Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix.
H-DNA, thought to play a regulatory role in transcription, exists in two isomeric forms, H-y3 and H-y5. We present the first solution structure of a DNA fragment representing the H-y5 fold. The structure shows the H-y5 triple helix, and for the first time how in an H-DNA isomer the purine strand extension interacts with the triplex loop. It gives direct insight into the mechanism of H-DNA formation, and explains a host of biochemical and biophysical data on the relative stability of the H-DNA isomers. In addition, the observed interaction of the purine strand extension and the triplex loop provides new clues to the design of clamp-type triple helix-forming oligonucleotides.
van Dongen
M J
MJ
NSR Centre for Molecular Structure, Design, and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, The Netherlands.
Doreleijers
J F
JF
van der Marel
G A
GA
van Boom
J H
JH
Hilbers
C W
CW
Wijmenga
S S
SS
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007536:Isomerism; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011687:Purines / Q000737:chemistry / Q000378:metabolism; D011743:Pyrimidines / Q000737:chemistry / Q000378:metabolism; D012996:Solutions
D009841:Oligonucleotides; D011687:Purines; D011743:Pyrimidines; D012996:Solutions; C051802:triplex DNA; D004247:DNA