Sudarsan N., Barrick J.E., Breaker R.R. Metabolite-binding RNA domains are present in the genes of eukaryotes // RNA. 2003. V.9. P.644–647.
Sudarsan N., Hammond M.C., Block K.F., Welz R., Barrick J.E., Roth A., Breaker R.R. Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions // Science. 2006. V.314. P.300-304.
Sudarsan N., Wickiser J.K., Nakamura S., Ebert M.S., Breaker R.R. An mRNA structure in bacteria that controls gene expression by binding lysine // Genes Dev. 2003. V.17. P.2688–2697.
Suess B., Fink B., Berens C., Stentz R., Hillen W. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo // Nucleic Acids Research. 2004. V.32. P.1610-1614.
Suess B., Hanson S., Berens C., Fink B., Schroeder R., Hillen W. Conditional gene expression by controlling translation with tetracycline-binding aptamers // Nucleic Acids Res. 2003. V.31. P.1853–1858.
Suga H., Cowan J.A., Szostak J.W. Unusual metal ion catalysis in an acyltransferase ribozyme // Biochemistry. 1998. V.37. P.10118-10125.
Suga H., Lohse P.A., Szostak J.W. Structural and kinetic characterization of an acyl transferase ribozyme // J. Am. Chem. Soc. 1998. V.120. P.1151-1156.
Sullenger B.A., Gilboa E. Emerging clinical applications of RNA // Nature. 2002. V.418. P.252–258.
Sussman D., Nix J.C., Wilson C. The structural basis for molecular recognition by the vitamin B12 RNA aptamer // Nat. Struct. Biol. 2000. V.7. P.53-57.
Sussman D., Wilson C. A water channel in the core of the vitamin B12 RNA aptamer // Structure. 2000. V.8. P.719-727.
Szwajkajzer D., Carey J. Molecular and biological constraints on ligand-binding affinity and specificity // Biopolymers. 1997. V.44. P.181–198.
Tahiri-Alaoui A., Frigotto L., Manville N., Ibrahim J., Romby P., James W. High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands // Nucleic Acids Res. 2002. V.30. P.e45.
Takemura K., Wang P., Vorberg I., Surewicz W., Priola S.A., Kanthasamy A., Pottathil R., Chen S.G., Sreevatsan S.. DNA Aptamers That Bind to PrPC and Not PrPSc Show Sequence and Structure Specificity // Experimental Biology and Medicine. 2006. V.231. P.204-214.
Tanabe T., Kuwabara T., Warashina M., Tani K., Taira K., Asano S. Oncogene inactivation in a mouse model // Nature. 2000. V.406. P.473–474.
Tanabe T., Takata I., Kuwabara T., Warashina M., Kawasaki H., Tani K., Ohta S., Asano S., Taira K. Maxizymes, novel allosterically controllable ribozymes, can be designed to cleave various substrates // Biomacromolecules. 2000. V.1. P.108–117.
Tang J., Breaker R.R. Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection // RNA. 1997. V.3. P.914–925.
Tang J., Breaker R.R. Mechanism for allosteric inhibition of an ATP-sensitive ribozyme // Nucleic Acids Res. 1998. V.26. P.4214–4221.
Tang J., Breaker R.R. Structural diversity of self-cleaving ribozymes // Proc. Natl Acad. Sci. USA. 2000. V.97. P.5784–5789.
Tang J., Xie J., Shao N., Yan Y. The DNA aptamers that specifically recognize ricin toxin are selected by two in vitro selection methods // Electrophoresis. 2006. V.27. P.1303-1311.
Tao J., Frankel A.D. Arginine-binding RNAs resembling TAR identified by in vitro selection // Biochemistry. 1996. V.35. P.2229-2238.
Tao J., Frankel A.D. // Proc. Natl. Acad. Sci. USA. 1992. V.89. P.2723.
Tarasow T.M., Kellogg E., Holley B.L., Nieuwlandt D., Tarasow S.L., Eaton B.E. The effect of mutation on RNA Diels-Alderases // J. Am. Chem. Soc. 2004. V.126. P.11843-11851.
Tarasow T.M., Tarasow S.L., Eaton B.E. RNA-catalysed carbon-carbon bond formation // Nature. 1997. V.389. P.54-57.
Tavitian B. In vivo imaging with oligonucleotides for diagnosis and drug development // Gut. 2003. V.52. P.iv40–iv47.
Tawfik D.S., Griffiths A.D. Man-made cell-like compartments for molecular evolution // Nat. Biotechnol. 1998. V.16. P.652-656.
Taylor S., Stojanovic M.N. Is There a Future for DNA-Based Molecular Devices in Diabetes Management? // Journal of Diabetes Science and Technology. 2007. V.1. P.440-444.
Teramoto N., Ichinari H., Kawazoe N., Imanishi Y., Ito Y. Peroxidase activity of in vitro-selected 2'-amino RNAs // Biotechnol. Bioeng. 2001. V.75. P.463-468.
Teramoto N., Imanishi Y., Ito Y. In vitro selection of a ligase ribozyme carrying alkylamino groups in the side chains // Bioconjug. Chem. 2000. V.11. P.744-748.
Teramoto N., Imanishi Y., Ito Y. In Vitro Selection of Ligase Ribozymes Containing 2'-Amino Groups // Journal of Bioactive and Compatible Polymers. 2000. V.15. P.297-308.
Tereshko V., Skripkin E., Patel D.J. Encapsulating Streptomycin within a small 40-mer RNA // Chem. Biol. 2003. V.10. P.175–187.
Theis M.G., Knorre A., Kellersch B., Moelleken J., Wieland F., Kolanus W., Famulok M. Discriminatory aptamer reveals serum response element transcription regulated by cytohesin-2 // Proc. Natl. Acad. Sci. USA. 2004. V.101. P.11221-11226.
Thompson K.M., Syrett H.A., Knudsen S.M., Ellington A.D. Group I aptazymes as genetic regulatory switches // BMC Biotechnol. 2002. V.2. P.21.
Thore S., Leibundgut M., Ban N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand // Science. 2006. V.312. P.1208–1211.
Thum O., Jager S., Famulok M. Functionalized DNA: A New Replicable Biopolymer // Angew. Chem. Int. Ed. 2001. V.40. P.3990-3993.
Tjandra N., Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium // Science. 1997. V.278. P.1111–1114.
Tian Y., Adya N., Wagner S., Giam C.Z., Green M.R., Ellington A.D. Dissecting protein:protein interactions between transcription factors with an RNA aptamer // RNA. 1995. V.1. P.317-326.
Tok J.B., Cho J., Rando R.R. RNA aptamers that specifically bind to a 16S ribosomal RNA decoding region construct // Nucleic Acids Res. 2000. V.28. P.2902-2910.
Tombelli S., Minunni M., Mascini M. Analytical applications of aptamers // Biosensors & Bioelectronics. 2005. V.20. P.2424–2434.
Tomsic J., McDaniel B.A., Grundy F.J., Henkin T.M. Natural Variability in S-Adenosylmethionine (SAM)-Dependent Riboswitches: S-Box Elements in Bacillus subtilis Exhibit Differential Sensitivity to SAM In Vivo and In Vitro // Journal of Bacteriology. 2008. V.190. P. 823–833.
