Parallel-stranded DNA with mixed sequence. Evidence for conformational transition in solution at low water activity.
Parallel-stranded deoxyoligonucleotide 5'd(CTATAGGGAT)3'/5'd(GATATCCCTA)3' (I-II) was shown to be stable in solution at 3 degrees-5 degrees C, 0.1-0.25 M NaCl, 10(-2) M phosphate buffer, pH 7.0 by means of a set of fluorescent techniques as well as of conventional optical methods. A cooperative change in the CD spectra is observed in trifluoroethanol (TFE) solutions at decreased water activity (relative humidity, r.h.). This distinctive change is supposed to stem from a cooperative conformational transition of parallel double helix from a B-like form with C2' endo sugar conformation to an A-like form designated as Ap. The free energy difference between the Ap and B-like conformation for the parallel duplex is 7.35 kcal/mol which is close to the value 7.40 kcal/mol for the antiparallel 5'd(CTATAGGGAT)3'/3'd(GATATCCCTA)5' (I-III). The ability of parallel helix to transit into Ap form is important for DNA-RNA parallel double helix formation.
Shchyolkina
A K
AK
V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow.
Borisova
O F
OF
Chernov
B K
BK
Tchurikov
N A
NA
D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004996:Ethidium; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D012995:Solubility; D013816:Thermodynamics; D014270:Trifluoroethanol; D014867:Water
D009838:Oligodeoxyribonucleotides; D014867:Water; D014270:Trifluoroethanol; D004247:DNA; D004996:Ethidium