Русская версия English version   
Том 6   Выпуск 2   Год 2011
Панюков Валерий Васильевич, Назипова Нафиса Наиловна, Озолинь Ольга Николаевна

Пакет программ aSHAPE для изучения пространственной конформации участков бактериального генома

Математическая биология и биоинформатика. 2011;6(2):211-227.

doi: 10.17537/2011.6.211.

Список литературы

  1. Coulombe B and Zachary FB. DNA Bending and Wrapping around RNA Polymerase: a "Revolutionary" Model Describing Transcriptional Mechanisms. Microbiol. Mol. Biol. Rev. 1999;63:457-478.
  2. Carmona M, Claverie-Martin F, Magasanik B. DNA bending and the initiation of transcription at σ54-dependent bacterial promoters. PNAS. 1997;94:9568-9572. doi: 10.1073/pnas.94.18.9568
  3. Bolshoy A, Nevo E. Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters. Genome Res. 2000;10:1185-1193. doi: 10.1101/gr.10.8.1185
  4. Hirvonen CA, Ross W, Wozniak CE, Marasco E, Anthony JR, Aiyar SA, Newburn VH, Richard L. Gourse Contributions of UP Elements and the Transcription Factor FIS to Expression from the Seven rrn P1 Promoters in Escherichia coli. J. Bacteriol. 2001;183:6305-6314. doi: 10.1128/JB.183.21.6305-6314.2001
  5. Kozobay-Avraham L, Hosid S, Bolshoy A. Involvement of DNA curvature in intergenic regions of prokaryotes. Nucleic Acids Res;34:2316-2327. doi: 10.1093/nar/gkl230
  6. Shultzaberger RK, Chen Z, Lewis KA, Schneider TD. Anatomy of Escherichia coli σ70 promoters. Nucleic Acids Res. 2007;35:771-788. doi: 10.1093/nar/gkl956
  7. Pul U, Lux B, Wurm R, Wagner R. Effect of upstream curvature and transcription factors H-NS and LRP on the efficiency of Escherichia coli rRNA promoters P1 and P2 – a phasing analysis. Microbiology. 2008;154:2546-2558. doi: 10.1099/mic.0.2008/018408-0
  8. Meysman P, Dang TH, Laukens K, De Smet R, Wu Y, Marchal K, Engelen K. Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. Nucleic Acids Res. 2011;39: e6. doi: 10.1093/nar/gkq1071
  9. Ozoline ON, Deev AA, Trifonov EN. DNA bendability – a novel feature in E.coli promoter recognition. J. Biomol. Struct. Dynamics. 1999;16:825-831.
  10. Ozoline ON, Masulis IS, Buckin VA. Deformable elements in promoter DNA as a basis for adaptive conformational transitions. J. Biomol. Struct. Dynamics. 2001;18(6):1002-1003.
  11. Shavkunov KS, Masulis IS, Tutukina MN, Deev AA, Ozoline ON. Gains and unexpected lessons from genome-scale promoter mapping. Nucleic Acids Res. 2009;37:4919-4931. doi: 10.1093/nar/gkp490
  12. Shatzky-Schwartz M, Shakked Z, Luisi BF. X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature. J. Mol. Biol. 1997;267:595-623.
  13. McAteer K, Aceves-Gaona A, Michalczyk R, Buchko GW, Isern NG, Silks LA, Miller JH, Kennedy MA. Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature. Biopolymers. 2004;75:497-511. doi: 10.1002/bip.20168
  14. Vlahovicek K, Kajan L, Pongor S. DNA analysis servers: plot.it, bend.it, model.it and IS. Nucleic Acids Res. 2003;31(13):3686-3687.  doi: 10.1093/nar/gkg559
  15. Faktornyi, diskriminantnyi i klasternyi analiz. Eniukov IS, ed.  Moscow, 1989. Translation of: Kim J-O, Mueller CU, and Klecka C. Factor, Discriminant, and Cluster Analysis.
  16. StatSoft. Electronic Statistics Textbook. URL: http://www.statsoft.com/textbook/discriminant-function-analysis/ (accessed 1 August 2011).
