
embodiment of this invention, the cleaved monomer is deposited onto
a surface in a orderly manner for detection by the aptamer. In a
more preferred embodiment of this invention, the surface onto which
the monomer is deposited is a patterned surface with regions of
differing hydrophilicity and/or is passivated against non-specific
adsorption of the recognition molecules. In a preferred embodiment
of this invention, the aptamer is labeled with an optically
detectable species. Preferred polymeric biomolecules for use with
the methods of this invention are DNA, RNA, polypeptides or
polysaccharides. Particularly preferred biomolecules of this
invention are polynucleotides.
[0029] The present invention provides an improved method for
producing aptamers with strong binding affinity and selectivity for
their target monomer comprising the steps of separating the desired
aptamer from a mixture of aptamers by exposing the mixture of
aptamers to an affinity system comprising the target monomer at low
temperature, amplifying the aptamer that bound to the affinity
system, and repeating the separation and amplification steps until
the aptamer(s) having the desired affinity and selectivity are
obtained. The low temperature is approximately a temperature
between less than 10.degree. C. to above freezing point. In a
preferred embodiment, the low temperature is closer to the freezing
point. The method of selection of this invention is particularly
useful for developing aptamers useful for sequencing and
characterizing DNA according to the methods of this invention.
[0030] The present invention also provides a method for producing
an aptamer for recognizing a target nucleotide or nucleoside
comprising the step of separating the aptamer from a mixture of
aptamers using an affinity system, wherein the affinity system
comprises the target nucleotide or nucleoside attached to a solid
support through the 5' carbon of the sugar ring. According to a
preferred embodiment of the invention the target nucleotide is
attached to the solid support through the phosphate on the 5'
carbon of the sugar ring. In a further embodiment of this method,
the separation step is carried out at low temperature, i.e.,
approximately a temperature between less than 10.degree. C. to
above freezing point. In a preferred embodiment, the temperature is
closer to the freezing point.
[0031] The invention provides a single-stranded nucleic acid
molecule that recognizes and binds to AMP and dAMP. The invention
also provides a single-stranded nucleic acid molecule that
recognizes and binds to CMP and dCMP. This invention further
provides a single-stranded nucleic acid molecule that recognizes
and binds to GMP and dGMP. The invention also provides several
specific nucleic molecules that recognize AMP, dAMP, CMP, dCMP, GMP
or dGMP. In one preferred embodiment of the invention, the binding
of the nucleic acid molecule to the nucleotide has a dissociation
constant that is less than 3 .mu.M.
BRIEF DESCRIPTION OF THE DRAWINGS
[0032] FIG. 1 depicts a schematic diagram of the process for
selecting a nucleotide-binding aptamer.
[0033] FIG. 2 is a diagram of the linkage that covalently couples
dAW to an agarose matrix through (a) a 4-atom ethylenediamine
linker, or (b) a 10-atom triethleneglycoldiamine linker
(Jeffamine).
[0034] FIG. 3 depicts the elution profile of round 14 pool for
aptamers that bind dAMP.
[0035] FIG. 4 discloses (a) the sequence of clones obtained from
Round 14 dAMP selection, and (b) the sequence of abridged clones.
DNA amplified from round 14 was either cloned without separating
the DNA based on oligomer length (unprimed clone numbers), or first
gel purified to isolate the band corresponding to 91-mers, (primed
clone numbers). Clone sequence is composed of fixed sequence (lower
case), variable sequence (uppercase), highly conserved or consensus
sequence (boldtype), and complimentary regions (underlined)
flanking the consensus. The sequences have been assigned the
following sequence identifier numbers:
1 Sequence Sequence Identifier dA20 SEQ ID NO:6 dA7' SEQ ID NO:7
dA3' SEQ ID NO:8 dA13' SEQ ID NO:9 dA19 SEQ ID NO:10 dA12' SEQ ID
NO:11 dA21 SEQ ID NO:12 dA18 SEQ ID NO:13 dA4 SEQ ID NO:14 dA6 SEQ
ID NO:15 dA12 SEQ ID NO:16 dA9' SEQ ID NO:17 dA9 SEQ ID NO:18 dA13
SEQ ID NO:19 dA33 SEQ ID NO:20 dA28 SEQ ID NO:21 dA17 SEQ ID NO:22
dA23 SEQ ID NO:23 dA22 SEQ ID NO:24 dA31 SEQ ID NO:25 dA1 SEQ ID
NO:26 dA14' SEQ ID NO:27 dA34.100 SEQ ID NO:28 dA20.77 SEQ ID NO:29
dA19.81 SEQ ID NO:30 dA13'.91 SEQ ID NO:31 dA19.30 SEQ ID NO:32
dA19.43 SEQ ID NO:33 dA13'.58 SEQ ID NO:34 dA13'.51 SEQ ID NO:35
dA13'.37 SEQ ID NO:36
[0036] FIG. 5 depicts the elution profiles for dAMP-aptamers tested
for binding affinity on columns of dAMP-agarose. (a) clone
dA34.100, (b) clone dA20.77, (c) clone dA19.81, (b) clone
dA13'.91.
[0037] FIG. 6 depicts the calculated secondary structure for clones
(A) dA19.30, (B) dA19.81, and (C) dA19.43.
[0038] FIG. 7 depicts the elution profiles providing relative
binding affinity for dAMP for clones (a) dA19.81, (b) dA19.30, and
(c) dA19.43.
[0039] FIG. 8 depicts the elution profile for Clone dA19.30 on
dAMP-agarose with an (a) ethylenediamine linker, (b) or
triethyleneglycoldiamine (Jeffamine) linker.
[0040] FIG. 9 depicts the elution profile on affinity columns of
dAMP-Jeffamine-agarose for clone dA13'.91 folded at (a) 75.degree.
C., and (b) 85.degree. C., for clone dA13'.58 folded at (c)
75.degree. C., and (d) 85.degree. C.
[0041] FIG. 10 depicts the calculated structure and free-energy for
clone dA13'.58 with free energy of (A) -6.6 kcal/mole, (B) -6.8
kcal/mole, and for clone dA13'.51 with free energy of (C) -12.5
kcal/mole.
[0042] FIG. 11 depicts the elution profile on affinity columns of
dAMP-Jeffamine-agarose for the dAMP-aptamers (a) dA13'.51, and (b)
dA13'.58.
[0043] FIG. 12 depicts the elution profiles for the dAMP-aptamer
dA13'.58 on affinity columns of dNMP-jeffamine-agarose, where the
nucleotide N is (a) dAMP, (b) dGMP, (c) TMP, and (d) dCMP.
[0044] FIG. 13 depicts the solution binding titration based on
analytical ultrafiltration for binding of dAMP and clone dA13'.58
at 4.degree. C.
[0045] FIG. 14 depicts the percentage of DNA specifically eluted
vs. round number for the dGMP selection.
[0046] FIG. 15 discloses the (a) sequence of clones obtained from
Round 16 dGMP selection, and (b) sequence of abridged clones. Clone
sequence is composed of fixed sequence (lower case), variable
sequence (uppercase), highly conserverd or consensus sequence
(boldtype), and complimentary regions (underlined) flanking the
consensus. The sequences have been assigned the following sequence
identifier numbers:
2 Sequence Sequence Identifier dG17 SEQ ID NO:37 dG20 SEQ ID NO:38
dG26 SEQ ID NO:39 dG5 SEQ ID NO:40 dG7 SEQ ID NO:41 dG4 SEQ ID
NO:42 dG32 SEQ ID NO:43 dG14 SEQ ID NO:44 dG29 SEQ ID NO:45 dG8 SEQ
ID NO:46 dG21 SEQ ID NO:47 dG36 SEQ ID NO:48 dG3 SEQ ID NO:49 dG35
SEQ ID NO:50 dG37 SEQ ID NO:51 dG15 SEQ ID NO:52 dG19 SEQ ID NO:53
dG17.44 SEQ ID NO:54 dG17.44.g SEQ ID NO:55 dG4.48 SEQ ID NO:56
dG21.52 SEQ ID NO:57 dG15.42 SEQ ID NO:58
[0047] FIG. 16 depicts the elution profiles on
dGMP-Jeffamine-agarose for the abridged clones (a) dG17.44, (b)
dG4.48, (c) dG21.52, and (d) dG15.42.
[0048] FIG. 17 depicts the Elution profile for clone dG17.44 on
affinity columns containing (a) dAMP, (b) dGMP, (c) TMP, and (d)
dCMP.
[0049] FIG. 18 depicts the relative binding affinities of various
G-analog nucleotides and nucleosides for dGMP-aptamer clone
dG17.44.
[0050] FIG. 19 depicts the elution profile for clone dG17.44 in
buffer containing either LiCl, KCl, or NaCl.
[0051] FIG. 20 depicts the solution binding titration based on
analytical ultrafiltration for binding of dGMP and clone dG17.44 at
4.degree. C.
[0052] FIG. 21 depicts the fraction of DNA eluted either
specifically by CMP, or non-specifically by urea, versus selection
round.
[0053] FIG. 22 depicts the elution profile of Round 22 selection
for a CMP-agarose column.
[0054] FIG. 23 discloses the (a) sequence of clones obtained from
Round 22 CMP selection, and (b) sequence of abridged clones. Clone
sequence is composed of fixed sequence (lower case), variable
sequence (uppercase), and highly conserved or consensus sequence
(boldtype). The sequences have been assigned the following sequence
identifier numbers:
3 Sequences Sequence Identfiers C3 SEQ ID NO:59 C10 SEQ ID NO:60
C30 SEQ ID NO:61 C9 SEQ ID NO:62 C25 SEQ ID NO:63 C12 SEQ ID NO:64
C8 SEQ ID NO:65 C32 SEQ ID NO:66 C29 SEQ ID NO:67 C6 SEQ ID NO:68
C1 SEQ ID NO:69 C38 SEQ ID NO:70 C21 SEQ ID NO:71 C17 SEQ ID NO:72
C5 SEQ ID NO:73 C2 SEQ ID NO:74 C3.48 SEQ ID NO:75 C9.58 SEQ ID
NO:76
[0055] FIG. 24 depicts the elution profile of the CMP-aptamer clone
C9.58 on either a CMP- or AMP-agarose affinity column.
[0056] FIG. 25 depicts the elution profile of the CMP-aptamer clone
C3.48 on a CMP-agarose affinity column in column-buffer containing
either NaCl or KCl.
[0057] FIG. 26 depicts the steps involved to fabricate silica
surfaces with amine-terminated linkers, for subsequent covalent
coupling of nucleotides, that exhibit very low non-specific binding
of aptamers.
[0058] FIG. 27 depicts the equilibrium binding curve of a
dGMP-aptamer (clone dG17.44) binding to surface-bound dGMP.
[0059] FIG. 28 discloses fluorescence images showing location of
single dGMP molecules on a surface by binding dye-labeled aptamers
(clone dG17.44 labeled with a single Cy5 dye). Surfaces are
derivatized with either dCMP or dGMP as indicated.
DETAILED DESCRIPTION OF THE INVENTION
[0060] The present invention provides methods for sequencing or
structually characterizing a polymeric biomolecule using an
aptamer, a method for producing an aptamer for recognizing the base
of a nucleotide and aptamers produced by the method.
