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Kinetic studies on the formation of acridine‐linked DNA triple helices
Author(s) -
Fox Keith R.
Publication year - 1995
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(94)01387-g
Subject(s) - triple helix , oligonucleotide , footprinting , chemistry , acridine , yield (engineering) , dna , reaction rate constant , intermolecular force , helix (gastropod) , stereochemistry , kinetics , crystallography , biochemistry , biology , base sequence , molecule , materials science , organic chemistry , physics , metallurgy , ecology , quantum mechanics , snail
We have used DNase I footprinting to measure the rate of intermolecular triple helix formation at the target sites A 6 G 6 · C 6 T 6 and G 6 A 6 · T 6 C 6 with the acridine‐linked oligonucleotides Acr‐T 5 C 5 , and Acr‐C 5 T 5 respectively. Under pseudo first‐order reaction conditions we find that the reactions are slow, with half‐lives of several minutes. The rates are dependent on the concentration of the third strand oligonucleotide and yield bimolecular association rate constants of 300 M −1 · s −1 for Acr‐T 5 C 5 binding to A 6 G 6 · C 6 T 6 and 2000 M −1 · s −1 for the interaction of Acr‐C 5 T 5 with G 6 A 6 · T 6 C 6 .