Kinetic studies on the formation of DNA triplexes containing the nucleoside analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine.
We have examined the kinetics of triple helix formation of oligonucleotides that contain the nucleotide analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine (bis-amino-U, BAU), which forms very stable base triplets with AT. Triplex stability is determined by both the number and location of the modifications. BAU-containing oligonucleotides generate triplexes with extremely slow kinetics, as evidenced by 14 degrees C hysteresis between annealing and melting profiles even when heated at a rate as slow as 0.2 degrees C min(-1). The association kinetics were measured by analysis of the hysteresis profiles, temperature-jump relaxation and DNase I footprinting. We find that the slow kinetics are largely due to the decreased rate of dissociation; BAU modification has little effect on the association reaction. The sequence selectivity is also due to the slower dissociation of BAU from AT than other base pairs.
Rusling
David A
DA
School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, SO16 7PX, UK. k.r.fox@soton.ac.uk.
Broughton-Head
Victoria J
VJ
Tuck
Alex
A
Khairallah
Hannah
H
Osborne
Sadie D
SD
Brown
Tom
T
Fox
Keith R
KR
D020137:Base Pair Mismatch; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D003850:Deoxyribonuclease I / Q000737:chemistry; D005453:Fluorescence; D007700:Kinetics; D009841:Oligonucleotides / Q000737:chemistry*; D010449:Peptide Mapping; D013696:Temperature; D013997:Time Factors; D044366:Transition Temperature; D014529:Uridine / Q000031:analogs & derivatives* / Q000737:chemistry*
C488802:2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine; D009841:Oligonucleotides; C051802:triplex DNA; D004247:DNA; D003850:Deoxyribonuclease I; D014529:Uridine