[0061] Structural information derived from the results of the
method of this invention includes information about any of the
following attributes of the primary structure of the polymeric
biomolecule which can be derived from the interaction of the
aptamer with a monomer of the polymeric biomolecule, e.g., the
monomeric composition of the biomolecule and the order in which the
monomers are linked, including the presence of any branched
structures; the linkage positions between the monomers; and the
linkage configuration.
[0062] A polymeric biomolecule according to this invention is a
molecule which comprises monomers covalently linked together such
as nucleic acids, polypeptides, polysaccharides. In a preferred
embodiment, the polymeric biomolecule is an nucleic acid (RNA or
DNA), a polypeptide or a polysaccharide. A polymeric biomolecule
used in this invention includes long chain biomolecules, e.g., DNA
molecules 50,000 base pairs in length as well as oligomers such as
oligosaccharides, oligonucleotides and peptides which are
approximately 100 monomers or less in length. A polymeric
biomolecule according to this invention may be artificially
synthesized, isolated from nature or modified for ease of use in
the methods of this invention (e.g., polysaccharides may be
neutralized by mild acid or neuraminidase to remove sialic acid, by
alkaline phosphatase to remove phosphate, or with sulfatases or by
chemical means to remove sulfate). A polymeric biomolecule
according to this invention may be bound to another molecule to
form, for example, a glycolipid or a glycoprotein. In this case,
the polymer to be analyzed according to the methods of this
invention may be cleaved off of the molecule to which it is
anchored by methods known in the art or may be analyzed while still
attached to the molecule to which it is anchored.
[0063] An aptamer according to this invention is a small single
stranded nucleic acid molecule approximately 10-120 nucleotides or
20-50 nucleotides that forms secondary and/or tertiary structures
which allows it to bind to a monomer of a polymeric biomolecule of
this invention. Preferred aptamers of this invention are those that
have high affinities, with equilibrium dissociation constants
ranging from 100 micromolar to sub-nanomolar depending on the
selection used, and/or have high selectivity. In a preferred
embodiment for the sequencing method according to this invention,
aptamers with equilibrium dissociation constants less than 3 .mu.M
are used.
[0064] Aptamers according to this invention may be modified to
improve binding specificity or stability as long as the aptamer
retains a portion of its ability to bind and recognize its target
monomer. For example, methods for modifying the bases and sugars of
nucleotides are known in the art. Typically, phosphodiester
linkages exist between the nucleotides of an RNA or DNA. An aptamer
according to this invention may have phosphodiester,
phosphoroamidite, phosphorothioate or other known linkages between
its nucleotides to increase its stability provided that the linkage
does not substantially interfere with the interaction of the
aptamer with its target monomer.
[0065] An aptamer suitable for use in the methods of this invention
may be synthesized by a polymerase chain reaction (PCR), a DNA or
RNA polymerase, a chemical reaction or a machine according to
standard methods known in the art. For example, an aptamer may be
synthesized by an automated DNA synthesizer from Applied
Biosystems, Inc. (Foster City, Calif) using standard
chemistries.
[0066] According to this invention, an aptamer useful for
recognizing and binding a AMP or a dAMP is a nucleic acid molecule
comprising the DNA sequence:
[0067] 5'-CGGRGGAGGNACGGRGGAG-3' (SEQ ID NO: 1),
[0068] wherein R is G or A and N is T, C, A or G. Examples of such
aptamers include SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID
NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13,
SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID
NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23,
SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID
NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32,
SEQ ID NO: 34, SEQ ID NO: 35 and SEQ ID NO: 36. Another aptamer
that recognizes and binds a AMP or dAMP is SEQ ID NO: 17.
Hereinafter, SEQ ID NO: 1 will also be referred to as the consensus
sequence for the A aptamer.
[0069] According to this invention, an aptamer useful for
recognizing and binding a CMP or a dCMP is a nucleic acid molecule
comprising the DNA sequence:
[0070] 5'-GGGAGGGTN.sub.1N.sub.2N.sub.3GGN.sub.4G-3' (SEQ ID NO:
2),
[0071] wherein N.sub.1, N.sub.2, N.sub.3, and N.sub.4 is any
monomer selected from the group consisting of A, C, G and T. In a
preferred embodiment, N.sub.4 is T or C. Examples of sequences of
such molecules include SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61,
SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID
NO: 67; SEQ ID NO: 75 and SEQ ID NO: 76.
[0072] Another aptamer useful for recognizing and binding CMP or
dCMP is a nucleic acid molecule comprising the DNA sequence:
[0073] 5'-GGT N.sub.1N.sub.2N.sub.3GGN.sub.4G-3' (SEQ ID NO: 3)
[0074] wherein N.sub.1, N.sub.2, N.sub.3, and N.sub.4 is any
monomer selected from the group consisting of A, C, G and T.
Examples of sequences of such aptamers include SEQ ID NO: 70, SEQ
ID NO: 71, SEQ ID NO: 72; SEQ ID NO: 73 or SEQ ID NO: 74. Other
sequences for making aptamers that are useful for recognizing and
binding a CMP or dCMP include SEQ ID NO: 65, SEQ ID NO: 68 and SEQ
ID NO: 69. Hereinafter, SEQ ID NOs: 2 and 3 will also be referred
to as the consensus sequences for the C aptamer.
[0075] According to this invention, an aptamer useful for
recognizing and binding a GMP or a dGMP is a nucleic acid molecule
comprising a DNA sequence
[0076] 5'-TGGGN.sub.1TGGGN.sub.2N.sub.3TGGGN.sub.4AGGGT-3' (SEQ ID
NO: 4 or SEQ ID NO: 90),
[0077] wherein N.sub.1, N.sub.2, and N.sub.4 is any monomer
selected from the group consisting of A, C, G and T and N.sub.3 is
no momomer or any monomer selected from the group consisting of A,
C, G and T. Examples of sequences of such aptamers include SEQ ID
NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 42; SEQ ID NO: 44,
SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 54, SEQ ID
NO: 55, SEQ ID NO: 56 and SEQ ID NO: 57. Other sequences that are
useful for making aptamers for recognizing and binding a GMP or
dGMP include SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID
NO: 45; SEQ ID NO: 48; SEQ ID NO: 50, SEQ ID NO: 51, SEQ IS NO: 52,
SEQ ID NO: 53 and SEQ ID NO: 58. Hereinafter, SEQ ID NO: 4 will
also be referred to as the consensus sequence for the G
aptamer.
[0078] To improve binding specificity, affinity and/or stability of
the aptamers comprising SEQ ID Nos. 1-4, the nucleic acid molecule
may be engineered to further contain sequences upstream and
downstream of any one of consensus sequences described above
(hereinafter, 5' flanking region and 3' flanking region,
respectively) to have Watson-Crick base pairing complementarity
with each other. Generally, a useful 5' flanking region according
to this invention will have several contiguous base pairs that are
complementary to the 3' flanking region. The optimal 5' and 3'
flanking regions for increasing the binding affinity, specificity
and/or stability of the aptamer may be determined by preparing an
aptamer pool comprising aptamers with a fixed DNA sequence for the
consensus region and randomized DNA sequences for the flanking
regions, and separating and amplifying the desired aptamer using
the methods of this invention.
[0079] In one embodiment, the nucleic acid molecule comprising SEQ
ID NO: 1 further comprises a 5' flanking region comprising the DNA
sequence 5'-CCTACT-3' and a 3' flanking region comprising the DNA
sequence 5'-AGTAGG-3'. In another embodiment, the nucleic acid
molecule comprising SEQ ID NO: 1 further comprises a 5' flanking
region comprising the DNA sequence 5'-AGATG-3' and a 3' flanking
region comprising the DNA sequence 5'-CATCG-3'. In one preferred
embodiment, the DNA sequences flanking SEQ ID NO: 1 is
5'-GCCTCATGTCGAACCTACTGGA-3' (SEQ ID NO: 77) and
5'-GGAAGTAGGTGAGGGAG-3' (SEQ ID NO: 78) upstream and downstream,
respectively.
[0080] In another embodiment, the aptamer comprising SEQ ID NO: 2
further comprises a 5' flanking region comprising the DNA sequence
5'-TCATGTCGAAGGGGCGTATGGGCTTTG-3' (SEQ ID NO: 79) and a 3' flanking
region comprising the DNA sequence 5'-ACATGT-3'. In another
embodiment, the aptamer comprising SEQ ID NO: 2 further comprises a
5' flanking region comprising the DNA sequence TGATCCGCGGCAGTGC-3'
(SEQ ID NO: 80) and a 3' flanking region comprising the DNA
sequence 5'-TGCTTGGAGCAATGGCGATGACGGATC-3' (SEQ ID NO: 81).
[0081] In another embodiment, the aptamer comprising SEQ ID NO: 4
further comprises a 5' flanking region comprising the DNA sequence
5'-AGTGACACCAC-3' (SEQ ID NO: 82) and a 3' flanking region
comprising the DNA sequence 5'-TGTGGAATCAC-3' (SEQ ID NO: 83). In
another embodiment, the aptamer comprising SEQ ID NO: 4 further
comprises a 5' flanking region comprising the DNA sequence
5'-AGATCGCCATAAG-3' (SEQ ID NO: 84) and a 3' flanking region
comprising the DNA sequence 5'-GGAGCAATGGCGAT-3' (SEQ ID NO:
85).
[0082] Selection of aptamers suitable for use in the methods of
this invention may be derived by creating an affinity column with a
monomer of the polymeric biomolecule attached to it, screening
mixtures of random aptamers using the affinity column, and then
amplifying the aptamers that bound, e.g., following the methods of
Gold, et al. (U.S. Pat. No. 5,270,163) which describes the "SELEX"
(Systematic Evolution of Ligands by Exponential Enrichment)
method.
[0083] The sequencing method according to this invention comprises
the step of separating a terminal monomer from the polymeric
biomolecule. The separation step comprises using a cleaving reagent
to catalyze the hydrolysis of the terminal monomer from the
polymeric biomolecule.
[0084] In a preferred embodiment of this invention, the method for
structurally characterizing the polymeric biomolecule comprises the
step of cleaving one or more linkages between the monomers using a
cleavage reagent. Thus, a cleavage reagent according to this
invention can act by liberating monomers at either termini of the
polymeric biomolecule, or by breaking internal bonds thereby
generating fragments or single monomers of the subject polymeric
biomolecule. Typically, the bond is a peptide bond for a
polypeptide, a glycosidic bond for a polysaccharide, or a
phosphodiester bond for a nucleic acid. A cleavage reagent for the
structural characterizing method may interrupt the primary sequence
by cleaving before or after a specific monomer(s) or may cleave
between all the monomers of the polymeric biomolecule. The cleavage
reagent(s) useful according to the methods of this invention will
depend upon the nature of the polymer and the sequence or type of
structural information desired. Several cleaving reagents are known
in the art for polymeric biomolecules.
