PDBsum entry 104d

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DNA-RNA hybrid PDB id
PDB id:
Name: DNA-RNA hybrid
Title: DNA duplexes flanked by hybrid duplexes: the solution structure of chimeric junctions in
Structure: DNA/RNA (5'-r( Cp Gp Cp G)- d(p Tp Ap Tp Ap Cp Gp Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: chemically synthesized
NMR struc: 1 models
Authors: L.Zhu,M.Salazar,B.R.Reid
Key ref:
L.Zhu et al. (1995). DNA duplexes flanked by hybrid duplexes: the solution structure of chimeric junctions in [r(cgcg)d(TATACGCG)]2. Biochemistry, 34, 2372-2380. PubMed id: 7857947
16-Dec-94     Release date:   31-Mar-95    


Biochemistry 34:2372-2380 (1995)
PubMed id: 7857947  
DNA duplexes flanked by hybrid duplexes: the solution structure of chimeric junctions in [r(cgcg)d(TATACGCG)]2.
L.Zhu, M.Salazar, B.R.Reid.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19022262 S.G.Sarafianos, B.Marchand, K.Das, D.M.Himmel, M.A.Parniak, S.H.Hughes, and E.Arnold (2009).
Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.
  J Mol Biol, 385, 693-713.  
16768458 W.P.Bohlayer, and J.J.DeStefano (2006).
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.
  Biochemistry, 45, 7628-7638.  
15220330 C.Dash, H.Y.Yi-Brunozzi, and S.F.Le Grice (2004).
Two modes of HIV-1 polypurine tract cleavage are affected by introducing locked nucleic acid analogs into the (-) DNA template.
  J Biol Chem, 279, 37095-37102.  
15205459 W.F.Lima, J.G.Nichols, H.Wu, T.P.Prakash, M.T.Migawa, T.K.Wyrzykiewicz, B.Bhat, and S.T.Crooke (2004).
Structural requirements at the catalytic site of the heteroduplex substrate for human RNase H1 catalysis.
  J Biol Chem, 279, 36317-36326.  
11250910 S.G.Sarafianos, K.Das, C.Tantillo, A.D.Clark, J.Ding, J.M.Whitcomb, P.L.Boyer, S.H.Hughes, and E.Arnold (2001).
Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
  EMBO J, 20, 1449-1461.
PDB code: 1hys
10684926 S.T.Hsu, M.T.Chou, and J.W.Cheng (2000).
The solution structure of [d(CGC)r(aaa)d(TTTGCG)](2): hybrid junctions flanked by DNA duplexes.
  Nucleic Acids Res, 28, 1322-1331.  
9369477 S.G.Kerr, and K.S.Anderson (1997).
RNA dependent DNA replication fidelity of HIV-1 reverse transcriptase: evidence of discrimination between DNA and RNA substrates.
  Biochemistry, 36, 14056-14063.  
9054564 T.Nishizaki, S.Iwai, E.Ohtsuka, and H.Nakamura (1997).
Solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at the center.
  Biochemistry, 36, 2577-2585.
PDB code: 1nao
8547252 J.Lingbeck, M.G.Kubinec, J.Miller, B.R.Reid, G.P.Drobny, and M.A.Kennedy (1996).
Effect of adenine methylation on the structure and dynamics of TpA steps in DNA: NMR structure determination of [d(CGAGGTTTAAACCTCG)]2 and its A9-methylated derivative at 750 MHz.
  Biochemistry, 35, 719-734.  
8679564 M.Salazar, O.Y.Fedoroff, and B.R.Reid (1996).
Structure of chimeric duplex junctions: solution conformation of the retroviral Okazaki-like fragment r(ccca)d(AATGA).d(TCATTTGGG) from Moloney murine leukemia virus.
  Biochemistry, 35, 8126-8135.
PDB code: 1oka
8756460 P.C.Bevilacqua, and T.R.Cech (1996).
Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR.
  Biochemistry, 35, 9983-9994.  
8672435 T.Nishizaki, S.Iwai, T.Ohkubo, C.Kojima, H.Nakamura, Y.Kyogoku, and E.Ohtsuka (1996).
Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC).
  Biochemistry, 35, 4016-4025.
PDB codes: 1dhh 1drn
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