title: Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix.
abstract: 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.
authors.affiliation: NSR Centre for Molecular Structure, Design, and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, The Netherlands.
authors.forename: M J
authors.initials: MJ
authors.lastname: van Dongen
authors.forename: J F
authors.initials: JF
authors.lastname: Doreleijers
authors.forename: G A
authors.initials: GA
authors.lastname: van der Marel
authors.forename: J H
authors.initials: JH
authors.lastname: van Boom
authors.forename: C W
authors.initials: CW
authors.lastname: Hilbers
authors.forename: S S
authors.initials: SS
authors.lastname: Wijmenga
mesh_terms: 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
chemical_list: D009841:Oligonucleotides; D011687:Purines; D011743:Pyrimidines; D012996:Solutions; C051802:triplex DNA; D004247:DNA