Solution Structure of a Homopyrimidine:Homopurine Dodecamer Encoded by the HIV-1 Envelope Gene: NMR and Molecular Simulation Studies

The solution structure of the nonpalindromic dodecanucleotide homopyrimidine:homopurine, d(5'-TTTCTCCTTTCT):d(5'-AGAAAGGAGAAA), was determined by two-dimensional nuclear magnetic resonance spectroscopy combined with molecular simulation. The dodecamer sequence studied was found within the...

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Bibliographic Details
Published in:Biochemistry (Easton) 1995-05, Vol.34 (20), p.6900-6910
Main Authors: Sodano, Patrick, Hartmann, Brigitte, Rose, Thierry, Wain-Hobson, Simon, Delepierre, Muriel
Format: Article
Language:English
Subjects:
AIDS/HIV
Base Sequence
Biochemistry, Molecular Biology
Computer Simulation
Deuterium
Gene Products, env
Gene Products, env - genetics
HIV-1
HIV-1 - genetics
human immunodeficiency virus 1
Life Sciences
Magnetic Resonance Spectroscopy
Models, Molecular
Molecular Sequence Data
Nucleic Acid Conformation
Oligodeoxyribonucleotides
Oligodeoxyribonucleotides - chemistry
Phosphates
Phosphates - chemistry
Protons
Solutions
Temperature
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Summary:The solution structure of the nonpalindromic dodecanucleotide homopyrimidine:homopurine, d(5'-TTTCTCCTTTCT):d(5'-AGAAAGGAGAAA), was determined by two-dimensional nuclear magnetic resonance spectroscopy combined with molecular simulation. The dodecamer sequence studied was found within the HIV-1 envelope sequence and had all four Gs substituted by A in two hypermutants. A set of low-energy B-DNA conformations satisfying the quantitative NOE data were obtained. These highly related structure had neither peculiar helical parameters for the base pairs nor axis curvature. Analysis of the dihedral angles (epsilon-zeta) suggests that the A stretches flanking the GpA dinucleotides were more flexible.
ISSN:0006-2960
1520-4995
DOI:10.1021/bi00020a038