[0085] When the biomolecule is to be sequenced according a method
of this invention, the preferred cleavage reagent is an
exohydrolase (i.e., cleaves the linkage between the terminal
monomer and the adjacent monomer). For example, when the
biomolecule to be sequenced is a polypeptide the preferred cleavage
reagent is a mono-exopeptidase. Exopeptidases may cleave at the
carboxy terminus (carboxypeptidases) or the amino-terminus
(aminopeptidases) of a polypeptide. Exopeptidases may be
mono-peptidases and poly-peptidases, such as di-peptidases and
tri-peptidases. This invention contemplates, in one particular
aspect of this invention, the use of carboxypeptidase Y,
carboxypeptidase P, carboxypeptidase A and carboxypeptidase B.
[0086] Also contemplated is the use of aminopeptidases, such as
leucine aminopeptidase, microsomal peptidase, aminopeptidase 1,
LAP, proline aminodipeptidase and cathepsin C and so forth.
Exopeptidases are commercially available, for example from reagent
suppliers such as Sigma Chemicals (St. Louis, Mo.) and Oxford
Glycosystems (Rosedale, N.Y.).
[0087] Preferred exoglycosidases for polysaccharide sequencing
include but are not limited to alpha-Mannosidese I,
alpha-Mannosidese, beta-Hexosaminidese, beta-Galactosidase,
alpha-Fucosidase I and II, alpha-Galactosidase, alpha-Neuraminidase
and, alpha-Glucosidase I and II. Representative lists of useful
exoglycosidases may be found, for example, in A. Kobata, Anal.
Biochem., 100, 1 (1979), R. Parekh et al., PCT Application No. WO
92/19768 (Nov. 12, 1992), T. W. Rademacher et al., U.S. Pat. No.
5,100,778 (Mar. 31, 1992), and R. J. Linhardt et al., U.S. Pat. No.
5,284,558 (Feb. 8, 1994), Kobata, A., in Biology of Carbohydrates,
Volume 2, V. Ginsburg et al., ed., John Wiley & Sons, New York,
pp. 88 ff. (1984)) all of which are incorporated herein by
reference. It is to be understood that these lists are illustrative
only and in no way limit the selection of exoglycosidases used
herein.
[0088] Preferred exonucleases for nucleic acid sequencing include,
but are not limited to lambda-exonuclease, t7 Gene 1 exonuclease,
exonuclease II, exonuclease I, exonuclease V, exonuclease II, DNA
polymerase II, venom phosphodiesterase, spleen phosphodiesterase,
Bal-31 nuclease, E. coli exonuclease I, E. coli exonuclease VII,
Mung Bean Nuclease, S1 Nuclease, an exonuclease activity of E. coli
DNA polymerase 1, an exonuclease activity of a Klenow fragment of
DNA polymerase 1, an exonuclease activity of T4 DNA polymerase, an
exonuclease activity of T7 DNA polymerase, an exonuclease activity
of Taq DNA polymerase, an exonuclease activity of DEEP VENT DNA
polymerase, and an exonuclease activity of VENTR DNA
polymerase.
[0089] The cleavage reagent according to this invention may
alternatively be a chemical compound, such as those known in the
art for catalyzing the cleavage of the terminal monomers of
polymeric biomolecules or partial or total cleavage of all the
linkages between the monomers of the polymeric biomolecules. See,
supra, background section of this application. Currently preferred
agents other than an enzyme include but are not limited to:
cyanogen bromide, hydrochloric acid, sulfuric acid, and
pentafluoroproprionic fluorohydride. In some embodiments,
hydrolysis can be accomplished using partial acid hydrolysis in
accordance with the methods disclosed herein.
[0090] Any of the aforementioned cleavage reagents may be suitable
for elucidating the structure of the polymeric biomolecule
according to the method of this invention. Enzymes which may
degrade the linkages between the internally located monomers of the
polymeric biomolecules are known, for example, endonucleases,
endopeptidases, and endogycosylases (e.g., A. Kobata, Anal.
Biochem., 100, 1 (1979)). The instant method provides for the use
of combinations of the above-described individual cleaving agents
to structurally characterize the polymeric biomolecules. For
example, chemical cleaving agents may be used with enzymatic
cleaving agents or enzymatic cleaving agents from one class or
different classes may be used together (e.g., a mixture of
exonucleases versus a mixture of an endoprotease and a
endopeptidase). Two or more cleaving agents may be used
simultaneously or sequentially on a polymeric biomolecule. The
exact combination and the circumstances under which such a
combination is appropriate will depend upon the nature of the
polymer and the information desired.
[0091] The methods of the invention is useful for polymeric
biomolecules of either known or unknown structure. In the case of a
known or putative structure, as where synthetic polymeric
biomolecules are obtained from a commercial supplier or isolated
from a glycoprotein of known or suspected structure, a combination
of cleavage agents can be designed to verify or confirm the
putative structure or sequence. For example, an enzymatic array may
be designed to cleave verify or confirm the structure of a
polysaccharide, as described in U.S. Pat. No. 5,753,454 (Lee)
incorporated by reference. If the oligosaccharide of unknown
structure is known to be an N-linked oligosaccharide, knowledge of
the common core structure of N-linked oligosaccharides, as
described above, can be used to design a suitable enzyme array.
[0092] The term "array" is used to convey the underlying principle
of the cleavage protocol utilized in U.S. Pat. No. 5,753,454 (Lee)
and further described as "Reagent Array Analysis" in Rademacher et
al., U.S. Pat. No. 5,100,778 (Mar. 31, 1992), incorporated herein
by reference. Essentially, two or more suitable cleaving agents are
selected, and an array of reagents is prepared such that each
reagent lacks one of the selected cleaving agents. In a variation
of the invention, one or more reagents can lack two of the selected
cleaving agents. Each aliquot is then reacted with a different
reagent to cleave the polymeric biomolecule and produce a plurality
of cleaved products. The reaction is typically carried out for a
predetermined amount of time, or to a predetermined end point, such
that the reaction is carried to completion. This method is
particularly useful for sequencing according to the method of this
invention. The released fragments or monomers are separated and/or
deposited onto a surface for analysis by aptamers which recognize
the monomers or monomers within the fragments.
[0093] In one preferred embodiment of this invention, polymeric
biomolecules are sequenced or characterized by (a) a separation
step comprising: cleaving the polymeric biomolecule which is
attached to a solid support, transporting the cleaved fragment or
monomer away from the uncleaved portion of the polymeric
biomolecule; and depositing the cleaved fragment or monomer onto a
surface; and (b) a detection step comprising the binding of
aptamers to the monomers on the surface or the monomers in the
fragment. In one embodiment of this invention, the polymeric
biomolecule is covalently attached to the solid support. In another
embodiment, the polymeric biomolecule is attached to the solid
support through a biotin-streptavidin interaction. In another
preferred embodiment of this invention, a mixture of exohydrolases
such as a mixture of exoglycosidases or a mixture of
carboxyexopeptidases are exposed to the polysaccharide or
polypeptide, respectively, under conditions which allow processive
degradation of the polymer from one terminus. In another preferred
embodiment of this invention, DNA sequencing is performed according
to the method provided in U.S. Pat. No. 5,674,743 (Ulmer)
(incorporated by reference) except that the detection step
comprises binding aptamers labeled with an optically detectable
species to each separated nucleotide and detecting each separated
nucleotide by the spectrosopic emission of the label.
[0094] Solid supports useful for binding to a polymeric biomolecule
according to this invention will depend upon the type of polymeric
biomolecule being analyzed and the type of method being performed.
For example, for carboxypeptidase sequencing, the polypeptide of
interest should not be attached to the solid support at or near its
C-terminus. Solid supports useful for binding to polysaccharides,
polypeptides, and nucleic acids are known in the art, e.g., glass
beads, cellulose beads, polystyrene beads, SEPHADEX beads,
SEPHAROSE beads, polyacrylamide beads and agarose beads (e.g.,
Ghosh, S. S. and Musso, G. F., "Covalent Attachment of
Oligonucleotides to Solid Supports," Nucleic Acids Research.
15:(13) 5353-5372 (1987); U.S. Pat. No. 4,992,383 (Farnsworth);
incorporated by reference). In one embodiment, the polymeric
biomolecule is covalently attached to the solid support. In another
embodiment, the polymeric biomolecule is attached to the support
through a biotin-streptavidin interaction.
[0095] The aptamers used in the sequencing or physical
characterization methods of this invention may be labeled or may be
tagged (e.g., biotinylated), but the label or tag should not
substantially interfere with the interaction of the aptamer with
the cleaved monomer or fragment. Alternatively, to boost the signal
derived from the binding of the aptamer to the monomer of the
polymeric biomolecule and/or increase the sensitivity of the
method, the methods of this invention may additionally comprise the
step of contacting a secondary factor to the aptamer that is bound
to the monomer. This secondary factor, for example, may be an
aptamer, an antibody, a protein or a compound which is labeled and
recognizes the aptamer or a tag which is bound to the aptamer.
Preferably, a label according to this invention is an optically
detectable species such as fluorophore. In one embodiment, such as
for sequencing DNA, aptamers for each nucleotide shall be labeled
with a different fluorophore. The aptamers may optionally have two
or more of the same fluorophores attached to them. Preferably, such
as for sequencing, the wavelength emissions of each fluorophore
should be measurably distinct from each other so as to facilitate
identification of the cleaved nucleotide. Fluorophores useful in
the methods of this invention are commercially available such as
TAMRA, Hoechst dye, fluorescein, rhodamine, Texas Red, or the 40 nm
fluorescent beads sold by Molecular Probes TransFluoSpheres, which
can attached to an aptamer or protein by standard methodologies.
Dye labels may be laser-excited using confocal, evanescent-wave or
other geometries for low background detection of the individual
labels.
[0096] In a preferred embodiment of this invention, the steps of
the sequencing method or the physical characterization method are
optimized for automation. In another preferred embodiment of this
invention, the cleaved monomer or the released portion of the
polymer biomolecule is deposited onto a surface in an orderly
manner such that it is separated from prior and subsequently
cleaved monomers/released portions of biomolecule. A mixture of
aptamers, at least one of which is expected to bind to a monomer,
can be applied to the surface having the cleaved monomer or
released portion of biomolecule under conditions which favor
aptamer binding. The surface onto which the monomer is deposited
may be washed before and after an aptamer is bound to the monomer
or released portion of the biomolecule. Then, the identity of the
aptamer can be determined as described above.
[0097] In a preferred embodiment, the surfaces according to this
invention which bind the cleaved monomer have been prepared to bind
the cleaved monmer in an orderly fashion. For example, the surface
will have binding sites for the monomer. In a preferred embodiment,
the binding site is situated such that a nucleotide will bind to it
through its 5' phosphate group thereby forming a phosphoroamidite
bond. In a further embodiment, the surface will be treated to
reduce non-specific binding, e.g., treated with polyethylene
glycol. In a further embodiment of this invention, the surface is
patterned so as to facilitate containment of the cleaved monomer to
a region on the surface and/or create a reaction chamber to
facilitate the binding of the monomer to the pre-treated
surface.
[0098] Preferably, fluorescent autoradiation from the label on the
aptamer, protein or compound used in the methods of this invention
will be detected by a microscope. The emitted autoradiation may be
directed by the microscope onto detection elements such as a
charged-coupled device (CCD) camera. For example, in the sequencing
method according to this invention, the microscope may have four
unique optical filters each connected to a CCD camera such that
only one of the four dyes used with each aptamer will be recorded
by each CCD camera. The CCD camera will then convert the emitted
autoradation into an electrical signal which is read by a computer.
Framing times can be faster than one field-of-view per second,
i.e., 25 bases/second per strand of DNA. A 50 kB DNA strand may
take approximately 30 minutes to read. One example of the DNA
sequencing envisioned by this invention described below.
Base-at-a-time sequencing of DNA is accomplished by the sequential
and repeated enzymatic hydrolysis of the terminal nucleotide of a
strand of DNA whose sequence of bases is to be determined. The DNA
strand is held fixed at the end distal to the enzymatic hydrolysis
in a channel containing aqueous buffer under laminar flow
conditions. Nucleotides released following enzymatic hydrolysis are
entrained in the flowing buffer, and move away from the stationary
DNA at an average speed determined by the buffer flow speed. The
channel containing the single DNA strand additionally acts as a
dispenser of the flowing buffer into isolated drops onto a moving
nucleotide-capture surface. Drop isolation prevents any mixing of a
nucleotide from one drop to another, thus preserving their order.
To minimize the probability that two nucleotides end up in one drop
(thereby confusing their order), this channel dispenser divides the
flowing buffer between entrained nucleotides into approximately
3-10 drops; i.e. more drops than nucleotides, to insure that any
two sequential nucleotides are spaced apart by drops containing no
nucleotides. The dimensions of the channel, the speed of the buffer
flow, the speed of the moving capture surface, the drop volume, and
the rate of enzymatic digestion are all chosen to provide drops on
the surface which preserve the order of hydrolyzed nucleotides at a
spacing larger than the resolution of the detection apparatus,
typically greater than 0.5 microns. This process of hydrolysis of
nucleotides into flowing buffer that is subsequently dispensed onto
a moving surface is continued until the full length of the DNA
strand in question is digested. Preferably, the process is
multiplexed, so that a plurality (Nchannels, each with one DNA
strand and side-by-side, dispense drops onto the nucleotide-capture
surface in N separate lanes, each lane containing the nucleotides
from only one DNA stand. Subsequent parallel processing and readout
of the surface-bound nucleotides greatly improves the effective
sequencing rate.
[0099] The use of the nucleotide-capture surface provides a
potentially permanent physical recording of the order of nucleotide
molecules from the DNA strand whose sequence was in question. To
make a permanent record which can subsequently be washed and
otherwise be treated in batch format, the nucleotides are
covalently coupled to the surface. The surface substrate is
preferably silica, silicon, glass, or plastic, functionalized to
enable covalent coupling of nucleotides. Functionalized surfaces
made be obtained using conventional silanization methods to
incorporate reactive groups, or by thin-film deposition of polymers
containing reactive functional moieties. The functional group is
chosen to facilitate covalently binding of nucleotides, preferably
through the phosphate or hydroxyl group of the nucleotide sugar,
i.e. a group common to a nucleotide of any base, either directly as
a consequence of droplet evaporation, or from droplet solution by
the action of a coupling reagent, that is either present on the
surface prior to drop dispensing, or mixed into the flowing buffer
prior to drop dispensing, or added after the drop has been
dispensed. Preferably, the surface is otherwise passive to the
absorption of nucleotides, or reagents that detect nucleotides.
Preferably, the functional group is an amine that terminates a
surface-bound linker, to which the nucleotide is covalently coupled
in the presence of imidazole and a carbodimide, e.g., EDAC. See
Example 4. The surface may additionally be patterned to help
maintain or contain the drops from the dispenser. Patterns of
hydrophillic patches separated by hydrophobic regions, or patterns
of surface depressions (nanowells) serve this purpose, and can be
obtained by replication from a master generated by standard
lithographic techniques.
[0100] The steps for detecting and identifing the nucleotides
spatially to determine their sequence could be carried out as
follows. Base-specific nucleotide affinity reagents such as the
aptamers are pooled into a solution, where each aptamer that binds
a specific base has been synthesized to include a unique label,
preferably a dye or group of dyes or dye FRET-dye pairs
(Fluorescent Resonant Energy Transfer) that yield a distinguishable
measurement, e.g. in their spectral or temporal fluorescence
properties. The concentration of each type of aptamer is adjusted
to be approximately 10-100 times the value of the equilibrium
binding constant for its specific ligand nucleotide. The substrate
containing the surface-bound nucleotides is incubated in the
solution containing the pooled aptamers for a sufficient time to
allow equilibrium to be reached. This surface is then washed free
of solution phase aptamers and the weak, non-specifically-bound
aptamers possibly on the surface. The wash time should be short
enough so that specifically-bound aptamers are not removed in any
significant number. The surface is then dried to immobilize the
specifically-bound aptamers at the location of their respective
nucleotide ligand. The substrate is then scanned under appropriate
illumination, and the fluorescence from the dye-labeled aptamers
recorded as a function of position on the surface. By
discrimination of the fluorescence properties, a map of the
identity and location of nucleotides on the surface is obtained,
and thus of the sequence of the original DNA in question.
[0101] The present invention provides a method for producing an
aptamer for recognizing a target monomer comprising the steps of
(1) separating the aptamer from a mixture of aptamers by subjecting
the mixture of aptamers to an affinity system comprising the target
monomer at low temperature, (2) amplifying the aptamer that bound
to the affinity system, and (3) repeating the separation and
amplification steps until the aptamer having the desired affinity
and selectivity for the target monomer is obtained. The low
temperature referred to above is approximately a temperature
between less than 10.degree. C. to above freezing point. In one
embodiment, the low temperature is 4.degree. C. In a preferred
embodiment, the temperature is closer to the freezing point.
[0102] An affinity system according to this invention is a system
for selecting the aptamer for the target monomer by using the
target monomer to bind to the desired aptamer and then eluting the
desired aptamer from binding to the target monomer. For example,
the affinity system may be a target nucleoside or nucleotide bound
to a solid support. In a preferred embodiment, an affinity system
according to this invention also comprises pre-selection and/or
counterselection to screen out undesireable aptamers.
[0103] Pre-selection involves filtering out aptamers which bind to
the matrix or solid support by, for example, exposing the aptamer
pool to the solid support of the affinity sytem, wherein the solid
support does not have target monomers bound to it.
[0104] Counterselection involves using a monomer of the polymeric
biomolecule to be sequenced, other than the target monomer, or some
part thereof, to bind and remove the undesirable aptamers.
Undesireable aptmers are aptamers that bind to a monomer other than
the target monomer and/or the matrix or solid support. Thus,
aptamers that did not bind to the other monomer or part thereof or
solid support, would be collected. For example, in order to obtain
an aptamer with high selectivity to dAMP, one could counterselect
with dCMP, dGMP and dTMP. The amplification step according to this
invention is carried out by using polymerase chain reaction
(PCR).
[0105] The present invention also provides a method for producing
an aptamer useful for nucleic acid sequencing. Specifically, the
method provides aptamers for recognizing the base of a target
nucleotide comprising the step of partitioning the aptamer from a
mixture of aptamers using an affinity system, wherein the affinity
system comprises the target nucleotide attached to a solid support
through the 5' carbon of the sugar ring of the target nucleotide.
Preferably, the target nucleotide is attached to the solid support
through the Hoogsteen on the 5' carbon of the sugar ring to allow
maximum interaction with the base and decreased background binding
to the surface. The selected apatmer is then subjected to
polymerase chain reaction (PCR) for amplification and converted to
single-stranded DNA by asymmetric PCR. The single-stranded DNA is
reformed into an aptamer, subjected to the same affinity system,
eluted from the affinity system, amplified by PCR and converted
into single-stranded DNA. This process is repeated for 11+
rounds.
[0106] In a particularly preferred embodiment, the target
nucleotides are orientated and positioned on the solid support in
approximately the same orientation and position that the cleaved
nucleotides take on the surface in the above sequencing method,
infra. In this way, the selection process and a sequencing method
of this invention are "self-consistent" with each other.
[0107] In another preferred embodiment, the 5' end of the primer
DNA used in the PCR reactions is labeled with a fluorophore such as
N,N,N',N'-tetramethyl-6-carboxyrhodamine (TAMRA), to allow
quantitative measurements of the amount of labeled aptamer DNA
recovered during elution.
[0108] Preferred solid supports for selecting aptamers for nucleic
acid sequencing are those that are capable of binding to the
nucleotide through the Hoogsteen on the 5' carbon of the sugar ring
and exhibit little non-specific binding to nucleotides. In another
preferred embodiment, the, surface of the solid support is modified
to reduce non-specific binding, for example using polyethylene
glycols (PEG) (Sigal et al., (1996) Anal Chem, 68, 490-497). Other
strategies for enhancing the affinities and selectivities of
aptamers are known (Eaton et al., (1997) Biorg & Med Chem., 5,
1087-1096; Kawakami J, et al. (1997) Nucleic Acids Symp Ser., 37,
201-202).
[0109] The concentration of the nucleotide on the surface of the
affinity column should be sufficient to isolate aptamers against
the individual nucleotides without recovering aptamers against
closely spaced dimers of nucleotide. Preferably, the concentration
range of the nucleotides attached to the surface of the affinity
column is 50 .mu.M-500 .mu.M (approximately 30 Angstrom to 300
Angstrom distance between nucletides). Preferably, the solid
support columns used in the later rounds of selection have a
decreasing concentration of target nucleotide attached to them.
[0110] In another preferred embodiment of the selection method, the
mixture of aptamers is subjected to counter selection against the
surface of the solid support alone and other non-target nucleotides
before or after the aptamer mixture is passed through the affinity
column to minimize the nonspecific binding of the selected
aptamers. In a more preferred embodiment, the mixture of aptamers
are subject to counter selection subsequent to the initial
selection. Preferentially, such counter selection is be
incorporated into the final selection rounds. Such counter
selection will decrease the representation of cross reacting
aptamers in the pool. Preferably, the selectivity of the aptamer
exceed 100 fold for the target nucleotide over a non-target
nucleotide (i.e. for 99% detection accuracy).
[0111] In one embodiment of the invention, the properties of the
selected aptamer may be improved by replacing selected residues in
the aptamer. For example, a pyrimidine may be replaced with a 2'
fluoro-pyrimidine to increase the affinity of the aptamer. In
another embodiment of the invention, the aptamer backbone may be
replaced by phosphorothioate or phosphoroamidite to increase the
stability of an aptamer or its affinity for its target. In another
embodiment of this invention, mixtures of aptamers may be exposed
to the target nucleotide and then subjected to crosslinking such
that a covalent linkage is formed between the relevant aptamers and
target nucleotides. However, the modifications to the DNA aptamer
should not substantially interfere with PCR amplification of
modified nucleotides. Alternatively, after selection of a suitable
group of aptamers, the aptamers may be modified and then be
partitioned to select for improved affinity and selectivity.
[0112] Modification may also be made to the aptamer to limit the
non-specific binding of the aptamer. For example, the Hoogsteen
backbone may be modified such that a peptide nucleic acid (PNA)
aptamer is formed. Given its neutral charge, a PNA should exhibit
improved binding to a negative nucleotide and essentially be inert
to any surface designed to bind nucleotide through interaction of
the Hoogsteens. This would have the double advantage of enhanced
affinity and decreased non-specific surface binding.
