PDBsum entry 1juu

Go to PDB code: 
dna_rna links
PDB id:
Name: DNA
Title: Nmr structure of a parallel stranded DNA duplex at atomic resolution
Structure: 5'-d(p Cp Cp Ap Tp Ap Ap Tp Tp Tp Ap Cp C)-3'. Chain: a. Engineered: yes. 5'-d(p Cp Cp Tp Ap Tp Tp Ap Ap Ap Tp Cp C)-3'. Chain: b. Engineered: yes
Source: Synthetic: yes. Other_details: the DNA duplex was synthesized with an applied biosystems model 380b DNA synthesizer using solid state phosphoramidate chemistry. Synthetic: yes
NMR struc: 20 models
Authors: V.R.Parvathy,S.R.Bhaumik,K.V.R.Chary,G.Govil,K.Liu, F.B.Howard,H.T.Miles
Key ref: V.R.Parvathy et al. (2002). NMR structure of a parallel-stranded DNA duplex at atomic resolution. Nucleic Acids Res, 30, 1500-1511. PubMed id: 11917010 DOI: 10.1093/nar/30.7.1500
28-Aug-01     Release date:   03-Apr-02    


DOI no: 10.1093/nar/30.7.1500 Nucleic Acids Res 30:1500-1511 (2002)
PubMed id: 11917010  
NMR structure of a parallel-stranded DNA duplex at atomic resolution.
V.R.Parvathy, S.R.Bhaumik, K.V.Chary, G.Govil, K.Liu, F.B.Howard, H.T.Miles.
DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences d(CCATAATTTACC) and d(CCTATTAAATCC) form a parallel-stranded duplex when dissolved at 1:1 stoichiometry in aqueous solution. This is due to the C:C+ clamps on either end and extensive mismatches in the antiparallel orientation. The structure is stable at neutral and acidic pH. At higher temperatures, the duplex melts into single strands in a highly cooperative fashion. All adenine, cytosine and thymine nucleotides adopt the anti conformation with respect to the glycosidic bond. The A:T base pairs form reverse Watson-Crick base pairs. The duplex shows base stacking and NOEs between the base protons T(H6)/A(H8) and the sugar protons (H1'/H2'/H2") of the preceding nucleotide, as has been observed in antiparallel duplexes. However, no NOEs are observed between base protons H2/H6/H8 of sequential nucleotides, though such NOEs are observed between T(CH3) and A(H8). A three-dimensional structure of the parallel-stranded duplex at atomic resolution has been obtained using molecular dynamics simulations under NMR constraints. The simulated structures have torsional angles very similar to those found in B-DNA duplexes, but the base stacking and helicoid parameters are significantly different.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18941894 R.Singh, J.Nitsche, and S.T.Andreadis (2009).
An integrated reaction-transport model for DNA surface hybridization: implications for DNA microarrays.
  Ann Biomed Eng, 37, 255-269.  
17693472 P.Guga, M.Janicka, A.Maciaszek, B.Rebowska, and G.Nowak (2007).
Hoogsteen-paired homopurine [RP-PS]-DNA and homopyrimidine RNA strands form a thermally stable parallel duplex.
  Biophys J, 93, 3567-3574.  
17905816 P.S.Pallan, P.Lubini, M.Bolli, and M.Egli (2007).
Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing.
  Nucleic Acids Res, 35, 6611-6624.  
17008216 W.R.Taylor (2006).
Transcription and translation in an RNA world.
  Philos Trans R Soc Lond B Biol Sci, 361, 1751-1760.  
12736295 S.H.Chou, K.H.Chin, and A.H.Wang (2003).
Unusual DNA duplex and hairpin motifs.
  Nucleic Acids Res, 31, 2461-2474.  
12466550 T.Sunami, J.Kondo, T.Kobuna, I.Hirao, K.Watanabe, K.Miura, and A.Takénaka (2002).
Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs.
  Nucleic Acids Res, 30, 5253-5260.
PDB code: 1ixj
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.