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PDBsum entry 104d

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DNA-RNA hybrid PDB id
104d
Jmol
Contents
DNA/RNA
PDB id:
104d
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
Date:
16-Dec-94     Release date:   31-Mar-95    
 Headers
 References

 

 
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.
 
  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.
 

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
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.