[0113] Unless specifically stated, the term "nucleotide" as used
herein is meant to include a nucleoside.
[0114] In order that the invention described herein may be more
fully understood, the following examples are set forth. These
examples are for illustrative purposes only and are not to be
construed as limiting this invention in any manner.
EXAMPLES
Example 1
[0115] Selection of dAMP-Specific Aptamers
[0116] The following example illustrates the selection, isolation,
and characterization of oligonucleotide aptamers that specifically
bind the nucleotide dAMP but not nucleotides containing the bases
guanine, cytosine, or thymine. In order to provide a highly diverse
initial pool of DNA sequence, from which ligand-binding aptamers
can be obtained, single-stranded DNA was synthesized that contained
a 42-base segment where at each position bases where incorporated
with equal probability. This variable sequence was flanked by
fixed-sequence segments: 5'-
4 GGCAAGCTTGGGCCTCATGTCGAA-(N).sub.42- (SEQ ID NO:5)
GAGCAATGGCGATGACGGATCCTCA-3'.
[0117] The fixed-sequence segments are necessary for subsequent
amplification, and are complimentary to the primers used for PCR.
The 42-base random sequence can in principle yield up to 10.sup.25
unique sequences, but practical constraints on DNA synthesis yield
(on order of nmoles) limits the diversity to at most 10.sup.15
sequences. Filtering of this initial pool of DNA is then obtained
by the process of repeated rounds of selection for a target ligand
(here dAMP) using affinity chromatography, followed by PCR
amplification of specifically-eluted oligos, to yield an enriched
pool of dAMP-binding DNA. This general scheme is indicated in FIG.
1.
[0118] An initial pool (3 nmole) of ssDNA containing a 42-base
segment of randomized sequence flanked by primers of fixed
sequence, was folded (75.degree. C. for 5 min, cooled to room
temperature over 20 min.) in 100 mL of column buffer (0.3 M NaCl,
20 mM Tris, pH 7.6) and applied to an affinity column containing a
1-mL bed of dAMP-ethylenediamine-agarose (350 nmole/mL) that had
been pre-equilibrated with 10 mL of column buffer. Nucleotide
coupling to the agarose matrix is shown in FIG. 2(a). After a
10-minute incubation, the column was washed with 10 mL of column
buffer to remove weakly-bound oligos. The bound oligos were then
eluted with 4 mL of 8M Urea. The wash and elution were collected in
2 mL fractions. The fractions containing the eluted DNA were
pooled, ethanol-precipitated, amplified by PCR, and purified for
size on an agarose gel. Size purification was important in later
rounds as increasing amounts of high-molecular weight DNA was
generated by PCR (which was subsequently found to be a PCR
artifact). This selection procedure was repeated up to round 6. For
all rounds after the first round, the elution profile was monitored
by fluorescence from a TAMRA dye that labeled the 5'-primer. At
round 7, the elutant for bound DNA was changed from urea to 4 mL of
3 mM dAMP, to force specificity in the pool for the dAMP
nucleotide. At round 8 and above, the selection conditions were
made more stringent by washing with 4 mL of 3 mM dGMP or dCMP prior
to elution, to remove the fraction of bound aptamers with
undesirable cross-specificity for a guanine- or cytosine-containing
nucleotide. At round 11, 5 mM MgCl.sub.2 was added to the column
buffer. This had a significant effect on improving the fraction of
the pool that specifically bound to the affinity column. Selection
continued to round 14, where the fraction of DNA eluted with dAMP
was 35%. The elution profile for round 14 is shown in FIG. 3.
[0119] The selected DNA aptamer from round 14 were primer-extended
to double-stranded DNA by PCR amplification, and cloned into the
pCRII cloning vector. The round 14 pool was cloned and sequenced
under two conditions. In the first batch, the pool was
PCR-amplified and cloned without gel-purification for size. Here,
36 clones were sequenced, of which 28 contained acceptable sequence
reads. In the second batch, the round 14 pool was amplified and
gel-purified for size, selecting only those sequences corresponding
to 91-mers. Here, 14 clones were sequenced, of which contained
acceptable sequence reads.
[0120] The sequences obtained from cloning are shown in FIG. 4(a).
The sequence derived from the 42-base variable segment is shown in
uppercase, while the fixed primer sequence is shown in lowercase.
The sequences are grouped to emphasize the consensus (boldtype)
sequence contained within flanking complimentary sequences
(underlined). The consensus consists of a 19-base sequence CGG RGG
AGG NAC GGR GGAG (SEQ ID NO: 1), of which 14 bases are absolutely
conserved, 2 bases very highly conserved (only clone 14 differs),
two bases that are strictly purines R, and one base N that is
mostly not a G. The consensus is guanine-rich (63% G) for the dAMP
aptamer clones. As FIG. 4(a) shows, the batch 1 clones obtained
without size selection are almost all 115-mers, although the
starting aptamer was 91 bases in length. As noted above, in early
rounds the PCR-amplified DNA pools, run on an agarose gel,
contained only 2 bands (ss and ds DNA of one size of .about.90
bases), while in later rounds additional bands appeared, and these
dominated the pool in the final rounds, even though they were
gel-isolated and rejected at each round. The additional bands
appear to be a sequence-dependent PCR artifact that produced a
ladder of bands from the 91-mer DNA. However, there is agreement in
the consensus sequence for both long (115-mers) and short (91-mers)
clones. Initially, clones from both size classes were examined.
[0121] Four clones (dA19, 20, 34, 13') were synthesized for binding
assays. In addition to the random sequence region, approximately 10
bases of the fixed sequence at the 5' end and all 24 bases of the
fixed sequence at the 3' end were included. These sequences are
shown in FIG. 4(b). The synthesized clones, each labeled with a
TAMRA dye at the 5' end, were folded and tested on separate
dAMP-ethylenediamine-agarose columns (350 nmole dAMP/mL of gel, 1
mL bed) to determine relative binding affinity. As shown in FIG. 5,
all four clones bind to the dAMP column, and differ mainly in the
fraction that passes through in the first 1-2 fractions, which for
each clone is the fraction not properly folded to bind dAMP.
[0122] In order to show that the consensus region present in all of
the clones is required for binding the dAMP ligand, clone dA 19 was
examined in greater detail. As shown in FIG. 6, the ssDNA oligo can
be predicted to be folded to contain two loop regions held together
by two stem regions (defined by Watson-Crick base-pairing). Of the
two loops, only one contains the consensus (in boldfaced).
[0123] Two abridged versions of clone dA19 were synthesized,
dA19.30 containing the loop with the consensus sequence and one
stem, and dA19.43 containing the second loop flanked by a stem on
either side but not containing the consensus region. As shown in
FIG. 7, the elution profiles run on separate
dAMP-ethylenediamine-agarose affinity columns for these oligos
indicate that while the 30-mer dA19.30 binds almost as well as the
81-mer dA19.81, the 43-mer, which does not contain the consensus,
washes of the column in the first three fractions. This test
indicates that the loop containing the consensus is necessary for
binding, and that much of the sequence of the 81-mer is
unnecessary.
[0124] The effect of the length of the linker used to covalently
bind nucleotide ligands to the agarose matrix for the affinity
columns used here was tested using the shortened aptamer dA19.30.
In FIG. 8, the elution profiles for this aptamer on aragose gel
containing 200 nmole/mL coupled via a 4-atom ethylenediamine linker
[FIG. 2(a)] or a 10-atom triethyleneglycol diamine (jeffamine)
linker [FIG. 2(b)] are shown. Both affinity columns exhibit the
same passthrough, as expected, but the amount of aptamer which
`leaks` off the column during washing is substantially higher for
the ethylenediamine linker. This suggests that the short
ethylenediamine linker leads to greater inhomogeneity than the
10-atom jeffamine linker. A preferred linker like jeffamine
minimizes this inhomogeneity, presumably by moving the nucleotide
ligand farther from the surface of the solid support, yielding a
more solution-like binding.
[0125] For any given aptamer clone, the fraction that passes
through the affinity column is presumably the fraction not properly
folded, and this fraction can be as high as 80%. This should be
distinguished from the affinity of the correctly folded fraction.
The avidity of an aptamer clone, the combination of affinity and
fraction of active species, can be improved with some
experimentation. For long sequences there may exist multiple
structures with comparable free energy and only one of which may
bind with high affinity to the nucleotide ligand. For example, the
91-base sequence of clone dA13' can form several different
structures with comparable free energy, based on predicted
secondary structure using the ssDNA folding program DNA Mfold [M.
Zucker, http://www.cbr.nrc.ca/zuk- erm/cgi-bin/form1-dna cgi;
Zucker, M., Meth. Enzy. 180, 261 (1989)]. By removing part of the
primer sequence at both the 5' and the 3' ends, one finds the
predicted number of structures decreases to just two.
[0126] This shortened version of clone dA13' was synthesized and
tested at two different folding temperatures. As shown in FIG. 9,
the fraction of aptamer retained by the dAMP-jefferamine-agarose
column, increases from .about.15% for the full length aptamer to
.about.40% for the shortened 58-mer, and that the 58-mer is less
sensitive to folding temperature. The structures formed by the
58-mer, shown in FIGS. 10(A) and 10(B), can be further tested by
removing bases 8-13 (i.e. removing TGTCGAA), which yields a unique
minimal-energy structure (based on calculation) shown in FIG.
10(C). This 51-mer was synthesized and tested on a
dAMP-jeffamine-agarose affinity column. As shown in FIG. 11, about
80% of dA13'.51 is retained by the column, a 5-fold improvement
over that for the original 91-mer version of this clone. Additional
improvements in aptamer avidity through removal of non-essential
sequence could be made but were not attempted here. (Programs such
as Mfold calculate energies based on Watson-Crick and G-T wobble
base-pairing; so that hairpins, base triples, pseudoknots, etc. are
not included. Structure calculations like these are useful as
guides, but are unlikely to reveal the actual structure of the
aptamer).
[0127] Several clones were tested for specifity using affinity
columns (1-mL beds) of agarose beads with the jeffamine linker and
derivatized with approximately equal concentrations (400 nM dNMP
per mL of gel) of either dAMP, dGMP, dCMP, or TMP. For example,
elution profiles on the four columns for the clone dA13'.58 are
shown in FIG. 12. For the G, C, and T gels, greater than 95% of the
aptamer passes through the columns in the first fraction of 2 mL,
indicating that the Kd for these nucleotides exceeds 0.1 mM. For
the A gel, 50% passes in the first fraction, while 33% of the
aptamer is retained after 10 fractions of washing, based on the
amount eluted with 3 mM dAMP. These measurements indicate a high
degree of specificity of the aptamer for the base A, but not for G,
C, or T.
