Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1995 Aug 1;92(16):7140–7142. doi: 10.1073/pnas.92.16.7140

Kinking of DNA and RNA by base bulges.

D M Lilley 1
PMCID: PMC41294  PMID: 7543675

Full text

PDF
7140

Images in this article

7140Fig. 1
on p.7140
7141Fig. 2
on p.7141
7141Fig. 3
on p.7141

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aboul-ela F., Murchie A. I., Homans S. W., Lilley D. M. Nuclear magnetic resonance study of a deoxyoligonucleotide duplex containing a three base bulge. J Mol Biol. 1993 Jan 5;229(1):173–188. doi: 10.1006/jmbi.1993.1016. [DOI] [PubMed] [Google Scholar]
  2. Bhattacharyya A., Lilley D. M. The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucleic Acids Res. 1989 Sep 12;17(17):6821–6840. doi: 10.1093/nar/17.17.6821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bhattacharyya A., Murchie A. I., Lilley D. M. RNA bulges and the helical periodicity of double-stranded RNA. Nature. 1990 Feb 1;343(6257):484–487. doi: 10.1038/343484a0. [DOI] [PubMed] [Google Scholar]
  4. Diekmann S., Wang J. C. On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities. J Mol Biol. 1985 Nov 5;186(1):1–11. doi: 10.1016/0022-2836(85)90251-7. [DOI] [PubMed] [Google Scholar]
  5. Dingwall C., Ernberg I., Gait M. J., Green S. M., Heaphy S., Karn J., Lowe A. D., Singh M., Skinner M. A. HIV-1 tat protein stimulates transcription by binding to a U-rich bulge in the stem of the TAR RNA structure. EMBO J. 1990 Dec;9(12):4145–4153. doi: 10.1002/j.1460-2075.1990.tb07637.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Gohlke C., Murchie A. I., Lilley D. M., Clegg R. M. Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11660–11664. doi: 10.1073/pnas.91.24.11660. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hare D., Shapiro L., Patel D. J. Extrahelical adenosine stacks into right-handed DNA: solution conformation of the d(C-G-C-A-G-A-G-C-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra. Biochemistry. 1986 Nov 18;25(23):7456–7464. doi: 10.1021/bi00371a030. [DOI] [PubMed] [Google Scholar]
  8. Hsieh C. H., Griffith J. D. Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: possible relevance to the folding of single-stranded nucleic acids. Proc Natl Acad Sci U S A. 1989 Jul;86(13):4833–4837. doi: 10.1073/pnas.86.13.4833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. LeBlanc D. A., Morden K. M. Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges. Biochemistry. 1991 Apr 23;30(16):4042–4047. doi: 10.1021/bi00230a031. [DOI] [PubMed] [Google Scholar]
  10. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Morden K. M., Gunn B. M., Maskos K. NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA).oligo(dT) tract. Biochemistry. 1990 Sep 18;29(37):8835–8845. doi: 10.1021/bi00489a047. [DOI] [PubMed] [Google Scholar]
  12. Nikonowicz E. P., Meadows R. P., Gorenstein D. G. NMR structural refinement of an extrahelical adenosine tridecamer d(CGCAGAATTCGCG)2 via a hybrid relaxation matrix procedure. Biochemistry. 1990 May 1;29(17):4193–4204. doi: 10.1021/bi00469a024. [DOI] [PubMed] [Google Scholar]
  13. Nikonowicz E., Roongta V., Jones C. R., Gorenstein D. G. Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex. Biochemistry. 1989 Oct 31;28(22):8714–8725. doi: 10.1021/bi00448a007. [DOI] [PubMed] [Google Scholar]
  14. Patel D. J., Kozlowski S. A., Marky L. A., Rice J. A., Broka C., Itakura K., Breslauer K. J. Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution. Biochemistry. 1982 Feb 2;21(3):445–451. doi: 10.1021/bi00532a004. [DOI] [PubMed] [Google Scholar]
