NMR study of self-paired parallel duplex of d(AAAAACCCCC) in solution.
The oligonucleotide d(A5C5) in solution forms a parallel self-duplex at neutral and low pH values. H2O NMR spectra at pH 5.1 indicate the presence of five imino resonances at lower temperatures; and the structure is stable up to 60 degrees C. These signals can arise only from the hemiprotonated C+.C pairs [Westhof, E. and Sundaralingham, M. (1980) Biochemistry 77, 1852-1856; Westhof, E. and Sundaralingham, M. (1980) J. Mol. Biol. 142, 331-361] and constitute the first direct observation of C+.C hemiprotonated pairs in solution. The cross peaks from H1's and more than five distinct AH8's in 500 MHz 1H 2D-NOESY spectra indicate that there are two conformationally different and energetically similar A-tracts. There is good qualitative agreement between NOESY data and two theoretically derived structures in which A-tracts are reverse Watson-Crick and reverse Hoogsteen base-paired, respectively.
Luo
J
J
Institute of Biomolecular Stereodynamics, State University of New York, Albany 12222.
Sarma
M H
MH
Yuan
R D
RD
Sarma
R H
RH
D001482:Base Composition; D001483:Base Sequence; D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009841:Oligonucleotides / Q000737:chemistry*; D011522:Protons; D012996:Solutions; D013696:Temperature
D009841:Oligonucleotides; D011522:Protons; D012996:Solutions