[0128] The ionic components of the buffer were tested to determine
their effect on aptamer binding. Assays were performed using clone
dA13'.58, in which modified buffer was used for both folding and
applying this aptamer to the affinity columns. The standard buffer
was 0.3 M NaCl, 20 mM Tris, 5 mM MgCl2, pH 7.6. Only one component
was changed in an assay. It was found that the binding affinity
disappears without Mg ions in the buffer, but there is little
difference in binding between 5 mM and 20 mM Mg ions. The sodium
salt concentration can be dropped to 50 mM with slightly better
binding affinity. There is no change in the binding affinity when
the Na+ cation is replaced by Li+ (at 0.3 M). Finally, at standard
buffer conditions, the binding affinity is improved 2-4 fold by
lowering the temperature from 23.degree. C. to 4.degree. C.
[0129] The equilibrium dissociation constant, K.sub.d, was
determined by ultrafiltration binding titration. For these
measurments, 100 .mu.L of 1 .mu.M dA13'.51 was incubated for 45 min
with .sup.32P-labeled dGMP at concentrations ranging from 10 nM to
50 .mu.M. Free and bound radio-labeled nucleotide were separated by
ultracentrifuge in a spin filter column, and the bound nucleotide
measured. These measurements, shown in FIG. 13, show that the
K.sub.d is 1.8 .mu.M at 4.degree. C.
Example 2
[0130] Selection of dGMP-Specific Aptamers
[0131] The following example illustrates the selection, isolation,
and characterization of oligonucleotide aptamers that specifically
bind the nucleotide dGMP and not nucleotides dNMP, N=A, C, or T. To
obtain aptamers with specific binding to dGMP, an initial pool (1.6
nmole) of ssDNA oligos containing a 42-base segment of randomized
nucleotides flanked by primers of fixed sequence, was folded
(heated to 85.degree. C. for 5 min, then cooled to 4.degree. C. at
6.degree. C./min) in 100 .mu.L of column buffer (0.3 M NaCl, 20 mM
Tris, 5 mM MgCL2, PH 7.6) and applied to an affinity column
containing a 1-mL bed of dGMP-jeffamine-agarose (500 nmole/mL) that
had been pre-equilibrated with 25 mL of column buffer. The
jeffamine (triethyleneglycoldiamine) linkage is shown in FIG. 2(b).
After a 10-min incubation, the column was washed with 20 mL of
column buffer to remove unbound DNA, followed by 6 mL of 8 M urea
to elute bound DNA. The wash and elution were collected in 2 mL
fractions. The amount of DNA in each fraction was measured by
fluorescence detection of a TAMRA dye label, attached to the DNA on
the 5' end. The fractions containing the eluted DNA were pooled,
ethanol-precipitated, amplified by PCR, and purified for size on
agarose gels, typically yielding 50-100 pmole of ssDNA. This
selection procedure was repeated on a new column for 1 additional
round.
[0132] For the 3rd round, the elution procedure was changed to
enhance specificity to dGMP. After loading and incubating the
amplified DNA from round 2, the column was washed with 20 mL of
column buffer, then 6 ML of 3 mM dGMP in column buffer to collect
bound DNA eluted by free dGMP, and then with 6 mL of 8 M urea to
determine the amount of DNA bound retained by the column. The
dGMP-eluted DNA was pooled, amplified, purified, folded and applied
to a new column for further selection.
[0133] At round 7, pre-selection against dAMP was performed. The
DNA-aptamer pool derived from round 6 was first applied to a dAMP
column, and the material that passed through this column was
applied to a dGMP column. For Round 9 and subsequent rounds, the
selection procedure was modified to include counter-selection, so
that the wash prior to elution included 2-3 fractions of 3 mM dAMP,
to remove bound oligos with affinity for dAMP. At round 11, the
aptamer pool was first passed through a blank column (derivatized
with linker but without nucleotides), then applied to a low-density
dGMP column (160 nmole of dGMP per mL of gel). A low density
dGMP-column was used for all subsequent rounds. Selection continued
to round 16, where the amount of DNA eluted with dGMP reached a
plateau at 20%. The fraction eluted versus round is shown in FIG.
14.
[0134] The round 16 pool was cloned into the pCRII cloning vector
and sequenced, and these sequences are shown in FIG. 15(a). A
number of clones contained identical sequence. For clarity, FIG.
15(a) condenses the redundancy and shows the 42-base randomize
segment distinguished (in uppercase) from the fixed primer
sequences (lower case). Bases that are conserved in these clones
(shown in boldface) are grouped to emphasize a consensus. The
consensus sequence for each clone is contained within flanking
sequences that differ from clone to clone but contain complimentary
sequence segments (underlined). For several clones (e. g. clones 4,
14, 21, etc) complimentary sequence segments can recruit part of
the primer sequence. The consensus sequence apart from point
mutations, TGGGNTGGGNNTGGGNAGGGT or TGGGNTGGGNTGGGNAGGGT (SEQ ID
NO: 4 or SEQ ID NO: 90, respectively) is 60% G-rich, whereas the
variable flanking regions, on average, are only slightly so
(29%).
[0135] Four clones (clones 17, 4, 21, and 15) were synthesized for
further tests. For practical reasons (e.g. synthesis yield), these
clones were reduced in length (FIG. 15(b)) by deleting the primer
sequences, unless these sequences appeared to base-pair with part
of the random sequence. For example, a portion of the 3' primer
sequence was included for clones 4 and 21, a portion likely to be
necessary for folding. In addition, a TAMRA dye molecule was
conjugated to these shortened clones at the 5' end. Each of these
four clones, after folding, were tested on separate dGMP-jeffamine
agarose columns (160 nmole dGMP/mL of gel, 1 mL bed) to determine
relative binding affinity. As shown in FIG. 16, clones 17 (dG17.44)
and 4 (dG4.48) bind strongly to the columns, whereas clones 21
(dG21.52) and 15 (dG15.42) have very low affinity, washing off the
column in the first few fractions. It is possible that for these
clones more of the primer sequence is necessary for formation of a
high affinity aptamer. However, in the case of clone 15, part of
the consensus region is missing, suggesting that affinity for dGMP
requires the full consensus region. Clone 21, on the other hand,
differs from clone 17 (a successful clone) in their consensus
region by just one base. To test whether this one-base change
significantly alters binding affinity, an oligo dG17.44.g (shown in
FIG. 15(b)) was synthesized. This oligo bound the dGMP affinity
column as well as dG17.44, so that the one base change within the
consensus region was not responsible for the reduced binding of
clone 21. This indicates that the sequence of the flanking region,
or the order and degree of complimentary base pairing in this
region, contributes to the binding affinity.
[0136] Both abridged clones dG17.44 and dG4.48 were further tested
for binding nucleotides other than dGMP. Each clone was tested on
affinity columns (1-mL beds) of agarose beads with the jeffamine
linker and derivatized with approximately equal concentrations (400
nmole dNMP per mL of gel) of either dAMP, dGMP, dCMP, or TMP.
Elution profiles on the four columns for clone 17 (dG17.44) are
shown in FIG. 17. For both clones on the A, C, or T gels, greater
than 90% of the aptamer passes thru the columns in the first two
fractions (4 mL), and no measurable aptamer is eluted by 3 mM dGMP.
For the dGMP gel, 60% is retained on the column after 10 fractions
of washing, and this is recovered in elution with 3 mM dGMP. For
both clones 17 and 4, the A, C, and T elution indicates that the
K.sub.d for binding these nucleotides exceeds 100 .mu.M, estimated
from the equations for isocratic elution. For comparison, an
isocratic elution profile for clone 17 on a dGMP column, using only
column buffer as the elutant (data not shown), indicated that the
affinity of clone 17 for dGMP is less than 1 .mu.M.
[0137] To determine what part of the dGMP nucleotide contributes to
binding specificity, measurements were made of the relative
affinity of clone 17 for nucleotides or nucleosides of various
G-analogs containing substitutions at locations around the purine
or sugar rings. The experiment involved loading dG17.44 on a dGMP
column, and measuring the fraction eluted by 3 mM of G-analog,
compared to that eluted by 3 mM of dGMP. As shown in FIG. 18, many
of the analogs tested had 30-100% of the affinity of dGMP, while
7-methylGMP had very weak affinity, and the deoxynucleotides of A,
C, or T had no measurable affinity. These results indicate that
clone 17 is tolerant to some modifications of the guanine
structure, but not for transformation to the other common
bases.
[0138] To shed light on the aptamer structure, the effect of the
salt and Mg used for the buffer was measured. The elution profile
of clone 17 on a dGMP-gel in a buffer where the NaCl was replaced
with either LiCl or KC was measured. The buffer was 300 mM salt
(either LiCl or KCl), 20 mM Tris, 5 mM MgCl.sub.2, pH 7.6. The
aptamer was folded in this buffer, applied to the column
pre-equilibrated in this buffer, and washed with this buffer. As
shown in FIG. 19, the dG17.44 aptamer has no affinity for dGMP in
either Li or K salts, indicating that both Li and K ions either
disrupt or alter the aptamer structure, or otherwise interfere with
ligand binding. In a separate experiment, a NaCl buffer without
MgCl.sub.2 was tested: 20 mM Tris, 300 mM NaCl, 1 mM EDTA, pH 7.6.
The EDTA was added to chelate any residual divalent ions present.
The elution profile (data not shown) was unchanged from that of the
standard buffer, indicating that the Mg ion does not play a role in
dGMP-aptamer binding.
[0139] The equilibrium binding constant K.sub.d was determined by
isocratic elution and by analytical ultrafiltration, to yield a
value for binding dGMP in solution. For the method of isocratic
elution, a 2.7 mL affinity gel bed (V.sub.t, is the total column
volume, with area of 0.2 cm.sup.2) containing 160 .mu.M of bound
dGMP, was loaded with 100 .mu.L of 3-mM clone 17 (dG17.44) aptamer.
Column buffer was applied at 0.25 mL/min, and 70 fractions
(1.75mL/fraction) were collected, at which point the remaining
bound aptamer (75%) was removed with 3 mM dGMP. The measured void
volume V.sub.o. was 1.4 mL, while the eluted volume V.sub.c. was
122 mL. The value of K.sub.d can be estimated from
(0.5)[dGMP].sub.bound(Vt-V.sub.o)/(V.sub.e-V.sub.o) to be less than
0.85 .mu.M.
[0140] For ultrafiltration binding measurements, 100 .mu.L of
1-.mu.M dGMP17.44 was incubated for 45 min with .sup.32P-labeled
dGMP at concentrations ranging from 10 nM to 10 .mu.M. Free and
bound radio-labeled nucleotide were separated by ultracentrifuge in
a spin filter column, and the bound nucleotide measured. These
measurements revealed that the solution K.sub.d is 350 nM at room
temperature and 45 nM at 4.degree. C. These are effective values of
K.sub.d. FIG. 20 shows the binding curve at 4.degree. C., and based
on a linear best fit to the data, the y- intercept is 0.65,
indicating that only 65% of the aptamers in solution are active,
but these have a K.sub.d of 30 nM. This fraction of active
aptamers, (i.e. that are properly folded and bind dGMP) is the same
as that found from the affinity column measurements (where the
fraction not active wash off the column in the first few
fractions).
