In Vitro Selection of DNA Aptamers on Chips Using a Method for Generating Point Mutations

References

• Ellington , A. D. and Szostak , J. W. 1990 . In vitro selection of RNA molecules that bind specific ligands . Nature , 346 ( 6287 ) : 818 – 822 . [PUBMED] [INFOTRIEVE]
   Google Scholar
• Tuerk , C. and Gold , L. 1990 . Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase . Science , 249 : 505 – 510 . [PUBMED] [INFOTRIEVE]
   Google Scholar
• Famulok , M. 1999 . Oligonucleotide aptamers that recognize small molecules . Curr. Opin. Struc. Biol. , 9 ( 3 ) : 324 – 329 . [CROSSREF] [CSA]
   Google Scholar
• Famulok , M. and Jenne , A. 1998 . Oligonucleotide libraries—variatio delectat . Curr. Opin. Chem. Biol. , 2 ( 3 ) : 320 – 307 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
   Google Scholar
• Lockhart , D. J. and Elington , A. 2000 . Winzeler genomics, gene expression and DNA arrays . Nature , 405 ( 6788 ) : 827 – 836 . [PUBMED] [INFOTRIEVE] [CROSSREF]
   Google Scholar
• McBeath , G. and Schreiber , S. L. 2000 . Printing proteins as microarrays for high‐throughput function determination . Science , 289 ( 5485 ) : 1760 – 1763 .
   Google Scholar
• Cox , J. , Rudolph , P. and Ellington , A. D. 1998 . Automated RNA selection . Biotechnol. Progr. , 14 : 845 – 850 . [CROSSREF] [CSA]
   Google Scholar
• Cox , C. J. and Ellington , A. D. 2001 . Automated selection of anti‐protein aptamers . Bioorgan. Med. Chem. , 9 ( 10 ) : 2525 – 2531 . [CROSSREF] [CSA]
   Google Scholar
• Nishimura , S.‐I. 2002 . A predator's selection of an individual prey from a group . Biosystems , 65 ( 1 ) : 25 – 35 . [PUBMED] [INFOTRIEVE] [CROSSREF]
   Google Scholar
• Nakano , T. , Kaminuma , T. , Sato , T. , Akiyama , Y. , Uebayasi , M. and Kitaura , K. 2000 . Fragment molecular orbital method: application to polypeptides . Chem. Phys. Lett. , 318 ( 6 ) : 614 – 618 . [CROSSREF]
   Google Scholar
• Takahashi , K. , Nakazawa , M. and Watanabe , Y. 2001 . DNA insight: a web based image processing system for large scale RLGS analysis . Genome Informatics , 12 : 212 – 221 . [CSA]
   Google Scholar
• Aita , T. and Hisimi , Y. 2000 . Theory of evolutionary molecular engineering through simultaneous accumulation of advantageous mutations . J. Theor. Biol. , 207 ( 4 ) : 543 – 556 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
   Google Scholar
• Aita , T. and Husimi , Y. 1998 . Fitness landscape of a biopolymer participating in a multi‐step reaction . J. Theor. Biol. , 191 ( 4 ) : 377 – 390 . [CROSSREF]
   Google Scholar
• Aita , T. , Ota , M. and Husimi , Y. 2003 . An in silico exploration of the neutral network in protein sequence space . J. Theor. Biol. , 221 : 599 – 613 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
   Google Scholar
• Asai , R. , Nishimura , S. I. and Takahashi , K. On‐chip Screening Method of DNA Aptamers . Japanese Patent Application No. 2003‐089494 . 2003 .
   Google Scholar
• Padmanabhan , K. , Padmanabhan , P. K. , Ferrara , J. D. , Sadler , J. E. and Tulinsky , A. 1993 . The structure of alpha‐thrombin inhibited by a 15‐mer single‐stranded DNA aptamer . J. Biol. Chem. , 268 ( 24 ) : 17651 – 17654 . [PUBMED] [INFOTRIEVE]
   Google Scholar
• Huizenga , D. E. and Szostak , J. W. 1995 . A DNA aptamer that binds adenosine and ATP . Biochemistry , 34 ( 2 ) : 656 – 665 . [PUBMED] [INFOTRIEVE]
   Google Scholar
• Proske , W. D. , Neumann , M. , Groschup , M. H. , Kretzschmar , H. A. , Famulok , M. and Winnacke , J. 1997 . Virol. , 71 : 8790
   Google Scholar
• Okazawa , A. , Maeda , H. , Fukusaki , E. , Katakura , Y. and Kobayashi , A. 2000 . In vitro selection of hematoporphyrin binding DNA aptamers . Bioorg. Med. Chem. Lett. , 10 ( 23 ) : 2653 – 2656 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
   Google Scholar
• Sugimoto , N. , Toda , T. and Ohmichi , T. 1998 . Reaction field for efficient porphyrin metallation catalysis produced by self‐assembly of a short DNA oligonucleotide . Chem. Commun. , : 1533 – 1535 . [CROSSREF]
   Google Scholar
• Fukusaki , E. , Kato , T. , Maeda , H. , Kawazoe , N. , Ito , Y. , Okazawa , A. , Kajiyama , S. and Kobayashi , A. 2000 . DNA aptamers that bind to chitin . Bioorg. Med. Chem. Lett. , 10 ( 5 ) : 423 – 425 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
   Google Scholar
• Tracy , R. B. , Baumohl , J. K. and Kowalczykowski , S. C. 1997 . The preference for GT‐rich DNA by the yeast Rad51 protein defines a set of universal pairing sequences . Gene. Dev. , 11 : 3423 – 3431 . [PUBMED] [INFOTRIEVE]
   Google Scholar
• Wilson , C. and Szostak , J. W. 1998 . Isolation of a fluorophore‐specific DNA aptamer with weak redox activity . Chem. Biol. , 5 : 609 – 617 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
   Google Scholar
• Strandh , M. , Persson , B. , Roos , H. and Ohlson , S. 1998 . Studies of interactions with weak affinities and low‐molecular‐weight compounds using surface plasmon resonance technology . J. Mol. Recognit. , 11 : 188 – 190 . [PUBMED] [INFOTRIEVE] [CROSSREF] [CSA]
   Google Scholar
• Kampranis , S. C. , Gormley , N. A. , Tranter , R. , Orphanides , G. and Maxwell , A. 1999 . Probing the binding of coumarins and cyclothialidines to DNA gyrase . Biochemistry , 38 ( 7 ) : 1967 – 1976 . [PUBMED] [INFOTRIEVE] [CROSSREF]
   Google Scholar
• Markgrena , P. O. , Hamalainenb , M. and Danielsona , U. H. 2000 . Kinetic analysis of the interaction between HIV‐1 protease and inhibitors using optical biosensor technology . Anal. Biochem. , 279 ( 1 ) : 71 – 78 . [CROSSREF]
   Google Scholar
• Adamczyka , M. , Moorea , J. A. and Yua , Z. 2000 . Application of surface plasmon resonance toward studies of low‐molecular‐weight antigen‐antibody binding interactions . Methods , 20 ( 3 ) : 319 – 328 . [CROSSREF] [CSA]
   Google Scholar
• Zuker , M. 2003 . Mfold web server for nucleic acid folding and hybridization prediction . Nucl. Acid. Res. , 31 ( 13 ) : 3406 – 3415 . [CROSSREF]
   Google Scholar