Изотермические и управляемые сменой температур реакции амплификации и высокочувствительной детекции специфичных последовательностей нуклеиновых кислот в реальном времени
Диссертация
В настоящее время практически ни одна работа в молекулярной биологии, где объектами исследований являются нуклеиновые кислоты, не обходится без этапа их амплификации или высокочувствительной детекции. Что касается диагностических анализов, то и они сейчас преимущественно рассчитаны на амплификацию, главным образом, с помощью ПЦР специфичных фрагментов ДНК или РНК, которые могут принадлежать… Читать ещё >
Список литературы
- Белохвостов А.С. Полимеразная цепная реакция и лигазные реакции, принципы, традиционные методики и нововведения // Молекулярная генетика, микробиология и вирусология. 1995. — № 1, — С.21−26.
- Гарафутдинов P.P. Новые методы детекции однонуклеотидных замен и общие принципы ДНК-идентификации личности на основе генетического штрих-кодирования: Автореф. дисс. канд. биол. наук / P.P. Гарафутдинов- Инст-т биохим. генет. УНЦ РАН Уфа, 2006. — 23 с.
- Лысов Ю.П., Флорентьев В. Л., Хорлин А. А. и др. Определение нуклеотидной последовательности ДНК гибридизацией с олигонуклеотидами. Новый метод // ДАН СССР. 1988. — Т.303. — С.1508−1511.
- Abravaya К., Carrino J. J., Muldoon S. Lee H.H. Detection of point mutations with a modified ligase chain reaction (Gap-LCR) // Nucleic Acids Res. 1995. -V. 23.-P. 675−682.
- Adler M., Schulz S., Fischer R., Niemeyer C.M. Detection of Rotavirus from stool samples using a standardized immuno-PCR («Imperacer») method with end-point and real-time detection // Biochem. Biophys. Res. Commun. 2005. -V.333.-P. 1289−1294.
- Adler M., Wacker R., Niemeyer M. A real-time immuno-PCR assay for routine ultrasensitive quantification of proteins // Biochem. Biophys. Res. Commun. -2003.-V. 308.-P. 240−250.
- Alves A.M., Can* F.J. Dot blot detection of point mutations with adjacently hybridising synthetic oligonucleotide probes // Nucleic Acids Res. 1988. -V.16.-P. 8723.
- An L., Tang W., Ranalli T.A. et al. Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification // J. Biol. Chem. 2005. — V. 280. — P. 28 952−28 958.
- Auer Т., Sninsky J.J., Gelfand D.H. et al. Selective amplification of RNA utilizing the nucleotide analog dITP and Thermus thermophilus DNA polymerase // Nucleic Acids Res. 1996. — V. 24. — P. 5021−5025.143
- Backman K. Ligase Chain Reaction: Diagnostic technology for the 1990s and beyond // Clin. Chem. 1992. — V. 38. — P. 457−458.
- Bains W., Smith G.C. A novel method for nucleic sequence determination // J. Theor. Biol. 1988. — V. 135. — P. 303−307.
- Barany F. Genetic disease detection and DNA amplification using cloned thermostable ligase // Proc. Natl. Acad. Sei. USA. 1991. -V. 88. — P. 189−193.
- Bar any F. The ligase chain reaction in a PCR world // PCR Methods Applic.1991a. V. l.-P. 5−16.
- Barletta J. Applications of real-time immuno-polymerase chain reaction (rt
- CR) for the rapid diagnoses of viral antigens and pathologic proteins // Mol.
- Aspects Med. 2006. — V. 27. — P. 224−253.
- Bekkaoui F., Poisson I., Crosby W. et al. Cycling probe technology with RNase H attached to an oligonucleotide // Biotechniques. 1996. — V.20. — P. 240−248.
- Bengtsson M., Karlsson H.J., Westman G. et al. A new minor groove binding asymmetric cyanine reporter dye for real-time PCR // Nucl. Acids Res. 2003. -V. 31. — e45.
- Bi W., Stambrook P.J. CCR: a rapid and simple approach for mutation detection // Nucleic Acids Res. 1997. — V. 25. — P. 2949−2951.
- Biesecker L.G., Bailey-Wilson J.E., Ballantyne J. et al. DNA identifications after the 9/11 World Trade Center attack // Science. 2005. — V. 310. — P. 1122−1123.
