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DNA duplexes flanked by hybrid duplexes: the solution structure of chimeric junctions in [r(cgcg)d(TATACGCG)]2.

Zhu L, Salazar M, Reid BR
Biochemistry 34 2372-80 (1995)
Cited: 13 times
EuropePMC logo PMID: 7857947

Abstract

Hybrid duplexes and chimeric duplexes containing hybrid segments linked to pure DNA (or pure RNA) segments are involved in transcription and replication, as well as reverse transcription. A complete understanding of the mechanism of these processes requires detailed information on such duplexes and the junctions between duplexes of differing structure. Using two-dimensional NMR, restrained molecular dynamics and mechanics, and back-calculation refinement against the nuclear Overhauser effect spectra at various mixing times, we have determined the solution structure of the chimeric duplex [r(cgcg)d-(TATACGCG)]2 containing a pure DNA segment in the center of a hybrid duplex. The solution structure differs from the previously determined X-ray structure of the analogous duplex [r(gcg)d(TATACGC)]2, which was found to be A-form throughout [Wang, A.H.-J., et al. (1982) Nature 299, 601-604]. The basic features of the solution structure are (a) the RNA residues are all A-form with C3'-endo sugar conformations, (b) the central DNA segment is B-form, (c) the transition from A-form RNA sugar conformations to B-form DNA sugar conformations involves only the dT5 base step, and (d) although the sugar conformations of the DNA residues A6-G12 are closer to B-form, the basic helical properties of the peripheral RNA.DNA hybrid segments are closer to typical A-form than to B-form.

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  1. Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E. J Mol Biol 385 693-713 (2009)
  2. Recognition of the unique structure of DNA:RNA hybrids. Shaw NN, Arya DP. Biochimie 90 1026-1039 (2008)

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  1. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. Sarafianos SG, Das K, Tantillo C, Clark AD, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E. EMBO J 20 1449-1461 (2001)
  2. NMR structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription. Szyperski T, Götte M, Billeter M, Perola E, Cellai L, Heumann H, Wüthrich K. J Biomol NMR 13 343-355 (1999)
  3. Tighter binding of HIV reverse transcriptase to RNA-DNA versus DNA-DNA results mostly from interactions in the polymerase domain and requires just a small stretch of RNA-DNA. Bohlayer WP, DeStefano JJ. Biochemistry 45 7628-7638 (2006)
  4. The solution structure of [d(CGC)r(aaa)d(TTTGCG)](2): hybrid junctions flanked by DNA duplexes. Hsu ST, Chou MT, Cheng JW. Nucleic Acids Res 28 1322-1331 (2000)
  5. Hydration of [d(CGC)r(aaa)d(TTTGCG)](2). Hsu ST, Chou MT, Chou SH, Huang WC, Cheng JW. J Mol Biol 295 1129-1137 (2000)
  6. The solution structure of [d(CGC)r(amamam)d(TTTGCG)]2. Tsao YP, Wang LY, Hsu ST, Jain ML, Chou SH, Huang C, Cheng JW. J Biomol NMR 21 209-220 (2001)
  7. Crystal structure of an RNA/DNA strand exchange junction. Cofsky JC, Knott GJ, Gee CL, Doudna JA. PLoS One 17 e0263547 (2022)
  8. The intrinsic curvature of a 51 bp K-DNA fragment of Leishmania tarentolae: a molecular model. Norberto de Souza O, Goodfellow JM. J Biomol Struct Dyn 15 905-930 (1998)


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