  17. Fedoseeva VB. DNK: izgiby dvoinoi spirali: struktura i funktsii (DNA: Bends of the Double Helix, Their Structure and Function). Available at: http://medbiol.ru/medbiol/dna_bend/00000a6c.htm#00013419.htm (accessed 1 August 2011) (in Russ.).
  18. Zheng G, Xiang-Jun Lu, Wilma K, Olson WK. Web 3DNA – a web server for the analysis, reconstruction, and visualization of threedimensional nucleic-acid structures. Nucleic Acids Research. 2009;37:W240-W246. doi: 10.1093/nar/gkp358
  19. Strahs D, Schlick T. Analysis of A-tract bending: Insights into experimental structues by molecular dynamics simulations. J. Mol. Biol. 2000;301:643-663. doi: 10.1006/jmbi.2000.3863
  20. Xiang-Jun Lu, Shakked Z, Olson WK. A-form Conformational Motifs in Ligand-bound DNA Structures. J. Mol. Biol. 2000;300:819-840.
  21. Dickerson RE. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 1998;26:1906-1926. doi: 10.1093/nar/26.8.1906
  22. Goodsell DS and Dickerson RE. Bending and curvature calculations in B-DNA. Nucleic Acids Res. 1994;22(24):5497-5503. doi: 10.1093/nar/22.24.5497
  23. Shpigelman ES, Trifonov EN and Bolshoy A. CURVATURE: software for the analysis of curved DNA. Comput. Appl. Biosci. 1993;9:435-440.
  24. Lavery R, Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 1988;6:63-91.
  25. Lee S, Park K, Kang C. Z-curve: a computer program calculating DNA helical axis coordinates for three-dimensional graphic presentation of curvature. Molecules and Cells. 1999;9(4):350-357.
  26. Barbic A, Crothers DM. Comparison of analyses of DNA curvature. J. Biomol. Struct. Dyn. 2003;21(1):89-97.
  27. Herisson J, Payen G, Gherbi R. A 3D pattern matching algorithm for DNA sequence. Bioinformatics. 2007;23(6):680-686. doi: 10.1093/bioinformatics/btl669
  28. Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu X-J, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung C-S, Westhof E, Wolberger C, Berman HM. A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry. J. Mol. Biol. 2001;313:229-237.
  29. Suzuki M, Amano N, Kakinuma J, Tateno M. Use of a 3D Structure Data Base for Understanding Sequence-dependent Conformational Aspects of DNA. J. Mol. Biol. 1997;274:421-435.
  30. Olson WK. Nucleic acid structural principles. Available at: http://128.6.69.24/lnotes/BioPhysChem_week5.pdf (accessed 1 August 2011).
  31. Handbook of applicable mathematics. Volume VI: Statistics. Part B. John Willey&Sons Ltd; 1984.
  32. Kanhere A, Bansal M. A novel method for prokaryotic promoter prediction based on DNA stability. BMC Bioinformatics. 2005;6(1). doi: 10.1186/1471-2105-6-1
  33. Wang H, Benham CJ. Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. BMC Bioinformatics. 2006;7(248).
  34. Sorokin AA, Osypov AA, Dzhelyadin TR, Beskaravainy PM, Kamzolova SG. Electrostatic properties of promoter recognized by E. coli RNA polymerase Esigma70. J Bioinform Comput Biol. 2006;4(2):455-467. doi: 10.1142/S0219720006002077
Содержание Оригинальная статья
Мат. биол. и биоинф.
2011;6(2):211-227
doi: 10.17537/2011.6.211
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы Перевод на англ. яз.
Мат. биол. и биоинф.
2011;6(2):t36-t52
doi: 10.17537/2011.6.t36

Полный текст (англ., pdf)

 

  Copyright ИМПБ РАН © 2005-2024