- Birkenmeyer L.G., Mushahwar I.K. DNA probe amplification methods // J. Virol. Methods. 1991. -V. 35. — P. 117−126.
- Birnboim H.C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA //Nucl. Acids Res. 1979. — V.7. — P.1513−1523.
- Birkenmeyer L., Armstrong A.S. Preliminary evaluation of the ligase chain reaction for specific detection of Neisseria gonorrhoeae // J. Clin. Microbiol. -1992.-V. 30.-P. 3089−3094.
- Bois J.S., Venkataraman S., Choi H.M. et al. Topological constraints in nucleic acid hybridization kinetics // Nucleic Acids Res. 2005. — V. 33. — P. 4090−4095.
- Bolton E., McCarthy B. A general method for the isolation of RNA complementary to DNA // Proc. Natl. Acad. Sci. USA. 1962. — V.48. — P.1390−1397.
- Britten R.J., Kohne D.E. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms//Science. 1968.-V. 161.-P. — 529−540.
- Bronstein I., Voyta J.C., Edwards B. A comparison of chemiluminescent and colorimetric substrates in a hepatitis B virus DNA hybridization assay // Anal. Biochem. 1989. — V. 180. — P. 95−98.
- Busti E., Bordoni R., Castiglioni B. et al. Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction) // BMC Microbiol. 2002. — V. 2. — P.27.
- Cairns M.J., Turner R., Sun L.Q. Homogeneous real-time detection and quantification of nucleic acid amplification using restriction enzyme digestion // Biochem. Biophys. Res. Comm. 2004. — V. 318. — P. 684−690.
- Cardullo R.A., Agrawal S., Flores C. et al. Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer // Proc. Natl. Acad. Sci. USA. 1988. -V. 85. — P. 8790−8794.
- Chen R., Huang W., Lin Z. et al. Development of a novel real-time RT-PCR assay with LUX primer for the detection of swine transmissible gastroenteritis virus // J. Virol. Methods. 2004. — V. 122. — P. 57−61.
- Chen X., Livak K.J., ICwok P.Y. A homogeneous, ligase-mediated DNA diagnostic test // Genome Res. 1998. — V. 8. — P. 549−556.
- Clegg R.M., Murchi A.I.H., Zechel A., Lilley D.M.J. Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer // Proc. Natl. Acad. Sci. USA. 1993. — V. 90. — P. 2994−2998.
- Chomczynski P., Sacchi N. Single-step method of RNA isolation by acid guanidium-thiocyanate-phenol-chloroform extraction // Anal. Biochem. 1987. -V. 162.-P. 156−159.
- Compton J. Nucleic acid sequence-based amplification // Nature. 1991. -V.350. — P.91−92.
- Costa J.M., Ernault P., Olivi M. et al. Chimeric LNA/DNA probes as a detection system for real-time PCR // Clin. Biochem. 2004. — V.37. — P.930−932.
- Crockett A.O., Wittwer C.T. Fluorescein-labeled oligonucleotides for real-time per: using the inherent quenching of deoxyguanosine nucleotides // Anal. Biochem. 2001. — V. 290. — P. 89−97.
- Dahl F., Baner J., Gullberg M. et al. Circle-to-circle amplification for precise and sensitive DNA analysis // Proc. Natl. Acad. Sci. USA. 2004. — V. 101. — P. 4548−4553.
- Demchinskaya A.V., Shilov I.A., Karyagina A.S., Plobner L. A new approach for point mutation detection based on a ligase chain reaction // J. Biochem. Biophys. Methods. 2001. — V. 50. № 1. — P. 79−89.
- Denhardt D.T. A membrane-filter technique for the detection of complementary DNA // Biochem. Biophys. Res. Commun. 1966. — V. 23. — P. 641−646.
- Didenko V.V. DNA probes using fluorescence resonance energy transfer (FRET): designs and applications // Biotechniques. 2001. — V. 31 — P. 1106−1111.
- Dirks R.M., Pierce N.A. Triggered amplification by hybridization chain reaction//Proc. Natl. Acad. Sci. USA. -2004. -V. 101. P. 15 275−15 278.
- Drmanac R., Labat I., Brukner I. et al. Sequencing of megabase plus DNA by hybridization: theory of the method // Genomics. 1989. — V. 4. — P. 114−128.
- Duck P., Alvarado-Urbina G., Burdick B., Collier B. Probe amplifier system based on chimeric cycling oligonucleotides // BioTechniques. 1990. — V. 9. — P. 142−148.
