References
- Alexandrov, N. N., & Mironov, A. A. (1990). Application of a new method of pattern recognition in DNA sequence analysis: A study of E. coli promoters. Nucleic Acids Research, 18, 1847–1852. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=330605&tool=pmcentrez&rendertype=abstract
- Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America, 98, 10037–10041. doi:10.1073/pnas.181342398.
- Cheetham, G. M., Jeruzalmi, D., & Steitz, T. A. (1999). Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature, 399, 80–83. doi:10.1038/19999.
- deHaseth, P. L., & Helmann, J. D. (1995). Open complex formation by Escherichia coli RNA polymerase: The mechanism of polymerase-induced strand separation of double helical DNA. Molecular Microbiology, 16, 817–824. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/7476180
- Dunn, J. J., Studier, F. W., & Gottesman, M. (1983). Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. Journal of Molecular Biology, 166, 477–535. doi:10.1016/S0022-2836(83)80282-4.
- Durniak, K., Bailey, S., & Steitz, T. (2008). The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation. Science, 322, 553–557.
- Golomb, M., & Chamberlin, M. (1974). Characterization of T7-specific ribonucleic acid polymerase. IV. Resolution of the major in vitro transcripts by gel electrophoresis. The Journal of Biological Chemistry, 249, 2858–2863. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/4828324
- Gordon, L., Chervonenkis, A. Y., Gammerman, A. J., Shahmuradov, I. A., & Solovyev, V. V. (2003). Sequence alignment kernel for recognition of promoter regions. Bioinformatics, 19, 1964–1971. doi:10.1093/bioinformatics/btg265.
- Gunderson, S. I., Chapman, K. A., & Burgess, R. R. (1987). Interactions of T7 RNA polymerase with T7 late promoters measured by footprinting with methidiumpropyl-EDTA-iron(II). Biochemistry, 26, 1539–1546. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/3036203
- Hertz, G. Z., & Stormo, G. D. (1996). Escherichia coli promoter sequences: Analysis and prediction. Methods in Enzymology, 273, 30–42. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/8791597
- Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447. doi:10.1021/ct700301q.
- Horton, P. B., & Kanehisa, M. (1992). An assessment of neural network and statistical approaches for prediction of E. coli promoter sites. Nucleic Acids Research, 20, 4331–4338. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=334144&tool=pmcentrez&rendertype=abstract
- Huerta, A. M., & Collado-Vides, J. (2003). Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals. Journal of Molecular Biology, 333, 261–278. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/14529615
- Ikeda, R. A., & Richardson, C. C. (1987). Interactions of a proteolytically nicked RNA polymerase of bacteriophage T7 with its promoter. The Journal of Biological Chemistry, 262, 3800–3808. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/3546320
- Joho, K. E., Gross, L. B., McGraw, N. J., Raskin, C., & McAllister, W. T. (1990). Identification of a region of the bacteriophage T3 and T7 RNA polymerases that determines promoter specificity. Journal of Molecular Biology, 215, 31–39. doi:10.1016/S0022-2836(05)80092-0.
- Jolliffe, L. K., Carter, A. D., & McAllister, W. T. (1982). Identification of a potential control region in bacteriophage T7 late promoters. Nature, 299, 653–656. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/7121598
- Jorgensen, W. L., & Tirado-Rives, J. (1988). The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110, 1657–1666.
- Kamzolova, S. G., & Postnikova, G. Y. B. (1981). Spin-labelled nucleic acids. Quarterly Reviews of Biophysics, 14, 223–288. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/6169107
- Kamzolova, S. G., Sivozhelezov, V. S., Sorokin, A. A., Dzhelyadin, T. R., Ivanova, N. N., & Polozov, R. V. (2000). RNA polymerase-promoter recognition. Specific features of electrostatic potential of “early” Т4 phage DNA promoters. Journal of Biomolecular Structure & Dynamics, 18, 325–334. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11149509
- Kamzolova, S. G., Sorokin, A. A., Dzhelyadin, T. R. D., Beskaravainy, P. M., & Osypov, A. A. (2005). Electrostatic potentials of E. coli genome DNA. Journal of Biomolecular Structure & Dynamics, 23, 341–346. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16218758
- Kamzolova, S. G., Ivanova, N. N., & Kamzalov, S. S. (1999). Long-range interactions in T2 DNA during its complex formation with RNA polymerase from E. coli. Journal of Biological Physics, 24, 157–161.
- Kamzolova, S. G., Osypov, A. A., Dzhelyadin, T. R., Beskaravainy, P. M., & Sorokin, A. A. (2006). Context-dependent effects of upstream A-tracts on promoter electrostatic properties and function. Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure, 1, 56–60.
- Kamzolova, S. G., Sorokin, A. A., Beskaravainy, P. M., & Osypov, A. A. (2006). Comparative analysis of electrostatic patterns for promoter and non promoter DNA in E. coli. Bioinformatics of Genome Regulation and Structure, II, 67–74.
- Kamzolova, S. G., Sorokin, A. A., Osipov, A. A., & Beskaravainy, P. M. (2009). Electrostatic map of bacteriophage T7 genome. Comparative analysis of electrostatic properties of sigma(70)-specific T7 DNA promoters recognized by RNA-polymerase of Escherichia coli. Biofizika, 54, 975–983.
