114D

INOSINE-ADENINE BASE PAIRS IN A B-DNA DUPLEX

Summary for 114D

• Entry DOI: 10.2210/pdb114d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*IP*AP*AP*TP*TP*AP*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: b-dna, double helix, modified, mismatched, dna
• Total number of polymer chains: 2
• Total formula weight: 7344.81

Authors

Corfield, P.W.R.,Hunter, W.N.,Brown, T.,Robinson, P.,Kennard, O. (deposition date: 1993-01-04, release date: 1993-07-15, Last modification date: 2024-02-07)

Primary citation

Corfield, P.W.,Hunter, W.N.,Brown, T.,Robinson, P.,Kennard, O.
Inosine.adenine base pairs in a B-DNA duplex.
Nucleic Acids Res., 15:7935-7949, 1987

PubMed Abstract: The structure of the synthetic deoxydodecamer d(C-G-C-I-A-A-T-T-A-G-C-G) has been determined by single crystal X-ray diffraction techniques at 2.5A resolution. The refinement converged with a crystallographic residual, R = 0.19 and the location of 64 solvent molecules. The sequence crystallises as a B-DNA helix with 10 Watson-Crick base-pairs (4 A.T. and 6 G.C) and 2 inosine.adenine (I.A) pairs. The present work shows that in the purine.purine base-pairs the adenine adopts syn orientation with respect to the furanose moiety while the inosine is in the trans (anti) orientation. Two hydrogen bonds link the I.A. base-pair, one between N-1(I) and N-7(A), the other between O-6(I) and N-6(A). This bulky purine.purine base-pair is incorporated in the double helix at two positions with little distortion of either local or global conformation. The pairing observed in this study is presented as a model for I.A base-pairs in RNA codon-anticodon interactions and may help explain the thermodynamic stability of inosine containing base-pairs. Conformational parameters and base stacking interactions are presented and where appropriate compared with those of the native compound, d(C-G-C-G-A-A-T-T-C-G-C-G) and with other studies of oligonucleotides containing purine.purine base-pairs.

PubMed: 3671069
DOI: 10.1093/nar/15.19.7935

Experimental method

X-RAY DIFFRACTION (2.5 Å)