Tor Y., Hermann T., Westhof E. // Chem. Biol. 1998. V.5. P.R277.
Toulme J.J., Di Primo C., Boucard D. Regulating eukaryotic gene expression with aptamers // FEBS Lett. 2004. V.567. P.55-62.
Travascio P., Bennet A.J., Wang D.Y., Sen D. A ribozyme and a catalytic DNA with peroxidase activity: active sites versus cofactor-binding sites // Chem. Biol. 1999. V.6. P.779-787.
Tsai D.E., Kenan D.J., Keene J.D. In vitro selection of an RNA epitope immunologically cross-reactive with a peptide // Proc. Natl. Acad. Sci. USA. 1992. V.89. P.8864-8868.
Tsang J., Joyce G.F. In vitro evolution of randomized ribozymes // Methods Enzymol. 1996. V.267. P.410-426.
Tsang J., Joyce G.F. Specialization of the DNA-cleaving activity of a group I ribozyme through in vitro evolution // J. Mol. Biol. 1996. V.262. P.31-42.
Tsukiji S., Pattnaik S.B., Suga H. An alcohol dehydrogenase ribozyme // Nat. Struct. Biol. 2003. V.10. P.713-717.
Tsukiji S., Pattnaik S.B., Suga H. Reduction of an aldehyde by a NADH/Zn2+- dependent redox active ribozyme // J. Am. Chem. Soc. 2004. V.126. P.5044-5045.
Tucker C.E., Chen L.S., Judkins M.B., Farmer J.A., Gill S.C., Drolet D.W. Detection and plasma pharmacokinetics of an anti-vascular endothelial growth factor oligonucleotide-aptamer (NX1838) in rhesus monkeys // J. Chromatogr. B. 1999. V.732. P.203-212.
Tuerk C., MacDougal S., Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase // Proc. Natl. Acad. Sci. USA. 1992. V.89. P.6988-6992.
Tuschl T., Eckstein F. Hammerhead ribozymes: importance of stem–loop II for activity // Proc. Natl Acad. Sci. USA. 1993. V.90. P.6991–6994.
Tuschl T., Sharp P.A., Bartel D.P. Selection in vitro of novel ribozymes from a partially randomized U2 and U6 snRNA library // EMBO J. 1998. V.17. P.2637-2650.
Uhlenbeck O.C. Less isn't always more // RNA. 2003. V.9. P.1415-1417.
Ule J., Jensen K., Mele A., Darnell R.B. CLIP: A method for identifying protein–RNA interaction sites in living cells // Methods. 2005. V.37. P.376–386.
Ulrich H. RNA aptamers: From basic science toward therapy // Handb. Exp. Pharmacol. 2006. V.173. P.305–326.
Ulrich H., Magdesian M.H., Alves M.J., Colli W. In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion // J. Biol. Chem. 2002. V.277. P.20756-20762.
Umezawa Y., Shimada T., Kori A., Yamada K., Ishihama A. The Uncharacterized Transcription Factor YdhM Is the Regulator of the nemA Gene, Encoding N-Ethylmaleimide Reductase // J. Bacteriol. 2008. V.190. P.5890-5897.
Unrau P.J., Bartel D.P. An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects // Proc. Natl. Acad. Sci. USA. 2003. V.100. P.15393-15397.
Vaidya A., Suga H. Diverse roles of metal ions in acyl-transferase ribozymes // Biochemistry. 2001. V.40. P.7200-7210.
Vaish N.K., Larralde R., Fraley A.W., Szostak J.W., McLaughlin L.W. A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality // Biochemistry. 2003. V.42. P.8842–8851.
Valegård K., Liljas L., Fridborg K., Unge T. // Nature. 1990. V.345. P.36.
Valegård K., et al. // J. Mol. Biol. 1997. V.270. P.724.
Valegård K., Murray J.B., Stockley P.G., Stonehouse N.J., Liljas L. // Nature. 1994. V.371. P.623.
Valencia-Sanchez M.A., Liu J., Hannon G.J., Parker R. Control of translation and mRNA degradation by miRNA and siRNAs // Genes Dev. 2006. V.20. P.515–524.
Vater A., Jarosch F., Buchner K., Klussmann S. Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX // Nucleic Acids Res. 2003. V.31. P.e130.
Vater A., Klussmann S. Toward third-generation aptamers: Spiegelmers and their therapeutic prospects // Curr. Opin. Drug Discov. Devel. 2003. V.6. P.253-261.
Verhelst S.H., Michiels P.J., van der Marel G.A., van Boeckel C.A., van Boom J.H. Surface plasmon resonance evaluation of various aminoglycoside-RNA hairpin interactions reveals low degree of selectivity // Chembiochem. 2004. V.5. P.937–942.
Vester B., Lundberg L.B., Sorensen M.D., Babu R., Douthwaite S., Wengel J. LNAzymes: incorporation of LNA-type monomers into DNAzymes markedly increases RNA cleavage // J. Am. Chem. Soc. 2002. V.124. P.13682–13683.
Vianini E., Palumbo M., Gatto B. In vitro selection of DNA aptamers that bind Ltyrosinamide // Bioorg. Med. Chem. 2001. V.9. P.2543-2548.
Vicens Q., Allen M.A., Gilbert S.D., Reznik B., Gooding A.R., Batey R.T. The Cech Symposium: A celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom // RNA. 2008. V.14. P.397-403.
Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation // Nucleic Acids Res. 2002. V.30. P.3141-3151.
Vo N.V., Oh J.-W., Lai M.M.C. Identification of RNA ligands that bind hepatitis C virus polymerase selectively and inhibit its RNA synthesis from the natural viral RNA templates // Virology. 2003. V.307. P.301.
von Ahsen U., Davies J., Schroeder R. Antibiotic inhibition of group I ribozyme function // Nature. 1991. V.353. P.368-370.
von Ahsen U., Davies J., Schroeder R. Non-competitive inhibition of group I intron RNA self-splicing by aminoglycoside antibiotics // J. Mol. Biol. 1992. V.226. P.935-941.
von Ahsen U., Schroeder R. Streptomycin and self-splicing // Nature. 1990. V.346. P.801.
von Ahsen U., Schroeder R. Streptomycin inhibits splicing of group I introns by competition with the guanosine substrate // Nucleic Acids Res. 1991. V.19. P.2261-2265.
Vuyisich M., Beal P.A. Controlling protein activity with ligand-regulated RNA aptamers // Chem. Biol. 2002. V.9. P.907-913.
Wadkins T.S., Been M.D. Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus // Nucleic Acids Res. 1997. V.25. P.4085–4092.
Wahlestedt C., Salmi P., Good L., Kela J., Johnsson T., Hokfelt T., Broberger C., Porreca F., Lai J., Ren K., Ossipov M., Koshkin A., Jakobsen N., Skouv J., Oerum H., Jacobsen M.H., Wengel J. Potent and nontoxic antisense oligonucleotides containing locked nucleic acids // Proc. Natl. Acad. Sci. USA. 2000. V.97. P.5633–5638.
Wallace S.T., Schroeder R. In vitro selection and characterization of streptomycin-binding RNAs: recognition discrimination between antibiotics // RNA. 1998. V.4. P.112–123.
Wallimann P., Marti T., Fürer A., Diederich F. // Chem. Rev. 1997. V.97. P.1567–1608.