  15. Puglisi J. D., Tan R., Calnan B. J., Frankel A. D., Williamson J. R. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science. 1992 Jul 3;257(5066):76–80. doi: 10.1126/science.1621097. [DOI] [PubMed] [Google Scholar]
  16. Riordan F. A., Bhattacharyya A., McAteer S., Lilley D. M. Kinking of RNA helices by bulged bases, and the structure of the human immunodeficiency virus transactivator response element. J Mol Biol. 1992 Jul 20;226(2):305–310. doi: 10.1016/0022-2836(92)90947-i. [DOI] [PubMed] [Google Scholar]
  17. Rosen M. A., Live D., Patel D. J. Comparative NMR study of A(n)-bulge loops in DNA duplexes: intrahelical stacking of A, A-A, and A-A-A bulge loops. Biochemistry. 1992 Apr 28;31(16):4004–4014. doi: 10.1021/bi00131a016. [DOI] [PubMed] [Google Scholar]
  18. Rosen M. A., Shapiro L., Patel D. J. Solution structure of a trinucleotide A-T-A bulge loop within a DNA duplex. Biochemistry. 1992 Apr 28;31(16):4015–4026. doi: 10.1021/bi00131a017. [DOI] [PubMed] [Google Scholar]
  19. Tang R. S., Draper D. E. Bulge loops used to measure the helical twist of RNA in solution. Biochemistry. 1990 Jun 5;29(22):5232–5237. doi: 10.1021/bi00474a003. [DOI] [PubMed] [Google Scholar]
  20. Tang R. S., Draper D. E. On the use of phasing experiments to measure helical repeat and bulge loop-associated twist in RNA. Nucleic Acids Res. 1994 Mar 11;22(5):835–841. doi: 10.1093/nar/22.5.835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Wang Y. H., Barker P., Griffith J. Visualization of diagnostic heteroduplex DNAs from cystic fibrosis deletion heterozygotes provides an estimate of the kinking of DNA by bulged bases. J Biol Chem. 1992 Mar 5;267(7):4911–4915. [PubMed] [Google Scholar]
  22. Wang Y. H., Griffith J. Effects of bulge composition and flanking sequence on the kinking of DNA by bulged bases. Biochemistry. 1991 Feb 5;30(5):1358–1363. doi: 10.1021/bi00219a028. [DOI] [PubMed] [Google Scholar]
  23. Weeks K. M., Ampe C., Schultz S. C., Steitz T. A., Crothers D. M. Fragments of the HIV-1 Tat protein specifically bind TAR RNA. Science. 1990 Sep 14;249(4974):1281–1285. doi: 10.1126/science.2205002. [DOI] [PubMed] [Google Scholar]
  24. Woodson S. A., Crothers D. M. Conformation of a bulge-containing oligomer from a hot-spot sequence by NMR and energy minimization. Biopolymers. 1989 Jun;28(6):1149–1177. doi: 10.1002/bip.360280608. [DOI] [PubMed] [Google Scholar]
  25. Woodson S. A., Crothers D. M. Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence. Biochemistry. 1987 Feb 10;26(3):904–912. doi: 10.1021/bi00377a035. [DOI] [PubMed] [Google Scholar]
  26. Woodson S. A., Crothers D. M. Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization. Biochemistry. 1988 May 3;27(9):3130–3141. doi: 10.1021/bi00409a004. [DOI] [PubMed] [Google Scholar]
  27. Zacharias M., Hagerman P. J. Bulge-induced bends in RNA: quantification by transient electric birefringence. J Mol Biol. 1995 Mar 31;247(3):486–500. doi: 10.1006/jmbi.1995.0155. [DOI] [PubMed] [Google Scholar]
  28. van den Hoogen Y. T., van Beuzekom A. A., van den Elst H., van der Marel G. A., van Boom J. H., Altona C. Extra thymidine stacks into the d(CTGGTGCGG).d(CCGCCCAG) duplex. An NMR and model-building study. Nucleic Acids Res. 1988 Apr 11;16(7):2971–2986. doi: 10.1093/nar/16.7.2971. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES