Determination of the conformation of d(GGAAATTTCC) sub 2 in solution by use of sup 1 H NMR and restrained molecular dynamics
- 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), Vol. 29:31; ISSN 0006-2960
- Country of Publication:
- United States
- Language:
- English
Similar Records
Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics
Molecular modeling studies of a deoxyoctanucleotide containing a dihydrouridine lesion
Related Subjects
37 INORGANIC
ORGANIC
PHYSICAL AND ANALYTICAL CHEMISTRY
OLIGONUCLEOTIDES
CONFORMATIONAL CHANGES
NUCLEAR MAGNETIC RESONANCE
AQUEOUS SOLUTIONS
DNA
MOLECULAR STRUCTURE
OVERHAUSER EFFECT
PROTONS
BARYONS
DISPERSIONS
ELEMENTARY PARTICLES
FERMIONS
HADRONS
MAGNETIC RESONANCE
MIXTURES
NUCLEIC ACIDS
NUCLEONS
ORGANIC COMPOUNDS
RESONANCE
SOLUTIONS
550200* - Biochemistry
400102 - Chemical & Spectral Procedures