Wallis M.G., Streicher B., Wank H., von Ahsen U., Clodi E., Wallace S.T., Famulok M., Schroeder R. In vitro selection of a viomycin-binding RNA pseudoknot // Chem. Biol. 1997. V.4. P.357-366.
Wallis M.G., von Ahsen U., Schroeder R., Famulok M. A Novel RNA motif for neomycin recognition // Chem. Biol. 1995. V.2. P.543–552.
Wang D.Y., Lai B.H., Feldman A.R., Sen D. A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes // Nucleic Acids Res. 2002. V.30. P.1735–1742.
Wang D.Y., Lai B.H., Sen D. A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes // J. Mol. Biol. 2002. V.318. P.33–43.
Wang D.Y., Sen D. A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate // J. Mol. Biol. 2001. V.310. P.723-734.
Wang D.Y., Sen D. Rationally designed allosteric variants of hammerhead ribozymes responsive to the HIV-1 Tat protein // Comb. Chem. High Throughput Screen. 2002. V.5. P.301–312.
Wang H., Tor Y. // Angew. Chem. Int. Ed. Engl. 1998. V.37. P.109.
Wang J., Jiang H., Liu F. In vitro selection of novel RNA ligands that bind human cytomegalovirus and block viral infection // RNA. 2000. V.6. P.571-583.
Wang K.Y., Krawczyk S.H., Bischofberger N., Swaminathan S., Bolton P.H. The tertiary structure of a DNA aptamer which binds to and inhibits thrombin determines activity // Biochemistry. 1993. V.32. P.11285-11292.
Wang K.Y., McCurdy S., Shea R.G., Swaminathan S., Bolton P.H. A DNA aptamer which binds to and inhibits thrombin exhibits a new structural motif for DNA // Biochemistry. 1993. V.32. P.1899-1904.
Wang Q.S., Unrau P.J. Ribozyme motif structure mapped using random recombination and selection // RNA. 2005. V.11. P.404-411.
Wang S., White K.A. Riboswitching on RNA virus replication // PNAS. 2007. V.104. P.10406-10411.
Wang W., Billen L.P., Li Y. Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes // Chem. Biol. 2002. V.9. P.507-517.
Wang Y., Killian J., Hamasaki K., Rando R.R. RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities // Biochemistry. 1996. V.35. P.12338–12346.
Wang Y., Rando R.R. Specific binding of aminoglycoside antibiotics to RNA // Chem. Biol. 1995. V.2. P.281–290.
Wang Y., Silverman S.K. Deoxyribozymes That Synthesize Branched and Lariat RNA // J. Am. Chem. Soc. 2003. V.125. P.6880-6881.
Wang Y., Silverman S.K. Efficient One-Step Synthesis of Biologically Related Lariat RNAs by a Deoxyribozyme // Angew. Chem. Int. Ed. 2005. V.44. P.5863-5866.
Warner R.G., Hundt C., Weiss S., Turnbull J.E. Identification of the heparan sulfate binding sites in the cellular prion protein // J. Biol. Chem. 2002. V.277. P.18421–18430.
Warren C.L., Kratochvil N.C.S., Hauschild K.E., Foister S., Brezinski M.L., Dervan P.B., Phillips Jr. G.N., Ansari A.Z. Defining the sequence-recognition profile of DNA-binding molecules // PNAS. 2006. V.103. P.867-872.
Wecker M., Smith D., Gold L. In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide // RNA. 1996. V.2. P.982-994.
Wedekind J.E., McKay D.B. Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis // Nat. Struct. Biol. 1999. V.6. P.261-268.
Wedekind J.E., McKay D.B. Crystal structure of the leadzyme at 1.8 Å resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation // Biochemistry. 2003. V.42. P.9554-9563.
Weigand J.E., Sanchez M., Gunnesch E.-B., Zeiher S., Schroeder R., Suess B. Screening for engineered neomycin riboswitches that control translation initiation // RNA. 2008. V.14. P.89-97.
Weigand J.E., Suess B. Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast // Nucleic Acids Res. 2007.|
Weigand B.S., Zerressen A., Schlatterer J.C., Helm M., Jäschke A. // Klussmann S., Ed. The Aptamer Handbook. Wiley-VCH, Weinheim, 2006. P.211–227.
Weill L., Louis D., Sargueil B. Selection and evolution of NTP-specific aptamers // Nucleic Acids Res. 2004. V.32. P.5045-5058.
Weinberg Z., Regulski E.E., Hammond M.C., Barrick J.E., Yao Z., Ruzzo W.L., Breaker R.R. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches // RNA. 2008. V.14. P.822-828.
Weinger J.S., Parnell K.M., Dorner S., Green R., Strobel S.A. Substrate-assisted catalysis of peptide bond formation by the ribosome // Nat. Struct. Mol. Biol. 2004. V.11. P.1101-1106.
Weiss S., Proske D., Neumann M., Groschup M.H., Kretzschmar H.A., Famulok M., Winnacker E.L. RNA aptamers specifically interact with the prion protein PrP // J. Virol. 1997. V.71. P.8790–8797.
Welz R., Breaker R.R. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis // RNA. 2007. V.13. P.573–582.
Werstuck G., Green M.R. Controlling gene expression in living cells through small molecule-RNA interactions // Science. 1998. V.282. P.296–298.
White R., Rusconi C., Scardino E., Wolberg A., Lawson J., Hoffman M., Sullenger B. Generation of species cross-reactive aptamers using "toggle" SELEX // Mol. Ther. 2001. V.4. P.567-573.
White R.R., Shan S., Rusconi C.P., Shetty G., Dewhirst M.W., Kontos C.D., Sullenger B.A. Inhibition of rat corneal angiogenesis by a nuclease-resistant RNA aptamer specific for angiopoietin-2 // Proc. Natl. Acad. Sci. USA. 2003. V.100. P.5028-5033.
White R.R., Sullenger B.A., Rusconi C.P. Developing aptamers into therapeutics // J. Clin. Invest. 2000. V.106. P.929–934.
Wiegand T.W., Janssen R.C., Eaton B.E. Selection of RNA amide synthases // Chem. Biol. 1997. V.4. P.675-683.
Wiegand T.W., Williams P.B., Dreskin S.C., Jouvin M.H., Kinet J.P., Tasset D. High-affinity oligonucleotide ligands to human IgE inhibit binding to Fcε receptor I // J. Immunol. 1996. V.157. P.221-230.
Williams K.P., Bartel D.P. PCR product with strands of unequal length // Nucleic Acids Res. 1995. V.23. P.4220-4221.
Williams K.P., Ciafre S., Tocchini-Valentini G.P. Selection of novel Mg2+-dependent self-cleaving ribozymes // EMBO J. 1995. V.14. P.4551-4557.
Williams K.P., Liu X.H., Schumacher T.N., Lin H.Y., Ausiello D.A., Kim P.S., Bartel D.P. Bioactive and nuclease-resistant L-DNA ligand of vasopressin // Proc. Natl. Acad. Sci. USA. 1997. V.94. P.11285-11290.
Willis M.C., Collins B.D., Zhang T., Green L.S., Sebesta D.P., Bell C., Kellogg E., Gill S.C., Magallanez A., Knauer S., Bendele R.A., Gill P.S., Janjic N. Liposome-anchored vascular endothelial growth factor aptamers // Bioconjug. Chem. 1998. V.9. P.573-582.
Wilson C., Nix J., Szostak J. Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot // Biochemistry. 1998. V.37. P.14410-14419.
Wilson C., Szostak J.W. In vitro evolution of a self-alkylating ribozyme // Nature. 1995. V.374. P.777-782.
Wilson C., Szostak J.W. Isolation of a fluorophore-specific DNA aptamer with weak redox activity // Chem. Biol. 1998. V.5. P.609-617.
3. Wilson D.S., Szostak J.W. In vitro selection of functional nucleic acids // Annu. Rev. Biochem. 1999. V.68. P.611–647.
Win M.N., Klein J.S., Smolke C.D. Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay // Nucleic Acids Research. 2006. V.34. P.5670-5682.
Win M.N., Smolke C.D. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function // PNAS. 2007. V.104. P.14283-14288.
Winkler W.C., Breaker R.R. Regulation of bacterial gene expression by riboswitches // Annu. Rev. Microbiol. 2005. V.59. P.487–517.
Winkler W.C., Breaker R.R. Genetic control by metabolite-binding riboswitches // Chembiochem. 2003. V.4. P.1024–1032.
Winkler W.C., Cohen-Chalamish S., Breaker R.R. An mRNA structure that controls gene expression by binding FMN // Proc. Natl Acad. Sci. USA. 2002. V.99. P.15908–15913.
Winkler W., Nahvi A., Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression // Nature. 2002. V.419. P.952–956.
Winkler W.C., Nahvi A., Roth A., Collins J.A., Breaker R.R. Control of gene expression by a natural metabolite-responsive ribozyme // Nature. 2004. V.428. P.281–286.
Winkler W.C., Nahvi A., Sudarsan N., Barrick J.E., Breaker R.R. An mRNA structure that controls gene expression by binding S-adenosylmethionine // Nat. Struct. Biol. 2003. V.10. P.701–707.
Wlotzka B., Leva S., Eschgfaller B., Burmeister J., Kleinjung F., Kaduk C., Muhn P., Hess-Stumpp H., Klussmann S. In vivo properties of an anti-GnRH Spiegelmer: an example of an oligonucleotide-based therapeutic substance class // Proc. Natl. Acad. Sci. USA. 2002. V.99. P.8898-8902.
Woese C.R., Winker S., Gutell R.R. // Proc. Natl. Acad. Sci. USA. 1990. V.87. P.8467.
Wright M.C., Joyce G.F. Continuous in vitro evolution of catalytic function // Science. 1997. V.276. P.614-617.
Wu H.N., Lin Y.J., Lin F.P., Makino S., Chang M.F., Lai M.M. Human hepatitis delta virus RNA subfragments contain an autocleavage activity // Proc. Natl Acad. Sci. USA. 1989. V.86. P.1831–1835.
Wu L.H., Curran J.F. An allosteric synthetic DNA // Nucleic Acids Res. 1999. V.27. P.1512–1516.
Wurster S.E., Maher III L.J. Selection and characterization of anti-NF-{kappa}B p65 RNA aptamers // RNA. 2008. V.14. P.1037-1047.
Xayaphoummine A., Viasnoff V., Harlepp S., Isambert H. Encoding folding paths of RNA switches // Nucleic Acids Res. 2007. V.35. P.614-622.
Xu W., Ellington A.D. Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope // Proc. Natl. Acad. Sci. USA. 1996. V.93. P.7475-7480.
Xu X., Hamhouyia F., Thomas S.D., Burke T.J., Girvan A.C., McGregor W.G., Trent J.O., Miller D.M., Bates P.J. Inhibition of DNA Replication and Induction of S Phase Cell Cycle Arrest by G-rich Oligonucleotides // J. Biol. Chem. 2001. V.276. P.43221-43230.
Yamamoto R., Katahira M., Nishikawa S., Baba T., Taira K., Kumar P.K. A novel RNA motif that binds efficiently and specifically to the Tat protein of HIV and inhibits the trans-activation by Tat of transcription in vitro and in vivo // Genes Cells. 2000. V.5. P.371-388.
Yamamoto-Fujita R., Kumar P.K.R. Aptamer-derived nucleic acid oligos: applications to develop nucleic acid chips to analyze proteins and small ligands // Anal. Chem. 2005. V.77. P.5460–5466.
Yang C.J., Jockusch S., Vicens M., Turro N.J., Tan W. Light-switching excimer probes for rapid protein monitoring in complex biological fluids // PNAS. 2005. V.102. P.17278-17283.
Yang C., Yan N., Parish J., Wang X., Shi Y., Xue D. RNA Aptamers Targeting the Cell Death Inhibitor CED-9 Induce Cell Killing in Caenorhabditis elegans // J. Biol. Chem. 2006. V.281. P.9137-9144.
Yang Q., Goldstein I.J., Mei H.Y., Engelke D.R. DNA ligands that bind tightly and selectively to cellobiose // Proc. Natl Acad. Sci. USA. 1998. V.95. P.5462–5467.
Yang W., Wang Q., Howell K.L., Lee J.T., Cho D.S., Murray J.M., Nishikura K. ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells // J. Biol. Chem. 2005. V.280. P.3946–3953.
Yang Y., Kochoyan M., Burgstaller P., Westhof E., Famulok M. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy // Science. 1996. V.272. P.1343–1347.
Yarus M. RNA-ligand chemistry: a testable source for the genetic code // RNA. 2000. V.6. P.475-484.
Ye X., Gorin A., Ellington A.D., Patel D.J. Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex // Nat. Struct. Biol. 1996. V.3. P.1026-1033.
Yen L., Svendsen J., Lee J.S., Gray J.T., Magnier M., Baba T., D'Amato R.J., Mulligan R.C. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage // Nature. 2004. V.431. P.471–476.
Ylera F., Lurz R., Erdmann V.A., Furste J.P. Selection of RNA aptamers to the Alzheimer's disease amyloid peptide // Biochem. Biophys. Res. Commun. 2002. V.290. P.1583-1588.
Yoshizawa S., Fourmy D., Puglisi J.D. // EMBO J. 1998. V.17. P.6437.
Zamore P.D., Haley B. Ribo-gnome: The big world of small RNAs // Science. 2005. V.309. P.1519–1524.
Zhang B., Cech T.R. Peptide bond formation by in vitro selected ribozymes // Nature. 1997. V.390. P.96-100.
Zhang H., Kolb F.A., Jaskiewicz L., Westhof E., Filipowicz W. Single processing center models for human Dicer and bacterial RNase III // Cell. 2004. V.118. P.57–68.
Zhang L., Kasif S., Cantor A.C.R. Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy // PNAS. 2007. V.104. P.3061-3066.
Zhang Q., Sun X., Watt E.D., Al-Hashimi H.M. Resolving the Motional Modes That Code for RNA Adaptation // Science. 2006. V.311. P.653-656.
Zhu L., Anslyn E.V. Signal amplification by allosteric catalysis // Angew. Chem. Int. Ed. Engl. 2006. V.45. P.1190–1196.
||Zhuang X., Bartley L.E., Babcock H.P., Russell R., Ha T., Herschlag D., Chu S. A single-molecule study of RNA catalysis and folding // Science. 2000. V.288. P.2048–2051.
Zimmermann G.R., Jenison R.D., Wick C.L., Simorre J.P., Pardi A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA // Nat. Struct. Biol. 1997. V.4. P.644–649.
Zimmermann G.R., Shields T.P., Jenison R.D., Wick C.L., Pardi A. A semiconserved residue inhibits complex formation by stabilizing interactions in the free state of a theophylline-binding RNA // Biochemistry. 1998. V.37. P.9186-9192.
Zimmermann G.R., Wick C.L., Shields T.P., Jenison R.D., Pardi A. Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer // RNA. 2000. V.6. P.659-667.
Zivarts M., Liu Y., Breaker R.R. Engineered allosteric ribozymes that respond to specific divalent metal ions // Nucleic Acids Res. 2005. V.33. P.622-631.
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction // Nucleic Acids Res. 2003. V.31. P.3406–3415.
Zuker M. Computer prediction of RNA structure // Methods Enzymol. 1989. V.183. P.202–287.
Pan K.M., Baldwin M., Nguyen J., Gasset M., Serban A., Groth D., Mehlhorn I., Huang Z., Fletterick R.J., Cohen F.E. Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins // Proc. Natl. Acad. Sci. USA. 1993. V.90. P.10962–10966.
Huang Z., Gabriel J.M., Baldwin M.A., Fletterick R.J., Prusiner S.B., Cohen F.E. Proposed three-dimensional structure for the cellular prion protein // Proc. Natl. Acad. Sci. USA. 1994. V.91. P.7139–7143.
Cohen F.E., Pan K.M., Huang Z., Baldwin M., Fletterick R.J., Prusiner S.B. Structural clues to prion replication // Science. 1994. V.264. P.530–531.
Scott M., Foster D., Mirenda C., Serban D., Coufal F., Walchli M., Torchia M., Groth D., Carlson G., DeArmond S.J. Transgenic mice expressing hamster prion protein produce species-specific scrapie infectivity and amyloid plaques // Cell. 1989. V.59. P.847–857.
Saborio G.P., Permanne B., Soto C. Sensitive detection of pathological prion protein by cyclic amplification of protein misfolding // Nature. 2001. V.411. P.810–813.
Castilla J., Saa P., Hetz C., Soto C. In vitro generation of infectious scrapie prions // Cell. 2005. V.121. P.195–206.
Gajdusek D.C. The transmissible amyloidoses: genetical control of spontaneous generation of infectious amyloid proteins by nucleation of configurational change in host precursors: kuru-CJD-GSS-scrapie-BSE // Eur. J. Epidemiol. 1991. V.5. P.567–577.
Prusiner S.B., McKinley M.P., Groth D.F., Bowman K.A., Mock N.I., Cochran S.P., Masiarz F.R. Scrapie agent contains a hydrophobic protein // Proc. Natl. Acad. Sci. USA. 1981. V.78. P.6675–6679.
McKinley M.P., Bolton D.C., Prusiner S.B. A protease-resistant protein is a structural component of the scrapie prion // Cell. 1983. V.35. P.57–62.
Bolton D.C., McKinley M.P., Prusiner S.B. Identification of a protein that purifies with the scrapie prion // Science. 1982. V.218. P.1309–1311.
Yokoyama T., Kimura K.M., Ushiki Y., Yamada S., Morooka A., Nakashiba T., Sassa T., Itohara S. In vivo conversion of cellular prion protein to pathogenic isoforms, as monitored by conformation-specific antibodies // J. Biol. Chem. 2001. V.276. P.11265–11271.
Winkler W., Nahvi A., Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression // Nature. 2002. V.419. P.952–956.
Filipowicz W., Jaskiewicz L., Kolb F.A., Pillai R.S. Post-transcriptional gene silencing by siRNAs and miRNAs // Curr. Opin. Struct. Biol. 2005. V.15. P.331–341.
Okazaki Y., Furuno M., Kasukawa T., Adachi J., Bono H., Kondo S., Nikaido I., Osato N., Saito R., Suzuki H., et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs // Nature. 2002. V.420. P.563–573.
Numata K., Kanai A., Saito R., Kondo S., Adachi J., Wilming L.G., Hume D.A., Hayashizaki Y., Tomita M. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection // Genome Res. 2003. V.13. P.1301–1306.
Huttenhofer A., Kiefmann M., Meier-Ewert S., O'Brien J., Lehrach H., Bachellerie J.P., Brosius J. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse // EMBO J. 2001. V.20. P.2943–2953.
Wassarman K.M., Repoila F., Rosenow C., Storz G., Gottesman S. Identification of novel small RNAs using comparative genomics and microarrays // Genes Dev. 2001. V.15. P.1637–1651.
Yuan G.Z., Klambt C., Bachellerie J.P., Brosius J., Huttenhofer A. RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs // Nucleic Acids Res. 2003. V.31. P.2495–2507.
Rivas E., Klein R.J., Jones T.A., Eddy S.R. Computational identification of noncoding RNAs in E-coli by comparative genomics // Curr. Biol. 2001. V.11. P.1369–1373.
Carter R.J., Dubchak I., Holbrook S.R. A computational approach to identify genes for functional RNAs in genomic sequences // Nucleic Acids Res. 2001. V.29. P.3928–3938.
Kim N., Shiffeldrim N., Gan H.H., Schlick T. Candidates for novel RNA topologies // J. Mol. Biol. 2004. V.341. P.1129–1144.
Gan H.H., Pasquali S., Schlick T. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design // Nucleic Acids Res. 2003. V.31. P.2926–2943.
Lim L.P., Lau N.C., Weinstein E.G., Abdelhakim A., Yekta S., Rhoades M.W., Burge C.B., Bartel D.P. The microRNAs of Caenorhabditis elegans // Genes Dev. 2003. V.17. P.991–1008.
Macke T.J., Ecker D.J., Gutell R.R., Gautheret D., Case D.A., Sampath R. RNAMotif, an RNA secondary structure definition and search algorithm // Nucleic Acids Res. 2001. V.29. P.4724–4735.
Rangan P., Masquida B., Westhof E., Woodson S.A. Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme // Proc. Natl. Acad. Sci. USA. 2003. V.100. P.1574–1579.
Kitagawa J., Futamura Y., Yamamoto K. Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures // Nucleic Acids Res. 2003. V.31. P.2006–2013.
Reinert G., Schbath S., Waterman M.S. Probabilistic and statistical properties of words: an overview // J. Comput. Biol. 2000. V.7. P.1–46.
Durbin R., Eddy S., Krogh A., Mitchison G. Biological Sequence Analysis Probabilistic Models of Proteins and Nucleic Acids, Cambridge, UK Cambridge University Press, 1998.
Rivas E., Eddy S.R. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs // Bioinformatics. 2000. V.16. P.583–605.
Keiper S., Bebenroth D., Seelig B., Westhof E., Jäschke A. Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket // Chem. Biol. 2004. V.11. P.1217–1227.
Seelig B., Jäschke A. A small catalytic RNA motif with Diels-Alderase activity // Chem. Biol. 1999. V.6. P.167–176.
Seelig B., Keiper S., Stuhlmann F., Jäschke A. Enantioselective ribozyme catalysis of a bimolecular cycloaddition reaction // Angew. Chem. Int. Ed. Engl. 2000. V.39. P.4576–4579.
Serganov A., Keiper S., Malinina L., Tereshko V., Skripkin E., Höbartner C., Polonskaia A., Phan A.T., Wombacher R., Micura R., et al. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation // Nature Struct. Mol. Biol. 2005. V.12. P.218–224.
Stuhlmann F., Jäschke A. Characterization of an RNA active site: interactions between a Diels-Alderase ribozyme and its substrates and products // J. Am. Chem. Soc. 2002. V.124. P.3238–3244.
Wombacher R., Keiper S., Suhm S., Serganov A., Patel D.J., Jäschke A. Control of stereoselectivity in an enzymatic reaction by backdoor access // Angew. Chem. Int. Ed. Engl. 2006. V.45. P.2469–2472.
Duckett D., Lilley D.M.J. // EMBO J. 1990. V.9. P.1659–1664.
Guo Q., Lu M., Churchill M.E.A., Kallenbach N.R. // Biochemistry. 1990. V.29. P.10927–10934.
Lu M., Guo Q., Kallenbach N.R. // Biochemistry. 1991. V.30. P.5815–5820.
Rimmer J.J., Hinde C.J. Acceptance of Context Sensitive Languages Using Ribonucleic Acid Computation // Boris Mirkin and George Magoulas, Eds. Proceedings of the 2005 UK Workshop on Computational Intelligence. London, UK, 5-7 September 2005. Birkbeck University of London, 2005. P.289-294.
Winfree E. Whiplash pcr for o(1) computing // Technical Report 1998.23, Caltech, 1998.
Hagiya M., Arita M., Kiga D., Sakamoto K., Yokoyama S. // H. Rubin and D. H Woods, editors. DNA Based Computers III. American Mathematical Society, 1999. P.55-72.
Sakamoto K., Kiga D., Komiya K., Gouzu H., Yokoyama S., Ikeda S., Sugiyama H., Hagiya M. State transitions by molecules // Biosystems. 1999. V.52. P.81–91.
Nishikawa A., Hagiya M. Towards a system for simulating DNA computing with whiplash PCR // P.J.Angeline, Z.Michalewicz, M.Schoenauer, X.Yao, A.Zalzala, editors. Proceedings of the Congress on Evolutionary Computation. V.2. Mayflower Hotel,Washington D.C., USA, 6-9 1999. IEEE Press, 1999. P.960-966.
Rose J.A., Deaton R.J., Hagiya M., Suyama A. Pna-mediated whiplash pcr // Lecture Notes In Computer Science 2340. 2001. P.104 – 116.
Matsuda D., Yamamura M. Cascading whiplash pcr with a nicking enzyme // Lecture Notes In Computer Science 2568. 2002. P.38 – 46.
Reif J.H., Majumder U. Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular Computation, Fourteenth International Meeting on DNA Based Computers (DNA14), Prague, Czech Republic (June, 2008). To appear in Lecture Notes for Computer Science (LNCS), NYC, NY, (edited by Ashish Goel and Friedrich C. Simmel), Springer-Verlag, New York, (2009). Электронный вариант доступен по адресу: ke.edu/~reif/paper/urmi/whipPCR/whipPCR.pub.pdf.
Wang H. Dominoes and the AEA Case of the Decision Problem // J. Fox, Eds. Mathematical Theory of Automata. Brooklyn, N.Y., Polytechnic Press, 1963. P.23-55.
Seeman N.C. Nucleicacid junctions and lattices // Journal of Theoretical Biology. 1982. V.2. P.237-247.
Winfree E. On the computational power of DNA annealing and ligation // Lipton E.J., Baum E.B., Eds. DNA Based Computing. Providence: Am. Math. Soc., 1996. P.199-219.
Winfree E., Liu F., Wenzler L.A., Seeman N.C. Design and selfassembly of twodimensional DNA crystals // Nature. 1998. V.394. P.539-544.
LaBean T.H., Winfree E., Reif J.H. Experimental Progress in Computation by Self-Assembly of DNA Tilings // DIMACS Series in Discrete Mathematics and Theoretical Computer Science. 2000. V.54. P.123-140.
Rothemund P., Winfree E. The programsize complexity of selfassembled squares // F. F. Yao, editor. Proceedings of the 32nd Annual ACM Symposium on Theory of Computing. Portland, OR, 21--23 May 2000.
Winfree E., Eng T., Rozenberg G. String tile models for DNA computing by selfassembly // A. Condon, G. Rozenberg, editors. DNA Based Computers VI. Leiden, The Netherlands, 13--17 June 2000.
Kao M., Ramachandran V. DNA Self-Assembly for Constructing 3D Boxes // Proc. ISAAC 2001, LNCS 2223. 2001. P.429-440.
Mao C., Sun W., Shen Z., Seeman N. A DNA nanomechanical device based on the B-Z transition // Nature. 1999. V.397. P.144-146.
Tian Y., Mao C. Molecular gears: A pair of DNA circles continously rolls against each other // J. Am. Chem. Soc. 2004. V.126. P.11410-11411.
Yan H., Zhang X., Shen Z., Seeman N. A robust DNA mechanical device controlled by hybridization topology // Nature. 2002. V.415. P.62-65.
Simmel F., Yurke B. Using DNA to construct and power a nanoactuator // Phys. Rev. E. 2001. V.63. P.41913.
Simmel F., Yurke B. A DNA-based molecular device switchable between three distinct mechanical states // Appl. Phys. Lett. 2002. V.80. P.883-885.
Yurke B., Turberfield A., Mills J.A.P., Simmel F., Neumann J. A DNA-fuelled molecu-lar machine made of DNA // Nature. 2000. V.406. P.605-608.
Alberti P., Mergny J. DNA duplex-quadruplex exchange as the basis for a nanomolecular machine // Proc. Natl. Acad. Sci. USA. 2003. V.100. P.1569-1573.
Feng L., Park S., Reif J., Yan H. A two-state DNA lattice switched by DNA nanoactuator // Angew. Chem. Int. Ed. 2003. V.42. P.4342-4346.
Li J., Tan W. A single DNA molecule nanomotor // Nano Lett. 2002. V.2. P.315-318.
Sherman W., Seeman N. A precisely controlled DNA biped walking device // Nano Lett. 2004. V.4. P.1203-1207.
Shin J., Pierce N. A synthetic DNA walker for molecular transport // J. Am. Chem. Soc. 2004. V.126. P.10834-10835.
Reif J.H. The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA // DNA Based Computers, Sapporo, Japan. Edited by Masami Hagiya and Azuma Ohuchi. LNCS. 2003. V.2568. P.22-37.
Yin P., Turberfield A.J., Sahu S., Reif J.H. Designs for Autonomous Unidirectional Walking DNA Devices // Tenth International Meeting on DNA Based Computers, Milano, Italy. Edited by C Ferretti, G. Mauri and C. Zandron. LNCS. 2005. V.3384. P.410-425.
Yin P., Yan H., Daniel X.G., Turberfield A.J., Reif J.H. A Unidirectional DNA Walker Moving Autonomously Along a Linear Track // Angewandte Chemie. 2004. V.43. N.37. P.4906-4911.
Chen Y., Wang M., Mao C. An autonomous DNA motor powered by a DNA enzyme // Angew. Int. Ed. 2004. V.43. P.2-5.
Sherman W.B., Seeman N.C. A precisely controlled DNA biped walking device // Nano. Lett. 2004. V.4. P.1203-1207.
Turberfield A., Mitchell J., Yurke B., Mills J.A.P., Blakey M., Simmel F. DNA fuel for free-running nanomachines // Phys. Rev. Lett. 2003. V.90. P.118102.
Barish R.D., Rothemund P.W.K., Winfree E. Two Computational Primitives for Algorithmic Self-Assembly: Copying and Counting // NanoLetters. 2005. V.5. P.2586-2592.
Mao C., LaBean T.H., Reif J.H., Seeman N.C. Logical Computation Using Algorithmic Self-Assembly of DNA Triple Crossover Molecules // Nature. 2000. V.407. P.493-496.
Rothemund P.W.K., Papadakis N., Winfree E. Algorithmic Self-Assembly of DNA Sierpinski Triangles // PLoS Biology. 2004. V.2.
Yan H., Feng L., LaBean T.H., Reif J. DNA Nanotubes, Parallel Molecular Computations of Pairwise Exclusive-Or (XOR) Using DNA "String Tile" Self-Assembly // Journal of American Chemistry Society(JACS). 2003. V.125. P.14246-14247.
Carbone A., Seeman N.C. Circuits and Programmable Self-Assembling DNA Structures // Proc. Nat. Acad. Sci. USA. 2002. V.99. P.12577-12582.
Reif J., Sahu S. Autonomous Programmable DNA Nanorobotic Devices Using DNAzymes // 13th International Meeting on DNA Computing (DNA 13), Memphis, Tennessee, June 4-8, 2007. P.1–16.
Yin P., Turberfield A., Sahu S., Reif J. Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion // Tenth International Meeting on DNA Computing. LNCS. 2005. V.3384. P.426--444.
Cavalcanti A. Assembly Automation with Evolutionary Nanorobots and Sensor-Based Control applied to Nanomedicine // IEEE Transactions on Nanotechnology. 2003. V. 2. P.82-87.
Douglas T. et al. Synthesis and structure of an iron(III) sulfide–ferritin bioinorganic nanocomposite // Science. 1995. V.269. P.54–57.
Meldrum F.C., Heywood B.R., Mann S. Magnetoferritin—in vitro synthesis of a novel magnetic protein // Science. 1992. V.257. P.522–523.
Ueno T. et al. Size-selective olefin hydrogenation by a Pd nanocluster provided in an apoferritin cage // Angew. Chem. Int. Edn. 2004. V.43. P.2527–2530.
Seebeck F.P., Woycechowsky K.J., Zhuang W., Rabe J.P., Hilvert D. A simple tagging system for protein encapsulation // J. Am. Chem. Soc. 2006. V.128. P.4516–4517.
Varpness Z., Peters J.W., Young M., Douglas T. Biomimetic synthesis of an H2 catalyst using a protein cage architecture // Nano Lett. 2005. V.5. P.2306–2309.
Douglas T., Young M. Host–guest encapsulation of materials by assembled virus protein cages // Nature. 1998. V.393. P.152–155.
Douglas T. et al. Protein engineering of a viral cage for constrained nanomaterials synthesis // Adv. Mater. 2002. V.14. P.415–418.
Douglas T., Young M. Viruses: Making friends with old foes // Science. 2006. V.312. P.873–875.
Flynn C.E., Lee S.-W., Peelle B.R., Belcher A.M. Viruses as vehicles for growth, organization and assembly of materials // Acta Mater. 2003. V.51. P.5867–5880.
Shenton W., Douglas T., Young M., Stubbs G., Mann S. Inorganic–organic nanotube composites from template mineralization of tobacco mosaic virus // Adv. Mater. 1999. V.11. P.253–256.
Dujardin E., Peet C., Stubbs G., Culver J.N., Mann S. Organization of metallic nanoparticles using tobacco mosaic virus templates // Nano Lett. 2003. V.3. P.413–417.
Mao C.B. et al. Virus-based toolkit for the directed synthesis of magnetic and semiconducting nanowires // Science. 2004. V.303. P.213–217.
Carette N. et al. A virus-based biocatalyst // Nature Nanotech. 2007. V.2. P.226–229.
Arora P.S., Kirshenbaum K. Nano-tailoring: Stitching alterations on viral coats // Chem. Biol. 2004. V.11. P.418–420.
Wang Q. et al. Bioconjugation by copper(I)-catalyzed azide-alkyne 3 ю 2 cycloaddition // J. Am. Chem. Soc. 2003. V.125. P.3192–3193.
Hooker J.M., Kovacs E.W., Francis M.B. Interior surface modification of bacteriophage MS2 // J. Am. Chem. Soc. 2004. V.126. P.3718–3719.
Comellas-Aragone M., Engelkamp H., Claessen V.I., Sommerdijk N.A.J.M., Rowan A.E., Christianen P.C.M., Maan J.C., Verduin B.J.M., Cornelissen J.J.L.M., Nolte R.J.M. A virus-based single-enzyme nanoreactor // Nature nanotechnology. 2007. V.2. P.635-639.
Venkataraman S., Dirks R.M., Rothemund P.W.K., Winfree E., Pierce N.A. An autonomous polymerization motor powered by DNA hybridization // Nature Nanotechnology. 2007. V.2. P.490-494.
Wang Y., Muller J.E., Kemper B., Seeman N.C. The assembly and characterization of 5-arm and 6-arm DNA branched junctions // Biochemistry. 1991. V.30. P.5667-5674.
LaBen T.H., Yan H., Kopatsch J., Liu F., Winfree E., Reif J.H, Seeman N.C. The Construction of DNA Triple Crossover Molecules // Journal of the American Chemical Society. 2000. V.122. P.1848-1860.
Park S.H., Pistol C., Ahn S.J., Reif J.H., Lebeck A.R., Dwyer C., LaBean T.H. Finite-size, fully addressable dna tile lattices formed by hierarchical assembly procedures // Angew. Chem. Int. Ed. 2006. V.45. P.735-739.
Chen J., Seeman N.C. The electrophoretic properties of a DNA cube and its sub-structure catenanes // Electrophoresis. 1991. V.12. P.607-611.
Ajo-Franklin C.M., Drubin D.A., Eskin J.A., Gee E.P.S., Landgraf D., Phillips I., Silver P.A. Rational design of memory in eukaryotic cells // Genes & Dev. 2007. V.21. P.2271-2276.
Anantharam A., Markowitz S.M., Abbott G.W. Pharmacogenetic considerations in diseases of cardiac ion channels // J. Pharmacol. Exp. Ther. 20003. V.307. P.831–838.
Anderson J.C., Clarke E.J., Arkin A.P., Voigt C.A. Environmentally controlled invasion of cancer cells by engineered bacteria // J. Mol. Biol. 2006. V.355. P.619–627.
Andrianantoandro E., Basu S., Karig D.K., Weiss R. Synthetic biology: New engineering rules for an emerging discipline // Mol. Syst. Biol. 2006. V.22006.0028.
Arkin A.P., Fletcher D.A. Fast, cheap and somewhat in control // Genome Biol. 2006. V.7. P.114.
Atkinson M.R., et al. Development of genetic circuit exhibiting toggle switch or oscillatory behavior in. Escherichia Coli // Cell. 2003. V.113. P.597–607.