- Kassavetis, G. A., & Chamberlin, M. J. (1979). Mapping of class II promoter sites utilized in vitro by T7-specific RNA polymerase on bacteriophage T7 DNA. Journal of Virology, 29, 196–208. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=353100&tool=pmcentrez&rendertype=abstract
- Kiefer, F., Arnold, K., Künzli, M., Bordoli, L., & Schwede, T. (2009). The SWISS-MODEL repository and associated resources. Nucleic Acids Research, 37(Database issue), D387–D392. doi:10.1093/nar/gkn750
- Leirmo, S., & Gourse, R. L. (1991). Factor-independent activation of Escherichia coli rRNA transcription. I. Kinetic analysis of the roles of the upstream activator region and supercoiling on transcription of the rrnB P1 promoter in vitro. Journal of Molecular Biology, 220, 555–568. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/1870123
- Mahadevan, I., & Ghosh, I. (1994). Analysis of E. coli promoter structures using neural networks. Nucleic Acids Research, 22, 2158–2165. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=308136&tool=pmcentrez&rendertype=abstract
- Margalit, H., Shapiro, B. A., Nussinov, R., Owens, J., & Jernigan, R. L. (1988). Helix stability in prokaryotic promoter regions. Biochemistry, 27, 5179–5188. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/3167040
- McAllister, W. T., & Carter, A. D. (1980). Regulation of promoter selection by the bacteriophage T7 RNA polymerase in vitro. Nucleic Acids Research, 8, 4821–4837. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=324390&tool=pmcentrez&rendertype=abstract
- McAllister, W. T., & Wu, H. L. (1978). Regulation of transcription of the late genes of bacteriophage T7. Proceedings of the National Academy of Sciences of the United States of America, 75, 804–808. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=411345&tool=pmcentrez&rendertype=abstract
- McAllister, W. T., Morris, C., Rosenberg, A. H., & Studier, F. W. (1981). Utilization of bacteriophage T7 late promoters in recombinant plasmids during infection. Journal of Molecular Biology, 153, 527–544. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/7040687
- McAllister, W. T., & McCarron, R. J. (1977). Hybridization of the in vitro products of bacteriophage T7 RNA polymerase to restriction fragments of T7 DNA. Virology, 82, 288–298. doi:10.1016/0042-6822(77)90004-6.
- Muller, D. K., Martin, C. T., & Coleman, J. E. (1989). T7 RNA polymerase interacts with its promoter from one side of the DNA helix. Biochemistry, 28, 3306–3313. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/2545254
- Niles, E. G., & Condit, R. C. (1975). Translational mapping of bacteriophage T7 RNAs synthesized In vitro by purified T7 RNA polymerase. Journal of Molecular Biology, 98, 57–67. doi:10.1016/S0022-2836(75)80101-X.
- Osypov, A. A., Krutinin, G. G., & Kamzolova, S. G. (2010). Deppdb – DNA electrostatic potential properties database: electrostatic properties of genome DNA. Journal of Bioinformatics and Computational Biology, 8, 413–425. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/20556853
- Pedersen, A. G., & Engelbrecht, J. (1995). Investigations of Escherichia coli promoter sequences with artificial neural networks: New signals discovered upstream of the transcriptional startpoint. Proceedings of International Conference on Intelligent Systems for Molecular Biology, 3, 292–199. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/7584449
- Pérez-Martín, J., Rojo, F., & De Lorenzo, V. (1994). Promoters responsive to DNA bending: A common theme in prokaryotic gene expression. Microbiological Reviews, 58, 268–290. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=372964&tool=pmcentrez&rendertype=abstract
- Polozov, R. V, Dzhelyadin, T. R., Sorokin, A. A., Ivanova, N. N., Sivozhelezov, V. S., & Kamzolova, S. G. (1999). Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences. Journal of Biomolecular Structure & Dynamics, 16, 1135–1143. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=10447198
- Sorokin, A. A. (2001). Functional analysis of E. coli promoter sequences. New promoter determinants (Doctoral dissertation). Institute of Theoretical and Experimental Biophysics, RAS.
- Sorokin, A. A., Dzhelyadin, T. R., Ivanova, N. N., Polozov, R. V, & Kamzolova, S. G. (2001). The quest for new forms of promoter determinants. Relationship of promoter nucleotide sequences to their electrostatic potential distribution. Journal of Biomolecular Structure & Dynamics, 18, 1020. Retrieved from http://www.jbsdonline.com/The-quest-for-new-forms-of-promoter-determinants-Relationship-of-promoter-nucleotide-sequences-to-their-electrostatic-potential-distribution-p10233.html
- Sorokin, A. A., Osypov, A. A., Dzhelyadin, T. R., Beskaravainy, P. M., & Kamzolova, S. G. (2006). Electrostatic properties of promoter recognized by E. coli RNA polymerase Esigma70. Journal of Bioinformatics and Computational Biology, 4, 455–467. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/16819795
- Sorokin, A. A., Osipov, A. A., Beskaravainyi, P. M., & Kamzolova, S. G. (2007). Analysis of the distribution of the nucleotide sequence and electrostatic potential of the Escherichia coli genome. Biofizika, 52, 223–227. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/17477048
- Studier, F. W., & Rosenberg, A. H. (1981). Genetic and physical mapping of the late region of bacteriophage T7 DNA by use of cloned fragments of T7 DNA. Journal of Molecular Biology, 153, 503–525. doi:10.1016/0022-2836(81)90405-8.
- Travers, A. A. (1989). DNA conformation and protein binding. Annual Review of Biochemistry, 58, 427–452. doi:10.1146/annurev.bi.58.070189.002235.
- Vanet, A., Marsan, L., & Sagot, M.-F. (1999). Promoter sequences and algorithmical methods for identifying them. Research in Microbiology, 150, 779–799. doi:10.1016/S0923-2508(99)00115-1.
- Von Hippel, P. H. (2004). Biochemistry. Completing the view of transcriptional regulation. Science, 305, 350–352. doi:10.1126/science.1101270
- Yada, T., Nakao, M., Totoki, Y., & Nakai, K. (1999). Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models. Bioinformatics, 15, 987–993. doi:10.1093/bioinformatics/15.12.987.