Все выпуски

Список литературы:

1. В. В. Адлер, А. М. Поверенный, В. Н. Подгородниченко, В. С. Шапот. Изучение процесса транскрипции с использованием антител к ДНК // Молекуляр. биология. — 1973. — Т. 7, № 2. — С. 203–208.
   • V. V. Adler, A. M. Poverennyj, V. N. Podgorodnichenko, V. S. Shapot. Transcription studying using antibodies against cDNA // Molekuljar. biologija. — 1973. — V. 7, no. 2. — P. 203–208. — in Russian.
2. А. С. Баев, Ю. Л. Любченко, Ю. С. Лазуркин, Э. Н. Трифонов, М. Д. Франк-Каменецкий. Изучение легкоплавких участков ДНК фага Т2 с помощью электронной микроскопии и кинетического формальдегидного метода // Мол. Биол. — 1972. — № 6. — С. 760–766. — MathSciNet: MR0359877.
   • A. S. Baev, Yu. L. Ljubchenko, Yu. S. Lazurkin, E. N. Trifonov, M. D. Frank-Kameneckij. Studying easily melted DNA regions of bacteriophage T2 by means of microscopy and kinetic formaldehyde method // Mol. Biol. — 1972. — V. 6. — P. 760–766. — in Russian.
3. С. Г. Камзолова, Р. И. Артюх, Л. И. Елфимова. Изучение матричных свойств Т2-ДНК, модифицированных 2,2',6,6'-тетрометил-4-бромацетоксипиперидин-1-оксилом, в РНК-полимеразной системе Е. coli II // Биохимия. — 1977. — Т. 42. — С. 1117–1122.
   • S. G. Kamzolova, R. I. Artjuh, L. I. Elfimova. Studying blueprint properties of T2- DNA modified with 2,2',6,6'-tetromhethyl-4-bromacetoxypiperidin-1-oxyl in E. coli RNA-polymerase system // Biohimija. — 1977. — V. 42. — P. 1117–1122. — in Russian.
4. С. Г. Камзолова, А. А. Сорокин, А. А. Осипов, П. М. Бескаравайный. Электростатическая карта генома бактериофага Т7. 1. Сравнительный анализ электростатических свойств сигма70- специфических промоторов Т7 ДНК, взаимодействующих с РНК-полимеразой E. coli // Биофизика. — 2009. — Т. 54, № (6). — С. 975–983.
   • S. G. Kamzolova, A. A. Sorokin, A. A. Osipov, P. M. Beskaravajnyj. Electrostatic map of bacteriophage T7 genome. Comparative analysis of electrostatic properties of sigma70-specific T7 DNA promoters recognized by RNA-polymerase of Escherichia coli // Biofizika. — 2009. — V. 54, no. 6. — P. 975–983. — in Russian.
5. А. А. Сорокин, Т. Р. Джелядин, М. А. Орлов, Е. А. Зыкова, С. Г. Камзолова. Пространственная организация электростатических взаимодействий Т7 РНК-полимеразы с поздними промоторами Т7 ДНК // Вестник биотехнологии и физико-химической биологии им Ю. А. Овчинникова. — 2016. — Т. 12, № 4. — С. 64–71.
   • A. A. Sorokin, T. R. Dzheljadin, M. A. Orlov, E. A. Zykova, S. G. Kamzolova. Spatial organization of electrostatic interactions between T7 RNA-polymerase and late T7 DNA promoters // Yu. A. Ovchinnikov Bulletin of Biotechnology and Physical and Chemical Biology. — 2016. — V. 12, no. 4. — P. 64–71. — in Russian.
6. C. J. Benham. Theoretical Analysis of Heteropolymeric Transitions in Superhelical DNA Molecules of Specified Sequence // Journal of Chemical Physics. — 1990. — V. 92. — P. 6294–6305. — DOI: 10.1063/1.458353. — ads: 1990JChPh..92.6294B.
7. C. J. Benham. Energetics of the strand separation transition in superhelical DNA // J. Mol. Biol. — 1992. — V. 225. — P. 835–847. — DOI: 10.1016/0022-2836(92)90404-8.
8. C. J. Benham. Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci // Proc. Natl. Acad. Sci. U.S.A. — 1993. — V. 90, no. 7. — P. 2999–3003. — DOI: 10.1073/pnas.90.7.2999. — ads: 1993PNAS...90.2999B.
9. C. J. Benham. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions // J. Mol. Biol. — 1996. — V. 255, no. 3. — P. 425–434. — DOI: 10.1006/jmbi.1996.0035.
10. C. Bi, C. J. Benham. WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA // Bioinformatics (Oxford, England). — 2004. — V. 20. — P. 1477–1479. — DOI: 10.1093/bioinformatics/bth304.
11. K. J. Breslauer, R. Frank, H. Blocker, L. A. Marky. Predicting DNA duplex stability from the base sequence // Proc. Natl. Acad. Sci. U.S.A. — 1986. — V. 83. — P. 3746–3750. — DOI: 10.1073/pnas.83.11.3746. — ads: 1986PNAS...83.3746B.
12. D. I. Cherny, A. A. Alexandrov, M. I. Zarudnaya, et al. Investigation of the binding of Escherichia coli RNA polymerase to DNA from bacteriophages T2 and T7 by kinetic formaldehyde method and electron microscopy // Eur. J. Biochem. — 1977. — V. 79. — P. 309. — DOI: 10.1111/j.1432-1033.1977.tb11811.x.
13. J. C. O. Guerra. Thermodynamics of Denaturation Transition of DNA Duplex Oligomers in the Context of Nearest Neighbor Models: A Short Review // Physics Procedia. — 2015. — V. 68. — P. 37–42. — DOI: 10.1016/j.phpro.2015.07.106. — ads: 2015PhPro..68...37G.
14. D. Imburgio, M. Rong, K. Ma, W. T. McAllister. Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants // Biochemistry. — 2000. — V. 39, no. 34. — P. 10419–10430. — DOI: 10.1021/bi000365w.
15. S. G. Kamzolova, G. B. Postnikova. Spin-labeled nucleic acids // Quart. Rev. Biophys. — 1981. — V. 14. — P. 223–288. — DOI: 10.1017/S0033583500002250.
16. S. G. Kamzolova, V. S. Sivozhelezov, A. A. Sorokin, et al. RNA polymerase–promoter recognition. Specific features of electrostatic potential of early T4 phage DNA promoters // J Biomol Struct Dyn. — 2000. — V. 18, no. 3. — P. 325–334. — DOI: 10.1080/07391102.2000.10506669.
17. S. G. Kamzolova, A. A. Sorokin, T. D. Dzhelyadin, et al. Electrostatic potentials of E. coli genome DNA // J Biomol Struct Dyn. — 2005. — V. 23, no. 3. — P. 341–345.
18. S. G. Kamzolova, R. M. Beskaravainy, A. A. Osypov, et al. Electrostatic map of T7 DNA: Comparative analysis of functional and electrostatic properties of T7 RNA polymerase-specific promoters // Journal of Biomolecular Structure and Dynamics. — 2014. — V. 32. — P. 1184–1192. — DOI: 10.1080/07391102.2013.819298.
19. H. Margalit, B. A. Shapiro, R. Nussinov, et al. Helix stability in prokaryotic promoter regions // Biochemistry. — 1988. — V. 27, no. 14. — P. 5179–5188. — DOI: 10.1021/bi00414a035.
20. W. T. McAllister, A. D. Carter. Regulation of promoter selection by the bacteriophage T7 RNA polymerase in vitro // Nucleic Acids Res. — 1980. — V. 8, no. 20. — P. 4821–4837. — DOI: 10.1093/nar/8.20.4821.
21. W. R. McClure. Mechanism and control of transcription initiation in prokaryotes // Annu. Rev. Biochem. — 1985. — V. 4. — P. 171–204. — DOI: 10.1146/annurev.bi.54.070185.001131.
22. T. Michoel, Y. Van de Peer. Helicoidal transfer matrix model for inhomogeneous DNA melting // Phys Rev E Stat Nonlin Soft Matter Phys. — 2006. — V. 73. — 011908. — DOI: 10.1103/PhysRevE.73.011908.
23. D. A. Natale, A. E. Schubert, D. Kowalski. DNA helical stability accounts for mutational defects in a yeast replication origin // Proc. Natl Acad. Sci. USA. — 1992. — V. 89. — P. 2654–2658. — DOI: 10.1073/pnas.89.7.2654. — ads: 1992PNAS...89.2654N.
24. A. A. Osypov, G. G. Krutinin, S. G. Kamzolova. DEPPDB — DNA electrostatic potential properties database: electrostatic properties of genome DNA // Journal of Bioinformatics and Computational Biology. — 2010. — V. 08, no. 03. — P. 413. — DOI: 10.1142/S0219720010004811.
25. J. Pérez-Martín, F. Rojo, V. de Lorenzo. Promoters responsive to DNA bending: a common theme in prokaryotic gene expression // Microbiol. Rev. — 1994. — V. 58. — P. 268–290.
26. D. Pribnow. Biological Regulation and Development. — New York: Plenum, 1979. — V. 1. — P. 219–277. — R. Goldberger, ed.
27. RefSeq database. — https://www.ncbi.nlm.nih.gov/refseq/. — (accessed: 22.12.2017).
28. J. SantaLucia, D. Hicks. The thermodynamics of DNA structural motifs // Annu Rev Biophys Biomol Struct. — 2004. — V. 33. — P. 415–440. — DOI: 10.1146/annurev.biophys.32.110601.141800.
29. I. A. Shahmuradov, R. M. Razali, S. Bougouffa, A. Radovanovic, V. B. Bajic. bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli // Bioinformatics. — 2017. — V. 33, no. 3. — P. 334–340.
30. A. A. Sorokin, A. A. Osypov, T. R. Dzhelyadin, et al. Electrostatic properties of promoter recognized by E. coli RNA polymerase Esigma70 // Journal of Bioinformatics and Computational Biology. — 2006. — V. 4, no. 2. — P. 455–467. — DOI: 10.1142/S0219720006002077.
31. N. Sugimoto, S. Nakano, M. Yoneyama, K. Honda. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes // Nucleic Acids Res. — 1996. — V. 24. — P. 4501–4505. — DOI: 10.1093/nar/24.22.4501.
32. W. Szybalski, H. Kubinski, P. Sheldrick. Pyrimidine clusters on the transcribing strand of DNA and their possible role in the initiation of RNA synthesis // Cold Spring Harb Symp Quant Biol. — 1966. — V. 14. — P. 123–127. — DOI: 10.1101/SQB.1966.031.01.019.
33. H. Wang, C. J. Benham. Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress // BMC Bioinformatics. — 2006. — V. 7. — P. 248. — ads: 2006IAUS..230..248W.
34. E. Yeramian. Genes and the physics of the DNA double-helix // Gene. — 2000. — V. 255, no. 2. — P. 139–150. — DOI: 10.1016/S0378-1119(00)00301-2.
35. D. Zhabinskaya, S. Madden, C. J. Benham. SIST: stress-induced structural transitions in superhelical DNA // Bioinformatics (Oxford, England). — 2015. — V. 31, no. 3. — P. 421–2.