Determination of the conformation of d(GGAAATTTCC) sub 2 in solution by use of sup 1 H NMR and restrained molecular dynamics

Journal Article · Tue Aug 07 04:00:00 EDT 1990 · Biochemistry; (USA)

DOI:https://doi.org/10.1021/bi00483a008· OSTI ID:6058214

Katahira, Masato; Sugeta, Hiromu; Kyogoku, Yoshimasa; Fujii, S ^[1]

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1. Osaka Univ. (Japan)

The conformation of the putative bent DNA d(GGAAATTTCC){sub 2} in solution was studied by use of {sup 1}H NMR and restrained molecular dynamics. Most of the resonances were assigned sequentially. A total of 182 interproton distance restraints were determined from two-dimensional nuclear Overhauser effect spectra with short mixing times. Torsion angle restraints for each sugar moiety were determined by qualitative analysis of a two-dimensional correlated spectrum. Restrained molecular dynamics was carried out with the interproton distances and torsion angles incorporated into the total energy function of the system in the form of effective potential terms. On the other hand, the conformations obtained by use of molecular dynamics without experimental restraints or restrained energy minimization depended heavily on the initial conformations, and convergence to a similar conformation was not attained. The conformation obtained by use of restrained molecular dynamics exhibits a few remarkable features. The second G residue takes on the BII conformation rather than the standard BI conformation. There is discontinuity of the sugar puckering between the eight T and ninth C. The minor groove of the oligo(dA) tract is rather compressed. As a result, d(GGAAATTTCC){sub 2} is bent.

• OSTI ID: 6058214
• Journal Information: Biochemistry; (USA), Journal Name: Biochemistry; (USA) Vol. 29:31; ISSN 0006-2960; ISSN BICHA
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
400102 -- Chemical & Spectral Procedures
550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
AQUEOUS SOLUTIONS
BARYONS
CONFORMATIONAL CHANGES
DISPERSIONS
DNA
ELEMENTARY PARTICLES
FERMIONS
HADRONS
MAGNETIC RESONANCE
MIXTURES
MOLECULAR STRUCTURE
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEONS
OLIGONUCLEOTIDES
ORGANIC COMPOUNDS
OVERHAUSER EFFECT
PROTONS
RESONANCE
SOLUTIONS