[0141] The structure of the G aptamer is discussed below. The
appearance of the triplet GGG four times in the consensus region
suggests that G-quartets are involved in the structure of the
aptamer. The thrombin DNA aptamer, a 15-mer containing four GG
repeats, is known from both solution NMR and X-ray crystallography
measurements to form a structure consisting of two tiers of
G-guartets. G-quartet structures are generally known to either form
intramolecular structures, intermolecular quadruplexes, or to not
form in solution depending on the buffer salt. Because G-quartets
involve Hoogsteen base pairing of the N7 position of the guanine
base, whereas Watson-Crick does not, protection studies were
performed on the clone dG17.44, to determine if the N7 position of
the guanines in the consensus region were involved in N7 bonding.
It was found that all of the guanines in the consensus region were
protected, while none of the guanines in the flanking regions
outside of the consensus were, suggesting the dGMP-aptamer adapts a
G-quartet structure for binding the dGMP ligand.
[0142] The salt dependance of the aptamer binding, noted above,
lends support to a G-quartet structure for the aptamer. It is known
that the Li+ cation diminishes the formation of quartet structures,
while high concentrations of K+ ions enhance formation of
intermolecular quaduplexes, and Na+ ions promote formation of the
unimolecular G-quartet. The measured salt dependence of the dG17.44
binding to dGMP correlates with the preferential formation of a
unimolecular G-quartet structure.
Example 3
[0143] Selection of CMP-Specific Aptamers
[0144] Selection for a CMP-binding aptamer followed the general
prescription used above, where the affinity column consisted of
CMP-agarose (Sigma) containing 2.8 .mu.mole of bound ligand per mL
of gel. Here, the nucleotide was linked to the solid matrix through
the sugar hydroxyls. Affinity columns of 1 mL bed volume were
pre-equilibrated with 20 mL of standard column buffer, to which a
nmole-quantity of randomized-sequence DNA, folded at 85.degree. C.,
was applied. After incubation and washing, 3 mM CMP in solution was
used to specifically elute bound DNA. PCR amplification and ssDNA
preparations were performed as previously described. The selection
continued for 21 additional rounds. By round 19, about 10% of the
DNA eluted with solution CMP. For subsequent rounds, both
pre-selection and counter-selection using AMP nucleotides was
employed to improve specificity for the CMP-nucleotide. The
percentage of DNA eluted by CMP versus selection round is shown in
FIG. 21. The elution profile for round 22 is shown in FIG. 22.
[0145] The fraction of CMP-eluted DNA from round 22 was amplified
by symmetric PCR, and gel-purified dsDNA was cloned into the pCRII
cloning vector and subsequently sequenced. Thirty-five out of
thirty-eight clones yielded acceptable sequence, shown in FIG.
23(a). The sequences are arranged to organize the variable-sequence
segments (upper case), fixed primer sequence (lower case), and
consensus (boldface). The redundancy in sequence for identical
clones is suppressed, with the number of clones with identical
sequence indicated. The clones appear to break into two groups,
with the first exhibiting a more complex consensus given by
GGGAGGGTNNNGGNG (SEQ ID NO: 2), wherein N is any base and the last
N is often a pyrimidine base. The less dominant consensus is
GGTNNNGGNG (SEQ ID NO: 3).
[0146] Two clones were selected for further tests. Abridged
sequences of clones 3 and 9, shown in FIG. 23(b), were synthesized
and tested for affinity. The choice of sequence reduction was
guided by secondary structure calculations using the program DNA
Mfold. As in previous examples, the 5' end of the shortened
aptamers were labeled with a TAMRA dye. Using standard column
buffer, clone 9 (C9.58) was folded, and applied to separate
affinity columns of either CMP or AMP (each with approximately 2
.mu.mole of bound ligand per mL of gel, and each employing the same
linker). As shown in FIG. 24, only the CMP column yields binding of
aptamers that specifically elutes with CMP. Both columns retain the
same small fraction of aptamers that are removed with urea and are
non-specifically bound to the matrix. From the elution profile of
clone 9 on the CMP column it is clear that the fraction of aptamers
properly folded is high (>90%), while the affinity, estimated
from the isocratic elution behavior of the aptamer during washing,
is about 35 .mu.M. Clone 3 yielded similar results, as shown in
FIG. 25, of high yield of properly-folded aptamers and a binding
constant K.sub.d of about 50 .mu.M. When clone 3 is folded in
column buffer containing KCl in place of NaCl, and applied to a CMP
column in this modified buffer, no binding is measured to the CMP
nucleotide, although some non-specific binding is still present.
The CMP-aptamers isolated here could be further improved by using
known methods of mutagenic PCR to obtain a low-diversity pool. This
would provide a starting pool for re-selection for a CMP aptamer
with better affinity, using more stringent selection conditions
such as lower concentration of nucleotide ligand on the affinity
column. Such a pool could also provide an initial pool for the
selection and isolation of aptamers that bind dCMP.
Example 4
[0147] Fabrication of Functionalized Surfaces for Coupling
Nucleotides
[0148] This example describes the fabrication of surfaces suitable
for coupling nucleotides and that have very low non-specific
binding of aptamers. The substrate material is chosen to be
optically-transparent silica, so that for single-nucleotide
detection, the excitation and emission light paths need not employ
the same optics, and excitation of fluorescence by total-internal
reflection (TIR) can be used. Silica is a very clean material and
generally free of contaminants, while its surface can also be made
clean using standard glass-cleaning methods. Cleanliness means that
the surface and substrate exhibit no significant auto-fluorescence
when illuminated by visible or infrared light. Hence the substrate
and surface do not contribute to false-positive detection of the
desired fluorescent signal from dye-labeled aptamers.
Alternatively, oxide-coated silicon can be used in an
epi-illumination geometry for exciting and detecting fluorescence
from surface-bound detection reagents. Silicon is at least as clean
as silica, and the surface chemistry reactions involving silanol
groups are the same. Silicon normally has a native oxide layer
about 1.5 nm thick. This thickness should be increased, by
oxidation for example, to more that 10 nm, since the silicon
substrate (the subsurface atomic silicon) quenches fluorescence of
fluorophores within about 5 nm of the uppermost layer of atomic
silicon. Such thick oxide silicon is available commercially. For
the case where an aptamer detection reagent is labeled with a
sufficiently bright fluorophore or group of fluorophores, glass or
plastic substrates can be used. Both of these materials exhibit
some autofluorescence and fluorescence from contaminants, but this
will not contribute to a false positive when very bright
fluorophores are used as labels. Surface chemistry for glass is the
same as silica, while plastic can be plasma-etched and cleaned and
converted to a hydrophilic surface for silica-like surface
chemistry.
[0149] While surface treatments are known for introducing a
functional group to the surface of silica, almost all methods lead
to some degree of non-specific binding of reagents that are not
intended to be retained by the surface.
[0150] One-millimeter thick silica substrates (from either ESCO
Products or CVI, Inc) were first cleaned using the base/acid wash
procedure known as SC1 and SC2. The surfaces were immersed in a
solution of 5 parts H.sub.2O, 1 part H.sub.2O.sub.2, 1 part
NH.sub.3OH, for 10 minutes at 80.degree. C., rinsed with
high-purity DI water (18 Mohm), then immersed in a solution of 5
parts H.sub.2O, 1 part H.sub.2O.sub.2, 1 part HCl for 10 minutes at
80.degree. C. and finally rinsed extensively with high-purity DI
water.
[0151] In order to accomplish silanization and activation, the
following procedure, modified from that of Potyrailo et al (Anal.
Chem. 70, 3419 [1998]), was used to first make a diol-silica
surface, and then to activate some fraction of the hydroxyl groups
with carbonyldiimidazole (CDI) for subsequent coupling of a diamine
linker. Clean silica substrates were silanized by immersion in an
aqueous solution of 10% Glycidoxypropyltrimethoxysilane (GOPS,
United Chemical Technologies) at pH 3.5 using HCl overnight at room
temperature, then heated at 90.degree. C. for 4 hrs. After cooling
back to room temperature, surfaces were briefly rinsed by dipping
in clean water (10-14 times), dried with N.sub.2 gas, and baked at
120.degree. C. for 1 hr. These diol-coated substrates (as shown in
FIG. 26) are then activated with CDI by reaction in a solution of
dry dioxane containing 3 mM CDI for 4 hours, then rinsed with clean
dioxane, and stored under vacuum in a dessicator. The treated
substrates could be stored for at least several days in the
dessicator without significant loss of activation.
[0152] For linker coupling, the CDI-activated surfaces were
immersed in a solution of 3.4 mM triethyleneglycoldiamine
(Jeffamine or ERD-148, Huntsman Corp.) in dry dioxane overnight,
then washed first with clean dioxane, then water. Surfaces were
then stored in column buffer (0.3 M NaCl, 20 mM Tris, 5 mM MgCl2,
pH 7.6) for at least 1 day, to passivate the surface by hydrolyzing
any active CDI-sites. This surface is then ready for use in
nucleotide coupling. This procedure results in about
1000/(micron).sup.2 jeffamine linkers coupled to the surface and
with one free amine group. Higher and lower surface concentrations
of surface-coupled jeffamine can be achieved by varying the
reaction solution concentrations of CDI or jeffamine.
[0153] Nucleotide coupling to the surface-bound jeffamine linker
was obtained using aqueous solutions of 50 mM
1-ethyl-3-(3-dimethylaminopropy- l) carbodiimide (EDC, Pierce
Chemical), 50 mM 1-methylimidazole, 100 mM MES buffer, 10 mM dNMP,
pH 6.0 for 2 hours at room temperature. Surfaces were then washed
with H20, and stored in column buffer.
[0154] To determine the binding characteristics of aptamers to
nucleotides linked to silica substrates, the dGMP-aptamer clone
dG17.44, labeled with a single tetramethylrhodamine dye, was folded
and then diluted to various concentrations, and each of these
applied to a surface containing dGMP linked to the surface via a
jeffamine linker. The surfaces were illuminated with 515-nm laser
light in a total-internal-reflection (TIR) geometry, and the
fluorescence monitored with a CCD camera. This arrangement allowed
measurement of both time dependent binding (i.e. to yield the
on-rate and off-rate) and equilibrium binding. FIG. 27 shows a plot
of the equilibrium data, and the hyperbolic curve expected for a
K.sub.d of 260 nM. From time-dependent measurements, the
association rate constant and dissociation rate were
1.5.times.10.sup.4 M.sup.-1sec.sup.-1 and 0.006 sec.sup.-1,
respectively. These values yield a K.sub.d value of 400 nM. These
surface measurements, made at room temperature, agree within 50% of
the solution binding measurements described in Example 2.
