Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase

American Association for the Advancement of Science (AAAS) - Tập 249 Số 4968 - Trang 505-510 - 1990
Craig Tuerk1, Larry Gold1
1Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO 80309.

Tóm tắt

High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.

Từ khóa


Tài liệu tham khảo

ANDRAKE, M, DNA-POLYMERASE OF BACTERIOPHAGE-T4 IS AN AUTOGENOUS TRANSLATIONAL REPRESSOR, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 85: 7942 (1988).

10.1073/pnas.86.18.7054

CHILDS, J, UCLA SYMPOSIA ON MOLECULAR AND CELLULAR BIOLOGY 30: 341 (1985).

FREEMONT, P.S., COCRYSTAL STRUCTURE OF AN EDITING COMPLEX OF KLENOW FRAGMENT WITH DNA, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 85: 8924 (1988).

GAUSS, P, THE BACTERIOPHAGE-T4 DEXA-GENE - SEQUENCE AND ANALYSIS OF A GENE CONDITIONALLY REQUIRED FOR DNA-REPLICATION, MOLECULAR & GENERAL GENETICS 206: 24 (1987).

GUATELLI, J.C., ISOTHERMAL, INVITRO AMPLIFICATION OF NUCLEIC-ACIDS BY A MULTIENZYME REACTION MODELED AFTER RETROVIRAL REPLICATION, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 87: 1874 (1990).

HALL, T.C., INTERNATIONAL REVIEW OF CYTOLOGY 60: 1 (1979).

HAWLEY, D.K., COMPILATION AND ANALYSIS OF ESCHERICHIA-COLI PROMOTER DNA-SEQUENCES, NUCLEIC ACIDS RESEARCH 11: 2237 (1983).

HUNTER, W.N., STRUCTURE OF AN ADENINE.CYTOSINE BASE PAIR IN DNA AND ITS IMPLICATIONS FOR MISMATCH REPAIR, NATURE 320: 552 (1986).

INNIS, M.A., DNA SEQUENCING WITH THERMUS-AQUATICUS DNA-POLYMERASE AND DIRECT SEQUENCING OF POLYMERASE CHAIN REACTION-AMPLIFIED DNA, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 85: 9436 (1988).

IRVINE D unpublished data.

JOYCE, G.F., RNA CATALYSIS SPLICI: 83 (1977).

KACIAN, D.L., REPLICATING RNA MOLECULE SUITABLE FOR A DETAILED ANALYSIS OF EXTRACELLULAR EVOLUTION AND REPLICATION, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 69: 3038 (1972).

KRAMER, F.R., EVOLUTION INVITRO - SEQUENCE AND PHENOTYPE OF A MUTANT RNA RESISTANT TO ETHIDIUM-BROMIDE, JOURNAL OF MOLECULAR BIOLOGY 89: 719 (1974).

LEUNG, D.W., TECHNIQUE 1: 11 (1989).

LEVISOHN, R, CLONING OF A SELF-REPLICATING RNA MOLECULE, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 60: 866 (1968).

LEVISOHN, R, FURTHER EXTRACELLULAR DARWINIAN EXPERIMENTS WITH REPLICATING RNA MOLECULES - DIVERSE VARIANTS ISOLATED UNDER DIFFERENT SELECTIVE CONDITIONS, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 63: 805 (1969).

MILLIGAN, J.F., OLIGORIBONUCLEOTIDE SYNTHESIS USING T7 RNA-POLYMERASE AND SYNTHETIC DNA TEMPLATES, NUCLEIC ACIDS RESEARCH 15: 8783 (1987).

MILLS, D.R., AN EXTRACELLULAR DARWINIAN EXPERIMENT WITH A SELF-DUPLICATING NUCLEIC ACID MOLECULE, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 58: 217 (1967).

MILLS, D.R., COMPLETE NUCLEOTIDE SEQUENCE OF A REPLICATING RNA MOLECULE, SCIENCE 180: 916 (1973).

MIN, K.T., SEARCH FOR THE OPTIMAL SEQUENCE OF THE RIBOSOME BINDING-SITE BY RANDOM OLIGONUCLEOTIDE-DIRECTED MUTAGENESIS, NUCLEIC ACIDS RESEARCH 16: 5075 (1988).

NINIO, J, CODON-ANTICODON RECOGNITION - MISSING TRIPLET HYPOTHESIS, JOURNAL OF MOLECULAR BIOLOGY 56: 63 (1971).

OLIPHANT, A.R., THE USE OF RANDOM-SEQUENCE OLIGONUCLEOTIDES FOR DETERMINING CONSENSUS SEQUENCES, METHODS IN ENZYMOLOGY 155: 568 (1987).

OLIPHANT, A.R., DEFINING THE SEQUENCE SPECIFICITY OF DNA-BINDING PROTEINS BY SELECTING BINDING-SITES FROM RANDOM-SEQUENCE OLIGONUCLEOTIDES - ANALYSIS OF YEAST GCN4 PROTEIN, MOLECULAR AND CELLULAR BIOLOGY 9: 2944 (1989).

OLIPHANT, A.R., DEFINING THE CONSENSUS SEQUENCES OF ESCHERICHIA-COLI PROMOTER ELEMENTS BY RANDOM SELECTION, NUCLEIC ACIDS RESEARCH 16: 7673 (1988).

PRIBNOW, D, NUCLEOTIDE-SEQUENCE OF AN RNA-POLYMERASE BINDING-SITE AT AN EARLY T7 PROMOTER, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 72: 784 (1975).

10.1038/344467a0

10.1126/science.2479982

SAFFHILL, R, IN-VITRO SELECTION OF BACTERIOPHAGE QBETA RIBONUCLEIC ACID VARIANTS RESISTANT TO ETHIDIUM BROMIDE, JOURNAL OF MOLECULAR BIOLOGY 51: 531 (1970).

Sambrook J. Molecular Cloning: A Laboratory Manual (1989).

SAMPSON, J.R., ROLE OF THE TERTIARY NUCLEOTIDES IN THE INTERACTION OF YEAST PHENYLALANINE TRANSFER-RNA WITH ITS COGNATE SYNTHETASE, BIOCHEMISTRY 29: 2523 (1990).

SCHNEIDER, T.D., INFORMATION-CONTENT OF BINDING-SITES ON NUCLEOTIDE-SEQUENCES, JOURNAL OF MOLECULAR BIOLOGY 188: 415 (1986).

SCHNEIDER, T.D., EXCESS INFORMATION AT BACTERIOPHAGE-T7 GENOMIC PROMOTERS DETECTED BY A RANDOM CLONING TECHNIQUE, NUCLEIC ACIDS RESEARCH 17: 659 (1989).

TUERK, C, AUTOGENOUS TRANSLATIONAL OPERATOR RECOGNIZED BY BACTERIOPHAGE-T4 DNA-POLYMERASE, JOURNAL OF MOLECULAR BIOLOGY 213: 749 (1990).

UHLENBECK, O.C., INTERACTION OF R17 COAT PROTEIN WITH ITS RNA-BINDING SITE FOR TRANSLATIONAL REPRESSION, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 1: 539 (1983).

WHITE, H.B., PYRIDINE NUCLEOTIDE: 1 (1982).

Thông tin
Thông tin xuất bản

American Association for the Advancement of Science (AAAS)

Tập 249 Số 4968

505-510

Thông tin tác giả