PMID: 9185574Jul 1, 1997Paper

Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: comparison with the DNA analogue d(CGCAAATTTGCG)2

Nucleic Acids Research
M R ConteA N Lane

Abstract

The thermodynamic stability of nine dodecamers (four DNA and five RNA) of the same base composition has been compared by UV-melting. TheDeltaG of stabilisation were in the order: r(GACUGAUCAGUC)2>r(CGCAAATTTGCG)2 approximately r(CGCAUAUAUGCG)2>d(CGCAAATTTGCG)2 approximately r(CGCAAAUUUGCG)2>d(CGCATATATGCG)2 approximately d(GACTGATCAGTC)2>r(CGCUUUAAAGCG)2 approximately d(CGCTTTAAAGCG)2. Compared with the mixed sequences, both r(AAAUUU) and r(UUUAAA) are greatly destablising in RNA, whereas in DNA, d(TTTAAA) is destabilising but d(AAATTT) is stabilising, which has been attributed to the formation of a special B'structure involving large propeller twists of the A-T base pairs. The solution structure of the RNA dodecamer r(CGCAAAUUUGCG)2has been determined using NMR and restrained molecular dynamics calculations to assess the conformational reasons for its stability in comparison with d(CGCAAATTTGCG)2. The structures refined to a mean pairwise r.m.s.d. of 0.89+/-0.29 A. The nucleotide conformations are typical of the A family of structures. However, although the helix axis displacement is approximately 4.6 A into the major groove, the rise (3.0 A) and base inclination ( approximately 6 degrees ) are different from standard A form R...Continue Reading

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Oct 1, 1996·Nucleic Acids Research·M R ConteA N Lane

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Citations

Oct 14, 2009·Journal of the American Chemical Society·Bastien CayrolHervé Isambert
Jul 16, 2014·Nature Structural & Molecular Biology·Andreas SchlundtMichael Sattler
Apr 4, 2014·Biochemistry·Daniel W BinzelPeixuan Guo
Jan 24, 2014·Clinical & Developmental Immunology·Kai NaumannJacques Rohayem
Nov 18, 2005·Bioorganic & Medicinal Chemistry·Myunji ParkThomas C Bruice
Jun 21, 2012·Biophysical Journal·Hannah S SteinertHarald Schwalbe
Jun 11, 2004·Biophysical Journal·Nicola H GreenStephanie Allen
Jul 18, 2016·Colloids and Surfaces. B, Biointerfaces·W AndrzejewskaM Kozak
Apr 20, 2011·The Journal of Physical Chemistry. B·Samanta PinoErnesto Di Mauro
Feb 27, 2013·The Journal of Physical Chemistry. B·Zhen XiaPengyu Ren
Feb 1, 2017·Organic & Biomolecular Chemistry·Rintaro Iwata HaraTakeshi Wada
Jan 8, 1999·Journal of Molecular Biology·C M Duarte, A M Pyle
Mar 14, 2018·Scientific Reports·Rintaro Iwata HaraTakeshi Wada
Jun 20, 2021·Immunologic Research·Asma KomalAttalla F El-Kott

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