- Efimov V.A., Chakhmakhcheva O.G., Choob M.V., Archdeacon D. Using chimeric DNA/RNA beacons for target-specific signal amplification. XllthV
- Symposium «Chemistry of Nucleic Acids Components». 2002. Spindleruv Mlyn, Czech Republic. Abstract Book. V.5. — P. 308−311.
- Eggerding F.A. A one-step coupled amplification and oligonucleotide ligation procedure for multiplex genetic typing // PCR Methods Appl. 1995. — V. 4. -P. 337−345.
- Fong W.K., Modrusan Z., McNevin J.P. et al. Rapid solid-phase immunoassay for detection of methicillin-resistant Staphylococcus aureus using cycling probe technology // J. Clin. Microbiol. 2000. — V.38. — P. 2525−2529.
- Forster T. Energiewanderung und fluoreszenz //Naturwissenschaften. 1946. -V. 6.-P. 166−175.ht. no Didenko, 2001).
- Forster T. Zwischenmoleculare energiewandenderung und fluoreszenz // Ann. Phys. (Leipzig). 1948. — V. 2. — P. 55−75. (ijht. no Didenko, 2001).
- French D.J., Archard C.L., Brown T., McDowell D.G. HyBeacon probes: a new tool for DNA sequence detection and allele discrimination // Mol. Cell. Probes. 2001.-V. 15.-P. 363−374.
- Getz M.J., Altenburg L.C., Saunders G.F. The use of RNA labeled in vitro with iodine-125 in molecular hybridization experiments // Biochim. Biophys. Acta. -1972.-V. 287.-P. 485−494.
- Gillespie D., Spiegelman S. A quantitative assay for DNA-RNA hybrids with DNA immobilized on a membrane // J. Mol. Biol. 1965. — V. 12. — P. 829−842.
- Gingeras T.R., Higuchi R., Kricka L.J. et al. Fifty years of molecular (DNA/RNA) diagnostics // Clin. Chem. 2005. — V.51. — P.661−671.
- Graham D.E. The isolation of high molecular weight DNA from whole organisms or large tissue masses // Anal. Biochem. 1978. — V.85. — P.609−613.
- Guatelli J.C., Whitfield K.M., Kwoh D.Y. et al. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication // Proc. Natl. Acad. Sei. USA. 1990. — V.87. — P.1874−1878.
- Hall B.D., Spiegelman S. Sequence complementarity of T2-DNA and T2-specific RNA // Proc. Natl. Acad. Sei. USA. 1961. — V. 47. — P. 137−146.
- Hall J.G., Eis P. S., Law S.M. et al. Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction Proc. Natl. Acad. Sei. USA. -2000.-V. 97.-P. 8272−8277.
- Harvey J.J., Lee S.P., Chan E.K. et al. Characterization and applications of CataCleave probe in real-time detection assays // Anal. Biochem. 2004. — V. 333.-P. 246−255.
- Hayashi M.N., Hayashi M., Spiegelman S. Chromatographic separation of annealed and enzymatically synthesized RNA-DNA hybrids // Biophys J. -1965.-V. 5.-P. 231−246.
- Higuchi R., Dollinger G., Walsh P. S. et al. Simultaneous amplification and detection of specific DNA sequences // Biotechnology. 1992. — V. 10. — P.413−417.
- Higuchi R., Fockler C., Dollinger G. et al. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions // Biotechnology. 1993. — V. 11.-P.1026−1030.
- Horii T., Monji A., Uemura K. et al. Rapid detection of fluoroquinolone resistance by isothermal chimeric primer-initiated amplification of nucleic acids from clinical isolates of Neisseria gonorrhoeae // J. Microbiol. Methods. 2006. V. 65.-P. 557−561.
- Horn T., Chang C.A., Urdea M.S. Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays // Nucleic Acids Res. 1997. — V. 25. — P. 4842−4849.
- Horn T., Chang C.A., Urdea M.S. An improved divergent synthesis of comb-type branched oligodeoxyribonucleotides (bDNA) containing multiple secondary sequences // Nucleic Acids Res. 1997. — V. 25. — P. 4835−4841.
- Housby J.N., Southern E.M. Thermus scotoductus and Rhodothermus marinus DNA ligases have higher ligation efficiencies than thermus thermophilus DNA ligase // Anal. Biochem. 2002. — V. 302. — P. 88−94.
