Mechanisms of triplex-caused polymerization arrest.
Pyrimidine/purine/purine triplexes are known to inhibit DNA polymerization. Here we have studied the mechanisms of this inhibition by comparing the efficiency of Vent DNA polymerase on triplex- and duplex-containing templates at different temperatures, Mg2+concentrations and time intervals with the thermal stability of the corresponding structures. Our results show that triplexes can only be by-passed at temperatures where thermal denaturation initiates, while duplexes, in contrast, are overcome at temperatures where they are quite stable. These results show that DNA polymerase cannot untangle triplex regions within DNA templates and seems to entirely depend on their thermal fluctuations. The high stability of triplexes at physiological temperatures and ambient conditions make them a barrier to polymerization.
Krasilnikov
A S
AS
Department of Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
Panyutin
I G
IG
Samadashwily
G M
GM
Cox
R
R
Lazurkin
Y S
YS
Mirkin
S M
SM
D001483:Base Sequence; D001704:Biopolymers / Q000378:metabolism; D004247:DNA / Q000096:biosynthesis*; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D018390:Gene Targeting; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D013379:Substrate Specificity; D013696:Temperature; D013698:Templates, Genetic
D001704:Biopolymers; C051802:triplex DNA; D004247:DNA; C088944:Deep Vent DNA polymerase; D004259:DNA-Directed DNA Polymerase; D008274:Magnesium