104D

DNA DUPLEXES FLANKED BY HYBRID DUPLEXES: THE SOLUTION STRUCTURE OF CHIMERIC JUNCTIONS IN

Summary for 104D

• Entry DOI: 10.2210/pdb104d/pdb
• Descriptor: DNA/RNA (5'-R(*CP*GP*CP*G)-D(P*TP*AP*TP*AP*CP*GP*CP*G)-3') (1 entity in total)
• Functional Keywords: dna, rna, junction, hybrid, duplex, dna-rna complex, dna-rna hybrid
• Total number of polymer chains: 2
• Total formula weight: 7454.78

Authors

Zhu, L.,Salazar, M.,Reid, B.R. (deposition date: 1994-12-16, release date: 1995-03-31, Last modification date: 2024-05-22)

Primary citation

Zhu, L.,Salazar, M.,Reid, B.R.
DNA duplexes flanked by hybrid duplexes: the solution structure of chimeric junctions in [r(cgcg)d(TATACGCG)]2.
Biochemistry, 34:2372-2380, 1995

PubMed 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.

PubMed: 7857947
DOI: 10.1021/bi00007a033

Experimental method

SOLUTION NMR