Distribution of potentially hairpin-loop structures in the genome of bovine retroviruses


Cite item

Full Text

Abstract

Inverted repeats which can form hairpin-loop structures in the genomic RNA and cruciform structures in the proviral DNA of bovine leukemia virus (BLV) and bovine immunodeficiency virus (BIV) have been determined. Localization diagrams have been made up for hairpins (one of the elements of signaling genome function). The retroviruses BLV and BIV, about 8.5 kbp in length, are characterized by the varying quantitative and qualitative composition of hairpin-loop structures. The BLV and BIV genomes have been found to have 7 and 18 hairpins with energy (-DG) of more than 10 kcal/mol, respectively. Furthermore, in the BIV genome, there are 3 thermodynamically stable (i.e. detectable on model systems in vitro) hairpins (with the loop up to 6 nucleotides), two of them are perfect. But thermodynamically stable hairpins have not been found in the BLV genome.

References

  1. Бродский Л. И., Драчев А. Л., Татузов Р. Л., Чумаков К. М. Пакет прикладных программ для анализа последовательностей биополимеров: GeneBee // Биополимеры и клетка. - 1991. - Т. 7, № 1. - С. 10-14.
  2. Зенгер В. Принципы структурной организации нуклеиновых кислот. - М., 1987.
  3. Лиманская О. Ю., Лиманский А. П. Визуализация элонгационных комплексов Т7 РНК-полимеразы с помощью атомно-силовой микроскопии // Молекул. биол. - 2008. - Т. 42, № 3. - С. 533-542.
  4. Лиманский А. П. Визуализация крестообразной структуры суперспиральной ДНК посредством атомно-силовой микроскопии // Биофизика. - 2000. - Т. 45, № 6. - С. 1039-1043.
  5. Лиманский А. П., Лиманская О. Ю., Волянский Ю. Л. Компьютерный анализ инвертированных повторов в геноме микобактерий туберкулеза // Журн. микробиол. - 2004. - № 5. - С. 48-52.
  6. Chatberg M. D., Englund P. T. The effect of template secondary structure on vaccinia DNA polymerase // J. Biol. Chem. - 1979. - Vol. 254. - P. 7820-7826.
  7. Gillet N., Florins A., Boxus M. Mechanisms of leukemogenesis induced by bovine leukemia virus: prospects for novel anti-retroviral therapies in human // Retrovirology. - 2007. - Vol. 4, N 18. - P. 1-32.
  8. Gonda M., Luther D., Fong S., Tobin J. Bovine immunodeficiency virus: molecular biology and virus-host interactions // Virus Res. - 1994. - Vol. 32, N 2. - P. 155-181.
  9. Kaguni L. S., Clayton D. A. Template-directed pausing in in vitro DNA synthesis by DNA polymerase a from Drosophila metanogaster embryos // Proc. Natl. Acad. Sci. USA. - 1982. - Vol. 79, N 4. - P. 983-987.
  10. Kang S., Ohshima K., Shimizu M. et al. Pausing of DNA synthesis in vitro at specific loci in CTG and CGG triplet repeats from human hereditary disease genes // J. Biol. Chem. - 1995. -Vol. 270, N 45. - P. 27014-27021.
  11. Kirn E., Peng H., Esparza F. et al. Cruciform-extruding regulatory element controls cell-specific activity of the tyrosine hydroxylase gene promoter // Nucl. Acids Res. - 1998. - Vol. 26, N 7. - P. 1793-1800.
  12. Komissarova N., Kashlev M. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded // Proc. Natl. Acad. Sci. USA. - 1997. - Vol. 94, N 5. - P. 1755-1760.
  13. Palecek E. Local supercoil-stahilized DNA structures // Crit. Rev. Biochem. Mol. Biol. - 1991. - Vol. 26, N 2. - P. 151-226.
  14. Panayotatos N., Fontaine A. A native cruciform DNA structure probed in bacteria by recombinant T7 endonuclease // J. Biol. Chem. - 1987. - Vol. 262, N 23. - P. 11364-11368.
  15. Panyutin I., Klishko V., Lyamichev V. Kinetics of cruciform formation and stability of cruciform structure in superhelical DNA // J. Biomol. Struct. Dyn. - 1984. - Vol. 1, N 4. - P. 1311-1324.
  16. pGEMEX-l and pGEMEX-2 vectors // Techn. Bull., Promega. - 2000. - N 253. - P. 1-13.
  17. Santangelo T., Roberts J. Forward translocation is the natural pathway of RNA release at an intrinsic terminator // Mol. Cell. - 2004. - Vol. 14, N 1. - P. 117-126.
  18. Sherman L. A., Getter M. L. Studies of the mechanism of enzymatic DNA elongation by Escherichia coli DNA polymerase II // J. Mol. Biol. - 1976. - Vol. 103. - P. 61-76.
  19. Voineagu I., Narayanan V., Lobachev K., Mirkin S. Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins // Proc. Natl. Acad. Sci. USA. - 2008. - Vol. 105, N 29. - P. 9936-9941.
  20. Weaver D. T., DePamphilis M. L. Specific sequences in native DNA that arrest synthesis by DNA polymerase alpha // J. Biol. Chem. - 1982. - Vol. 257, N 4. - P. 2075-2086.

Supplementary files

Supplementary Files
Action
1. JATS XML
Download

Copyright (c) 2009 Limanskaya O.Y., Limanskiy A.P., Limanskaya O.Y., Limansky A.P.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
СМИ зарегистрировано Федеральной службой по надзору в сфере связи, информационных технологий и массовых коммуникаций (Роскомнадзор).
Регистрационный номер и дата принятия решения о регистрации СМИ: серия ПИ № ФС77-77676 от 29.01.2020.


This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies