PMID: 11311717Apr 20, 2001Paper

Solution conformation of an RNA--DNA hybrid duplex containing a pyrimidine RNA strand and a purine DNA strand

International Journal of Biological Macromolecules
E HantzT Huynh Dinh

Abstract

RNA--DNA hybrid duplexes are involved in transcription, replication and reverse transcription of nucleic acids. Information on such duplexes may shed some light on the mechanism of these processes. For this purpose, the influence of base composition on the structure of a polypyrimidine--polypurine RNA--DNA duplex r(cucuccuucucuu). d(GAGAGGAAGAGAA) has been studied using 1H, 31P and 13C NMR experiments, molecular modeling (JUMNA program) and NOE back-calculation methods. The resulting structure of the 13-mer hybrid duplex shows that the RNA strand is in the expected A-type conformation while the DNA strand is in a very flexible conformation. In the DNA strand, the desoxyribose sugars retain the C2'-endo B-type conformation. The duplex helical parameters (such as inclination, twist and displacement of the bases) are close to the A-type conformation. No bending was observed for the global axis curvature. The major groove width is close to the B-form value and the minor groove width is intermediate between standard values for A and B-forms. These results are in favour of the independence of minor groove size (where RNase H interacts) and the base composition of the hybrid duplexes.

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Citations

Mar 30, 2011·Biochemistry·Christopher N JohnsonMarkus W Germann
Jan 17, 2008·The Journal of Physical Chemistry. B·U Deva Priyakumar, Alexander D Mackerell
May 9, 2012·Proceedings of the National Academy of Sciences of the United States of America·Christopher CozensPhilipp Holliger
Feb 19, 2015·Biophysical Journal·Yan SunCharles P Scholes
Dec 18, 2015·Nucleic Acids Research·Irina AnosovaMartin Egli
May 20, 2008·Biochimie·Nicholas N Shaw, Dev P Arya
Jul 17, 2018·Chemical Communications : Chem Comm·Rintaro Iwata HaraTakeshi Wada
Sep 12, 2020·Current Opinion in Structural Biology·Miri KrupkinElisabetta Viani Puglisi
Mar 15, 2008·Journal of the American Chemical Society·David M Parish, Thomas Szyperski
May 20, 2021·Physical Review. E·Taigang LiuWenbing Zhang
Feb 27, 2008·Journal of the American Chemical Society·Agnes NoyModesto Orozco
Mar 31, 2005·Journal of the American Chemical Society·Agnes NoyModesto Orozco

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