- Isacsson J., Cao H., Ohlsson L. et al. Rapid and specific detection of PCR products using light-up probes // Mol Cell Probes. 2000. — V. 14. — P. 321−328.
- Jeon H.J., Shin H.J., Choi J.J. et al. Mutational analyses of the thermostable NAD±dependent DNA ligase from Thermus filiformis // FEMS Microbiol. Lett.-2004.-V. 237.-P. 111−118.
- Kalin I., Shephard S., Candrian U. Evaluation of the ligase chain reaction (LCR) for the detection of point mutations // Mutat Res. 1992. — V.283. — P. 119−123.
- Kandimalla E.R., Agrawal S. «Cylicons» as hybridization-based fluorescent primer-probes: Synthesis, properties and application in real-time PCR // Bioorg. Med. Chem. -2000. V. 8.-P. 1911−1916.
- Koo K., Jaykus L.A. Detection of single nucleotide polymorphisms within the Listeria genus using an 'asymmetric' fluorogenic probe set and fluorescence resonance energy transfer based-PCR // Lett. Appl. Microbiol. 2002. — V. 35. -P. 513−517.
- Kutyavin I.V., Afonina I.A., Mills A. et al. 3'-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures // Nucleic Acids Res. 2000. — V. 28. — P. 655−661.
- Laing T.D., Mah D.C.W., Poirier R.T. et al. Genomic DNA detection using cycling probe technology and capillary gel electrophoresis with laser-induced fluorescence // Mol. Cell. Probes. 2004. — V.18. — P. 341−348.
- Landegren U., Kaiser R., Sanders J., Hood L. A ligase-mediated gene detection technique // Science. 1988. — V. 241. — P. 1077−1080.
- Landegren U. Molecular mechanics of nucleic acid sequence amplification // Trends Genet. 1993. — V. 9. — P. 199−204.
- Leary J.J., Brigati D.J., Ward D.C. Rapid and sensitive colorimetric method for visualizing biotin-labeled DNA probes hybridized to DNA or RNA immobilized on nitrocellulose: Bio-blots // Proc. Natl. Acad. Sci. USA. 1983. — V.80. -P.4045−4049.
- Lee L.G., Connell C.R., Bloch W. Allelic discrimination by nick-translation PCR with fluorogenic probes // Nucl. Acids Res. 1993. — V. 21. — P. 3761−3766.
- Lee M.A., Siddle A.L., Page R.H. ResonSense®: simple linear fluorescent probes for quantitative homogenous rapid polymerase chain reaction // Anal. Chim. Acta. 2002. V.457. P.61−70.
- Li J., Chu X,. Liu Y. et al. A colorimetric method for point mutation detection using high-fidelity DNA ligase // Nucleic Acids Res. 2005. — V. 33. — el68.
- Liew M., Pryor R., Palais R. et al. Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons // Clin. Chem. 2004.-V.50.-P.1156−1164.
- Little M.C., Andrews J., Moore R. et al. Strand displacement amplification and homogeneous real-time detection incorporated in a second-generation DNA probe system, BDProbeTecET // Clin. Chem. 1999. — V. 45. — P. 777−784.
- Livak K.J., Flood S.J., Marmaro J. et al. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization // PCR Methods Appl. 1995. — V.4. — P.357−362.
- Lizardi P.M., Huang X., Zhu Z. et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification // Nat. Genet. 1998. -V.19.-P. 225−232.
- Lomeli H., Tyagi S., Pritchard C.G. et al. Quantitative assays based on the use of replicatable hybridization probes // Clin. Chem. 1989. — V. 35. — P. 1826−1831.
- Luo J., Bergstrom D.E., Barany F. Improving the fidelity of Thermus thermophilus DNA ligase //Nucleic Acids Res. 1996. — V. 24. — P. 3071−3078.
- Lyamichev V.I., Kaiser M.W., Lyamicheva N.E. et al. Experimental and theoretical analysis of the invasive signal amplification reaction // Biochemistry. -2000.-V. 39.-P. 9523−9532.
- Marras S.A., Kramer F.R., Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes // Nucl. Acids Res. 2002. — V.30. — el22.
- Marshall R.L., Laffler T.G., Cerney M.B. et al. Detection of HCV RNA by the asymmetric gap ligase chain reaction // PCR Methods Appl. 1994. — V.4. -P.80−84.
- Mori N., Motegi Y., Shimamura Y. et al. Development of a new method for diagnosis of rubella vims infection by reverse transcription-loop-mediated isothermal amplification // J. Clin. Microbiol. 2006a. — V. 44. — P. 3268−3273.
- Mori Y., Nagamine K., Tomita N. et al. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation // Biochem. Biophys. Res. Commun. 2001. — V. 289. — P. 150−154.
- Mori Y., Kitao M., Tomita N. et al. Real-time turbidimetry of LAMP reaction for quantifying template DNA // J. Bioch. Bioph. Meth. 2004. — V.59. — P. 145−157.
- Mori Y., Hirano T., Notomi T. Sequence specific visual detection of LAMP reactions by addition of cationic polymers // BMC Biotechnol. 2006. — V.6. — P.3.
- Moser M.J., Marshall DJ., Grenier J.K. et al. Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system // Clin. Chem. 2003. — V.49. — P.407−414.
- Nadeau J.G., Pitner J.B., Linn C.P. et al., Real-time, sequence-specific detection of nucleic acids during strand displacement amplification // Anal. Biochem. 1999. — V. 276. — P. 177−187.
- Nagamine K., Hase T., Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers // Mol. Cell Probes. 2002. — V.16. -P. 223−229.
- Nazarenko I.A., Bhatnagar S.K., Hohman R.J. A closed tube format for amplification and detection of DNA based on energy transfer // Nucleic Acids Res. 1997. — V. 25. — P. 2516−2521.
- Nazarenko I., Lowe B., Darfler M. et al. Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore // Nucleic Acids Res. -2002.-V. 30. e37.
- Nelson N.C., Kacian D.L. Chemiluminescent DNA probes: a comparison of the acridinium ester and dioxetane detection systems and their use in clinical diagnostic assays // Clin. Chim. Acta. 1990. — V. 194. — P. 73−90.
- Nickerson D.A., Kaiser R., Lappin S. et al. Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay // Proc. Natl. Acad. Sci. USA. -1990.-V. 87.-P. 8923−8927.
- Niemeyer C.M., Adler M., Wacker R. Immuno-PCR: high sensitivity detection of proteins by nucleic acid amplification // Trends Biotechnol. 2005. — V.23. -P.208−216.
- Nilsson M., Malmgren H., Samiotaki M. et al. Padlock probes: circularizing oligonucleotides for localized DNA detection // Science. 1994. — V. 265. — P. 2085−2088.
- Nilsson M., Barbany G., Antson D.O. et al. Enhanced detection and distinction of RNA by enzymatic probe ligation //Nat. Biotechnol. 2000. — V. 18. -P.791−793.
- Nilsson M., Antson D.O., Barbany G., Landegren U. RNA-templated DNA ligation for transcript analysis // Nucleic Acids Res. 2001. — V. 29. — P. 578−581.152
- Nilsson M., Dahl F., Larsson C. et al. Analyzing genes using closing and replicating circles // Trends Biotechnol. 2006. — V. 24. — P. 83−88.
- Notomi T., Okayama H., Masubuchi H. et al. Loop-mediated isothermal amplification of DNA // Nucleic Acids Res. 2000. — V. 28. — E63.
- Nuovo G.J., Hohman R.J., Nardone G.A. et al. In situ amplification using universal energy transfer-labeled primers // J. Histochem. Cytochem. 1999. V.47. P.273−279.
- Nurmi J., Ylikoski A., Soukka T. et al. A new label technology for the detection of specific polymerase chain reaction products in a closed tube // Nucleic Acids Res. 2000. — V. 28. — e28.
- Pham H.M., Nakajima C., Ohashi K. et al. Loop-mediated isothermal amplification for rapid detection of Newcastle disease virus // J. Clin. Microbiol. -2005. -V. 43.-P. 1646−1650.
- Pickering J., Bamford A., Godbole V. et al. Integration of DNA ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms // Nucleic Acids Res. 2002. — V. 30. — e60.
- Prensky W., Steffensen D.M., Hughes W.L. The use of iodinated RNA for gene localization//Proc. Natl. Acad. Sci. USA. 1973. -V. 70. — P. 1860−1864.
- Pritchard C.E., Southern E.M., Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases // Nucleic Acids Res. 1997. — V. 25. -P. 3403−3407.
- Rasmussen T.B., Uttenthal A., de Strieker K. et al. Development of a novel quantitative real-time RT-PCR assay for the simultaneous detection of all serotypes of foot-and-mouth disease virus // Arch. Virol. 2003. — V. 148. — P. 2005−2021.
- Renz M., Kurz C. A colorimetric method for DNA hybridization // Nucleic Acids Res. 1984. — V. 12. — P. 3435−3444.153
- Rizzo J., Gifford L.K., Zhang X. et al. Chimeric RNA-DNA molecular beacon assay for ribonuclease H activity // Mol.&Cell. Probes. 2002. — V. 16. — P. 277−283.
- Rosler A., Bailey L., Jones S. et al. Rolling circle amplification for scoring single nucleotide polymorphisms // Nucleosides Nucleotides Nucleic Acids. -2001.-V. 20.-P. 893−894.
- Proc. Natl. Acad. Sei. USA. 1997. — V. 94. — P. 4262−4266. 128. Schachter J. DFA, EIA, PCR, LCR and other technologies: what tests should be used for diagnosis of chlamydia infections? // Immunol Invest. — 1997. — V. 26. — P. 157−161.
- Seeman N.C. DNA engineering and its application to nanotechnology // Trend.
- Biotechnol. 1999. — V. 17. — P. 437−443. 132. Seeman N.C. From genes to machines: DNA nanomechanical devices //
- Trends Biochem. Sei. 2005. — V. 30. — P. 119−25. 133. Shchepinov M.S., Udalova I.A., Bridgman A.J. et al. Oligonucleotide dendrimers: synthesis and use as polylabelled DNA probes // Nucleic Acids Res. — 1997. — V. 25. — P. 4447−4454.
- Shengqi W., Xiaohong W., Suhong C. et al. A new fluorescent quantitative polymerase chain reaction technique // Anal. Biochem. 2002. — V.309. — P. 206−211.
- Sherril C.B., Marshall D.J., Moser M.J. et al. Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence // J. Am. Chem. Soc. 2004. V.126. P.4550−4556.
- Sismour A.M., Benner S.A. The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system // Nucl. Acids Res. 2005. V.33. P.5640−5646.
- Smolina I.V., Demidov V.V., Cantor C.R. et al. Real-time monitoring of branched rolling-circle DNA amplification with peptide nucleic acid beacon // Anal. Biochem. 2004. — V. 335. — P. 326−329.
- Solinas A., Brown L.J., McKeen C. et al. Duplex Scorpion primers in SNP analysis and FRET applications // Nucleic Acids Res. 2001. — V. 29. — E96.
- Southern E.M. Detection of specific sequences among DNA fragments separated by gel electrophoresis // J. Mol. Biol. 1975. — V. 98. — P. 503−517.
- Southern E.M., Maskos U., Elder J.K. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models // Genomics. 1992. — V. 13. — P. 1008−1017.
- Spargo C.A., Fraiser M.S., Van Cleve M. et al. Detection of M. tuberculosis DNA using thermophilic strand displacement amplification // Mol. Cell Probes. 1996.-V. 10.-P. 247−256.
- Stryer L., Haugland R.P. Energy transfer: a spectroscopic rule // Proc. Natl. Acad. Sci. USA. 1967. -V. 58.-P. 719−726.
- Svanvik N., Stahlberg A., Sehlstedt U. et al. Detection of PCR products in real time using light-up probes // Anal. Biochem. 2000. — V. 287. — P. — 179−182.
- Thomas D.C., Nardone G.A., Randall S.K., Amplification of padlock probes for DNA diagnostics by cascade rolling circle amplification or the polymerase chain reaction // Arch. Pathol. Lab. Med. 1999. — V. 123. — P. 1170−1176.
- Tian P., Mandrell R. Detection of norovirus capsid proteins in faecal and food samples by a real time immuno-PCR method // J. Appl. Microbiol. 2006. — V. 100.-P. 564−574.
- Todd A.V., Fuery C.J., Impey H.L. et al DzyNA-PCR: use of DNAzymes to detect and quantify nucleic acid sequences in a real-time fluorescent format // Clin. Chem. 2000. — V. 46. — P. 625−630.
- Tong J., Cao W., Barany F. Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D // Nucleic Acids Res. 1999. — V. 27. — P. 788−794.
- Tong J., Barany F., Cao W. Ligation reaction specificities of an NAD (+)-dependent DNA ligase from the hyperthermophile Aquifex aeolicus // Nucleic Acids Res. 2000. — V. 28. — P. 1447−1454.
- Tyagi S., Kramer F.R. Molecular beacons: probes that fluoresce upon hybridization//Nat. Biotechnol. 1996. -V. 14. — P. 303−308.
- Tyagi S., Marras S.A., Kramer F.R. Wavelength-shifting molecular beacons // Nat. Biotechnol.-2000. V. 18.-P. 1191−1196.
- Van Ness J., Van Ness L.K., Galas D.J. Isothermal reactions for the amplifica-tion of oligonucleotides //Proc. Natl. Acad. Sci. USA. -2003. V. 100. -P.4504−4509.
- Vaughn C.P., Elenitoba-Johnson K.S. Hybridization-induced dequenching of fluorescein-labeled oligonucleotides: a novel strategy for PCR detection and genotyping // Am. J. Pathol. 2003. — V. 163. — P. 29−35.
- Vincent M., Xu Y., Kong H. Helicase-dependent isothermal DNA amplification // EMBO Reports. 2004. — V.5. — P. 795−800.
- Walker G. T, Fraiser M. S, Schram J.L. et al. Strand displacement amplification~an isothermal, in vitro DNA amplification technique // Nucleic Acids Res. 1992. — V. 20. -1691−1696.
- Walker G. T, Little M. C, Nadeau J.G. et al. Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system // Proc. Natl. Acad. Sei. USA. 1992. — V. 89. — P. 392−396.
- Warmaar S.O., Cohen J A. A quantitative assay for DNA-DNA hybrids using membrane filters // Biochem. Biophys. Res. Commun. 1966. — Y.24. — P.554−558.
- Watson E. J, Templeton A, Russell I. et al. The accuracy and efficacy of screening tests for Chlamydia trachomatis: a systematic review // J. Med. Microbiol. 2002. — V. 51. — P. 1021 -1031.
- Whitcombe D, Brownie J, Gillard H.L. et al. A homogenous fluorescence assaya for PCR amplicons: its application to real-time, single-tube genotyping // Clin. Chem. 1998. V.44,P.918−923.
- Wiedmann M, Wilson W. J, Czajka J. et al. Ligase chain reaction (LCR) -overview and applications // PCR Methods Applic. 1994. — V. 3. — P. S51-S64.
- Winn-Deen E.S. Multi-mutation screening using PCR and ligation principles and applications // Trends Biotechnol. — 1996. — V. 14. — P. 112−114.
- Wittwer C. T, Herrmann M. G, Moss A.A., Rasmussen R.P. Continuous fluorescence monitoring of rapid cycle DNA amplification // Biotechniques. -1997.-V. 22.-P. 130−131, 134−138.
- Wittwer C. T, Ririe K.M., Andrew R.Y. et al. The LightCycler: a microvolume multisample fluorimeter with rapid temperature control // Biotechniques. -1997a.-V. 22.-P. 176−181.
- Wittwer C, Reed G, Gundry C.N. et al. High-resolution genotyping by amplicon melting analysis using LCGreen // Clin. Chem. 2003. — V.49. — P.853−860.
- Wu D. Y, Wallace R.B. The ligation amplification reaction (LAR)~ amplification of specific DNA sequences using sequential rounds of template-dependent ligation // Genomics. 1989. — V. 4. — P. 560−569.157
- Wu D.Y., Wallace R.B. Specificity of the nick-closing activity of bacteriophage T4 DNA ligase // Gene. 1989a. V.76. — P.245−254.
- Yamane A. MagiProbe: a novel fluorescence quenching-based oligonucleotide probe carrying a fluorophore and an intercalator // Nucl. Acids Res. 2002. -V.30. — e97.
- Yang J.Q., Tata P.V., Park-Turkel H.S., Waksal H.W. The application of AmpliProbe in diagnostics // Biotechniques. 1991. — V. 11. — P. 392−397.
- Zhang D.Y., Zhang W., Li X., Konomi Y. Detection of rare DNA targets by isothermal ramification amplification // Gene. 2001. — V.274. P.209−216.
- Zhang Y., Zhang D., Li W. et al. A novel real-time quantitative PCR method using attached universal template probe // Nucleic Acids Res. 2003. — V. 31. — el23.
- Zhou L., Myers A.N., Vandersteen J.G. et al. Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye // Clin. Chem. -2004.-V. 50.-P. 1328−1335.