Structural Influence of RNA Incorporation in DNA: Quantitative Nuclear Magnetic Resonance Refinement of d(CG)r(CG)d(CG) and d(CG)r(C)d(TAGCG)

T. N. Jaishree, Andrew H.J. Wang, Gijs A. van der Marel, Jacques H. van Boom

研究成果: 雜誌貢獻文章同行評審

40 引文 斯高帕斯(Scopus)

摘要

RNA and DNA adopt different types of conformations, i.e., A-type with C3′-endo sugar pucker for RNA and B-type with C2′-endo sugar pucker for DNA, respectively. The structural influence of the incorporation of RNA nucleotides into DNA is less understood. In this paper, we present the three-dimensional structures of two RNA-containing oligonucleotides, d(CG)r(CG)d(CG) and d(CG)r(C)d-(TAGGG), as determined by the NMR refinement procedure, and assess the possible structural perturbation of DNA induced by RNA. With a single RNA insertion into an octamer DNA, its overall conformation remains as the canonical B-DNA, except that the sugar pucker of the rC3 residue is C3′-endo (pseudorotation angle P = 3.6°). In contrast, the hybrid hexamer is neither the pure B-DNA nor the pure A-DNA conformation. Instead, we propose a model in which the DNA parts adopt B conformation, whereas the RNA part adopts A conformation, with the overall conformation closer to A-DNA. To ensure an exhaustive search of the conformational space, the model was subjected to 100-ps simulated annealing with slow cooling or 100-ps molecular dynamics with subsequent quenching. Models obtained at different time points of the trajectories were further subjected to the SPEDREF NOE refinement [Robinson & Wang (1992) Biochemistry 31, 3524] and they appeared to arrive at a convergent model (<0.5 Å RMSD for the central four base pairs). The consensus hexamer structure contains a significant discontinuity at the (rG4)p(dC5) step with a base pair tilt angle of 6.7° and roll angle of 11.5°. This discontinuity may be related to the structural “bend” that occurs at the junction of the RNA and DNA helices.

原文英語
頁(從 - 到)4903-4911
頁數9
期刊Biochemistry
32
發行號18
DOIs
出版狀態已發佈 - 1993
對外發佈

ASJC Scopus subject areas

  • 生物化學

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