Atsumi S., Little J.W. Regulatory circuit design and evolution using phage // Genes & Dev. 2004. V.18. P.2086–2094.
Babu M.M., Teichmann S.A. Evolution of transcription factors and the gene regulatory network in Escherichia coli // Nucleic Acids Res. 2003. V.31. P.1234–1244.
Basu S., Mehreja R., Thiberge S., Chen M.T., Weiss R. Spatiotemporal control of gene expression with pulse-generating networks // Proc. Natl. Acad. Sci. 2004. V.101. P.6355–6360.
Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R. A synthetic multicellular system for programmed pattern formation // Nature. 2005. V.434. P.1130–1134.
Becskei A., Serrano L. Engineering stability in gene networks by autoregulation // Nature. 2000. V.405. P.590–593.
Becskei A., Seraphin B., Serrano L. Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion // EMBO J. 2001. V.20. P.2528–2535.
Beyer P., Al-Babili S., Ye X., Lucca P., Schaub P., Welsch R., Potrykus I. Golden Rice: Introducing the -carotene biosynthesis pathway into rice endosperm by genetic engineering to defeat vitamin A deficiency // J. Nutr. 2002. V.132. P.506S–510S.
Bhattacharyya R.P., Remenyi A., Yeh B.J., Lim W.A. Domains, motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits // Annu. Rev. Biochem. 2006. V.75. P.655–680.
Bintu L., et al. Transcriptional regulation by the numbers: applications // Curr. Opin. Genet. & Dev. 2005. V.15. P.125–135.
Cello J., Paul A.V., Wimmer E. Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template // Science. 2002. V.297. P.1016–1018.
Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators // Nature. 2000. V.403. P.335–338.
Elowitz M.B., Levine A.J., Siggia E.D., Swain P.S. Stochastic gene expression in a single cell // Science. 2002. V.297. P.1183–1186.
Endy D. Foundations for engineering biology // Nature. 2005. V.438. P.449–453.
Feng X.J., et al. Optimizing genetic circuits by global sensitivity analysis // Biophys. J. 2004. V.87. P.2195–2202.
Kolisnychenko V., Plunkett III G., Herring C.D., Feher T., Posfai J., Blattner F.R., Posfai G. Engineering a reduced Escherichia coli genome // Genome Res. 2002. V.12. P.640–647.
Marchisio M.A., Stelling J. Computational design of synthetic gene circuits with composable parts // Bioinformatics. 2008. V.24. P.1903-1910.
Morimoto T., Kadoya R., Endo K., Tohata M., Sawada K., Liu S., Ozawa T., Kodama T., Kakeshita H., Kageyama Y., et al. Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis // DNA Res. 2008. V.15. P.73-81.
Seet B.T., Dikic I., Zhou M.M., Pawson T. Reading protein modifications with interaction domains // Nat. Rev. Mol. Cell Biol. 2006. V.7. P.473–483.
Chen L., Aihara K. A model of periodic oscillation for genetic regulatory systems // IEEE Trans. Circuits Syst. I. 2002. V.49. P.1429-1436.
Chen L., Wang R., Kobayashi T., Aihara K. Dynamics of gene regulatory networks with cell division cycles // Phys. Rev. E. 2004. V.70. P.1-13.
Crosthwaite S.K., Dunlap J.C., Loros J.J. Neurospora wc-1 and wc-2: transcription, photoresponses, and the origin of circadian rhythmicity // Science. 1997. V.276. P.763-769.
Leloup J., Gonze D., Goldbeter A. Limit cycle models for circadian rhythms based on transcription regulation in Drosophila and Neurospora // J. Biol. Rhythms. 1999. V.19. P.10-21.
Belair J., Campbell S.A., Driessche P. Frustration, stability, and delay-induced oscillations in a neural network model // SIAM J. Appl. Math. 1996. V.56. P.245-255.
Deng Y., Ding M., Feng J. Synchronization in stochastic coupled systems: theoretical results // J. Phys. A: Math. Gen. 2004. V.37. P.2163-2173.
Elowitz M.B., Leibler S. Asynthetic oscillatory network of transcriptional regulators // Nature. 2000. V.403. P.335-338.
Garcia-Ojalvo J., Elowitz M., Strogatz S.H. Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing // PNAS. 2004. V.101. P.10955-10960.
Goldbeter A. Amodel for circadian oscillations in the Drosophila period protein (PER) // Proc. R. Soc. Lond. B. 1995. V.261. P.319-324.
Golden S.S., Ishiura M., Johnson C.H., Kondo T. Cyanobacterial circadian rhythms // Annu. Rev. Plant. Physiol. Plant. Mol. Biol. 1997. V.48. P.327-354.
Kunz H., Achermann P. Simulation of circadian rhythm generation in the suprachiasmatic nucleus with locally coupled self-sustained oscillators // J. Theor. Biol. 2003. V.224. P.63-78.
Malpel S., Klarsfeld A., Rouyer F. Circadian synchronization and rhythmicity in larval photoperceptiondefective mutation of Drosophila // J. Biol. Rhythms. 2004. V.19. P.10-21.
McMillen D., Kopell N., Hasty J., Collins J.J. Synchronizing genetic relaxation oscillators by intercell signaling // PNAS. 2002. V.99. P.679-684.
Pecora L.M., Carrol T.L. Master stability functions for synchronized coupled systems // Phys. Rev. Lett. 1998. V.80. P.2105-2109.
Pikovsky A., Rosenblum M., Kurths J. Synchronization: AUniversal Concept in Nonlinear Sciences. Cambridge, UK: Cambridge University Press, 2001.
Taga M.E., Bassler B.L. Chemical communication among bacteria // PNAS. 2003. V.100. P.14549-14554.
Ueda H., Hirose K., Iino M. Intercellular coupling mechanism for synchronized and noise-resistant circadian oscillators // J. Theor. Biol. 2002. V.216. P.501-512.
Wang R., Chen L. Synchronizing Genetic Oscillators by Signaling Molecules // J. Biol. Rhythms. 2005. V.20. P.257-269.
Wang R., Jing Z., Chen L. Modelling periodic oscillation in gene regulatory networks by cyclic feedback networks // Bull. Math. Biol. 2004. V.67. P.339-367.
Wang R., Zhou T., Jing Z., Chen L. Modelling periodic oscillation of biological systems with multiple time scale networks // Syst. Biol. 2004. V.1. P.71-84.
Winfree A.T. The Geometry of Biological Time. Berlin: Springer-Verlag, 2000.
Weiss R., Knight T.F. Engineering communications for microbial robotics // DNA6. 2000.
Heinlein M. Plasmodesmata: dynamic regulation and role in macromolecular cell-to-cell signaling // Curr. Opin. Plant. Biol. 2002. V.5. P.543-552.
Perbal B. Communication is the key // Cell Commun. Signaling. 2003. V.1. P.1-4.
Chen L.,Wang R., Zhou T., Aihara K. Noise-induced cooperative behavior in a multi-cell system // Proceedings of IEEE International Symposium on Circuits and Systems. 2005.
// Genes & Dev. 2004. V.18. P.2086–2094. 
-carotene biosynthesis pathway into rice endosperm by genetic engineering to defeat vitamin A deficiency // J. Nutr. 2002. V.132. P.506S–510S.