1BUF

SELF-COMPLEMENTARY DNA 5'-D(CAATTG)2, NMR, MINIMIZED AVERAGE STRUCTURE

Summary for 1BUF

• Entry DOI: 10.2210/pdb1buf/pdb
• Related: 1UQA 1UQB 1UQC 1UQD 1UQE 1UQF 1UQG
• Descriptor: DNA (5'-D(*CP*AP*AP*TP*TP*G)-3') (1 entity in total)
• Functional Keywords: deoxyribonucleic acid, dna
• Total number of polymer chains: 2
• Total formula weight: 3616.46

Authors

Lam, S.L.,Au-Yeung, S.C.F. (deposition date: 1996-06-24, release date: 1997-01-27, Last modification date: 2024-05-22)

Primary citation

Lam, S.L.,Au-Yeung, S.C.
Sequence-specific local structural variations in solution structures of d(CGXX'CG)2 and d(CAXX'TG)2 self-complementary deoxyribonucleic acids.
J.Mol.Biol., 266:745-760, 1997

PubMed Abstract: In this study, the solution structures of eight self-complementary deoxyribonucleic acid molecules, d(CGXX'CG)2 and d(CAXX'TG)2 (where X = C, G, T or A and X' is complementary to X), have been determined using NMR interproton distances, endocyclic sugar torsion angles, backbone torsion angles and hydrogen bond constraints. Based on the structural data obtained in solution, a novel sequence-specific local structure function, sigma LS, composed of the sum of the contributions from the helix twist omega, base roll rho, base-pair slide delta delta and propeller twist omega, is introduced to describe their sequence-specific local structures. Sigma LS is found to produce an acceptable correlation (r = 0.96) with the relative local stability (delta G0 10) of a base-pair-step. This result demonstrates that in addition to the inter-strand purine-purine clashes, the base morphology of nearest-neighbor base-pairs is also important in defining the local geometry of base-pairs. Thus, in analyzing the base-pair structural parameter blocks of trimers are used as the basic unit whereas for the base-pair-step structural parameters, the basic unit is composed of blocks of tetramers. The omega LS-delta G(zero) 10 correlation is the first experimental evidence demonstrating the relationship between the relative local stabilities and the sequence-specific local structures of DNA duplexes. It also forms the basis for using the trimer-tetramer model for the prediction of sequence-specific local structures of deoxyribonucleic acid molecules.

PubMed: 9102467
DOI: 10.1006/jmbi.1996.0783

Experimental method

SOLUTION NMR