Example 5
[0155] Base Specific Detection of Single Nucleotides Using Aptamer
Affinity Probes
[0156] In order to demonstrate base-specific detection of single
nucleotides, nucleotides (either dGMP or dCMP) were first coupled
to the jeffamine linker using an EDC/Methylimidazole reaction,
purified by HPLC, and then applied to the CDI-activated surfaces
described above in Example 4, from an aqueous solution of 50 mM
Hoogsteen buffer, pH 8.3. Concentrations and time were chosen to
load about 0.1 nucleotide/micron.sup.2, a surface coverage that
allows individual nucleotides to be resolved optically. After
incubation, the surfaces were washed and soaked in column buffer
for two hours, then incubated in a solution of 1 micromolar dG17.44
aptamer labeled with a single Cy5 dye in column buffer (CB)
containing 0.1% Tween-20 for 15 minutes. These surfaces were then
washed with 10 ml CB plus 0.1% tween-20 for 10 sec from a squirt
bottle, dried and measured in a microscope set up for single
molecule detection. Surfaces were imaged using a 100.times., 0.9 NA
dry objective onto a LN.sub.2-cooled CCD camera (Princeton
Instruments). Surfaces were illuminated with 7 mW of 633-nm laser
light, focused onto the surface in TIR in a spot approximately 30
microns in diameter. A bandpass filter, centered at 670 nm and of
width 40 nm, was used after the microscope objective, to pass
fluorescence but block laser light. The CCD camera acquires an
image of the surface in 2 seconds, a time sufficient to provide a
S/N>20 for detection of individual Cy5-labeled aptamers, which
appear as isolated bright dots on the image.
[0157] As shown in FIG. 28, based on the number of single aptamers
detected, non-specific binding of dG17.44 aptamers on surfaces
containing dCMP is very small (approximately 0.003
aptamer/micron.sup.2). The surface containing dGMP retains a much
larger number of aptamers, close to the expected number of dGMP
molecules on the surface. (The exact number of surface-bound dGMP
cannot be measured directly. The amount is estimated by
extrapolation from measurements made at higher loading
concentrations.)
[0158] Based on these measurements, the specificity of the dG17.44
aptamer for dGMP is at least 100.times.greater than the specificity
for dCMP, in agreement with the specificity measurements made on
affinity columns as described in Example 2. In addition, the
functionalized silica surfaces used here have very low non-specific
binding.
Example 6
[0159] Methods and Materials of Fabricating Affinity Matrix
[0160] Adenosine-monoHoogsteen was covalently coupled to beaded
agarose via ethylenediamine using carbodiimide chemistry, resulting
in the linkage shown in FIG. 2(a). The agarose gel (CM Bio-Gel A,
BIORAD) was carboxylate-modified, with 20 .mu.mole COOH groups per
mL of gel. The gel was first column-washed with 4 column volumes of
high-purity water, adjusted to pH 5, then resuspended in H.sub.20
at 50% V/V. To couple ethylenediamine to the COOH-agarose via EDAC
(Sigma), a 45 mL aqueous solution of 0.23 M EDAC and 5 mM
ethylenediamine (Sigma) was made nd adjusted to pH 5 with 1M HCl.
Next, 45 mL of gel was poured into two polypropylene tubes and
rotated end-over-end for 1 hr. (HCl was added at 1/2 hour to
maintain pH at 5). The gel was drained and rinsed with H.sub.2O
(20.times.column volumes) and then resuspend in H.sub.2O at 50%
V/V. To couple the nucleotide to the amine-derivatized gel, a 45 mL
aqueous solution of 0.23 M EDAC, 0.17 M 1-methylimidazole, and 20
mM dAMP, at pH 6.2 was added to 45 mL of diamine-reacted gel,
adjusted to pH 6.2, and rotated end-over-end for 2 hrs. In order to
terminate excess free amines on the gel, succinic acid was used to
cap terminal amines with carboxylates. A 5 mL solution of 0.46 M
EDAC and 150 mM succinic acid, adjusted to pH 6, was added to 45 mL
of nucleotide-modified gel and rotated end-over-end for 2 hrs.
Then, it was drained and rinsed in a column with H.sub.2O (2 column
volumes) and then with Buffer A (40 column volumes). Buffer A is
0.3 M NaCl, 20 mM Tris, pH 7.6. The derivative gel was then
resuspended in Buffer A at 50% v/v and store at 4.degree. C.
[0161] dNMP-Jeffamine-Agarose affinity matrix.:
Nucleoside-monoHoogsteens were covalently coupled to agarose beads
via the triethyleneglycoldiamine linker Jeffamine (XTJ-504,
Huntsman) using carbodiimide chemistry, resulting in the linkage
shown in FIG. 2(b). Typically, 50 ml of carboxy-modified agarose
gel (Biorad) was washed with 500 mL of high purity deionized water
and resuspended at 50% V/V in a reaction mixture of 0.1 M EDC
(Pierce), 20 mM of Jeffamine, and 0.1 M MES buffer at pH 5.2 for 90
min. under gentle mixing conditions. This slurry was column-washed
with 500 mL of high-purity deionized water, and resuspended in
reaction mixture B. This mixture consisted of first reacting 0.2 M
EDC, 0.2 M Methylimidazole (Sigma), and 40 mM dNMP at pH 6.2 for 30
min, then adding the diamine-reacted gel at 50% V/V overnight
(about 14 hr) with gentle mixing. This slurry was column-washed
with 2.5 Liters of 0.3 M NaCl, 20 mM Tris, pH 7.6 buffer, and
resuspended in this buffer at 50% V/V. The quantity of nucleotide
coupled to the agarose gel was measured by uv absorption after
melting the reacted nucleotide-agarose gel using perchloric acid.
Typically, 0.25 mL of perchloric acid was added to 0.25 mL of 50%
V/V gel, placed in a 37.degree. C. heat bath for 30 sec until the
agarose beads melted, then diluted to 2 mL with high-purity water.
After subtracting the absorption of gel reacted without a
nucleotide, and using acid-pH extinction coefficients, [dNMP]
concentrations for the reacted gel at 50% V/V were typically 180
mM, or 360 nmoles of nucleotide coupled per ml of gel. Storage at
4.degree. C. resulted in no apparent degradation over periods of
greater than 1 month.
Example 7
[0162] Molecular Biology Methods
[0163] DNA Pools: The pool of random-sequence DNA used for the
initial selections was prepared by commercial synthesis of the
91-mer oligo 5'-GGC AAG CTT GGG CCT CAT GTC GAA (N).sub.42 GAG CAA
TGG CGA TGA CGG ATC CTC A-3' (SEQ ID NO: 5), where N is any one of
the four nucleotides occurring with an equal probability.
[0164] Folding Procedure: Prior to use in a selection, the initial
pool or amplified ssDNA were folded at either 75.degree. C. (for
dAMP selection) or 85.degree. C. (for G or C selections) for 5 min,
then cooled to 4.degree. C. at 6.degree. C./min.
[0165] Affinity Columns: Nucleotide-agarose columns (Area=0.77
cm.sup.2) of 1 mL bed volume were pre-equilibrated with
approximately 25 mL of column buffer (300 mM NaCl, 5 mM MgCl2, 20
mM Tris, pH 7.6). For each round of selection a fresh column and
gel was used. Eluted fractions containing the DNA of interest were
pooled, ethanol precipitated (1 .mu.g tRNA or glycogen was added to
facilitate the precipitation), and amplified by PCR.
[0166] PCR. The PCR reactions contained 200 .mu.M of each dNTP, 10
mM Tris-HCl, pH 8.4, 50 mM KCl, 2.5mM MgCl2, and 2.5 units of Taq
polymerase per 100 .mu.L reaction. The primer concentrations were 1
.mu.M HPLC purified oligonucleotide. The 5' primer was 5'-LGG CAA
GCT TGG GCC TCA TGT CGA A-3' (SEQ ID NO: 86), where L=Amino
linker+TAMRA dye. The 3'-primer was 5'-TGA GGA TCC GTC ATC GCC ATT
GCT C-3' (SEQ ID NO: 87). Thermal cycling was 94.degree. C. for 45
sec, 55.degree. C. for 30 sec, and 72.degree. C. for 60 sec (30-35
cycles) for both Symmetric PCR and Asymmetric PCR. However,
preheating time for symmetric PCR was 5 minutes while for
asymmetric PCR was 2 minutes. For symmetric PCR, 1 .mu.M for both
primers were used. For asymmetric PCR, 6 .mu.M 5'-primer and 0.2
.mu.M 3'-primer were used. All of PCR amplified DNA mix were loaded
onto 4% NuSieve GTG agarose gel (FMC) for TAMRA-labeled
single-stranded aptamer purification. This was also important for
isolating the bands of the right length.
[0167] Cloning: The single-stranded DNA aptamer pool recovered from
the last round of selection was amplified by PCR to give a single
identifiable double-stranded DNA band. The primers to the ends of
the aptamer were 5'-GGC AAG CTT GGG CCT CAT GTC GAA-3' (SEQ ID NO:
88), and 5'-TGA GGA TCC GTC ATC GCC ATT GCT C-3' (SEQ ID NO: 89).
The cycling steps were as follows: 1. 94.degree. C. or 3 minutes,
2. 94.degree. C. for 0.5 minutes, 3. 60.degree. C. for 0.5 minutes,
4. 72.degree. C. for 0.5 minutes, repeat steps 1-4 30 times, then
5. 72 o for 5 minutes, then 4.degree. C. for storage. The annealing
temperature and the 5 minutes at 72.degree. C. were empirically
found to be necessary for obtaining the correct sized PCR product
with a single 3' A overhang suitable for subsequent cloning. The
double-stranded DNAs were gel purified and isolated using the QIAEX
II Agarose Gel extraction Kit (Qiagen). Purified DNA was ligated
directly into PCR2.1 vector (Invitrogen) and transformed into the
E. coli SURE strain (Invitrogen) to minimize rearrangements.
Individual aptamer clones were then isolated for sequencing.
[0168] Binding Assays. Nucleotide-jeffamine-agarose columns
(Area=0.77 cm2) of 1 mL bed volume were pre-equilibrated with
approximately 25 mL of column buffer (unless noted, this was 300 mM
NaCl, 5 mM MgCl2, 20 mM Tris, pH 7.6). Solutions of aptamers were
folded in the same buffer and then applied to the column for 10
minutes, after which the column was washed for 10-100 mL of
buffer.
[0169] Dissociation Constants. K.sub.d by Equalibrium
Ultrafiltration The interaction of aptamers and dNMPs was measured
by ultrafiltration using the method of Menguy et al. (Anal.Biochem.
264, 141-148 (1998)). In brief, TAMRA-labeled aptamer was incubated
in the presence of a32P-dNMP under the specified binding conditions
in a total volume of 100 .mu.l. The reactions were placed in
MicroCon 10 spin filters (Millipore) and centrifuged at
11,800.times.g for 8 minutes. The filtrate and retentate were
collected. Aptamer concentration was determined by comparing the
TAMRA fluorescence against the fluorescence of samples of known
aptamer concentration. The concentration of nucleotide was
determined by liquid scintillation counting. Control experiments
indicate the dNMP passes freely through these filters and greater
than 90% of a 58-mer aptamer is retained.
[0170] Throughout the specification and claims, the word
"comprise," or variations such as "comprises" or "comprising," will
be understood to imply the inclusion of a stated integer or group
of integers but not the exclusion of any other integer or group of
integers.
[0171] U.S. Provisional application No. 60/135,863 and other United
States applications cited herein are hereby incorporated by
reference.
[0172] While hereinbefore a number of embodiments of this invention
have been presented, it is apparent that the basic construction can
be altered to provide other embodiments which can utilize the
methods of this invention. Therefore, it will be appreciated that
the scope of this invention is to be defined by the claims and
specification rather than the specific embodiments which are
exemplified here.
Sequence CWU 0
0
* * * * *
References