The detection of B-form/A-form junction in a deoxyribonucleotide duplex.
The transition of the 14-meric deoxyoligonucleotide duplex d-(ACCCCCTTTTTTTG).d-(CAAAAAAAGGGGGT) from the B- to the A-conformation in water/trifluorethanol (TFE) solution was studied with the use of circular dichroism. An increase in the fraction of TFE induces a two-step B-A transition. In the first step, up to 73% TFE, the A-form is generated from the GC-rich part; in the second step, 73-82% TFE, the AT-rich part shifts to the A-form. By this we suggest the existence of a B/A junction near 73% TFE. Emergence of the B/A junction has been directly confirmed with the use of distamycin A and netropsin, ligands known to selectively bind to AT stretches of B-DNA. It can be shown that both ligands suppress formation of the A-form in the B-philic part. The free energy value for the B/A junction was estimated to be 2.1 kcal/mol, which agrees well with known data for polymeric DNAs. The obtained results may have biological relevance in connection with recently published x-ray data about the occurrence of the B/A junction in the complex of DNA with reverse transcriptase of HIV.
Ivanov
V I
VI
W. A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
Minchenkova
L E
LE
Burckhardt
G
G
Birch-Hirschfeld
E
E
Fritzsche
H
H
Zimmer
C
C
D001482:Base Composition; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D000431:Ethanol; D006813:Humidity; D007700:Kinetics; D008961:Models, Structural; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D014867:Water
D009838:Oligodeoxyribonucleotides; D014867:Water; D000431:Ethanol; D004247:DNA