Journal of Nucleic Acids

Review Article

Kinetic Approaches to Understanding the Mechanisms of Fidelity of the Herpes Simplex Virus Type 1 DNA Polymerase

Table 1

Summary of presteady-state kinetics of nucleotide incorporation by HSV-1 DNA polymerase.
EnzymePrimer/template end after incorp.dNTP:Template N a kpol (sec-1) b š¾ d (dNTP) apparent ( šœ‡ M ) c Efficiency (Ī¼M-1 sec-1)(inverse rel. discrim) d
WT polMatcheddATP:dT 2 5 8 Ā± 3 8 h , j (estimated) N D e ND
dTTP:dA 1 5 7 Ā± 3 1 f 1 2 . 2 Ā± 5 . 7 f 1 2 . 9 Ā± 2 . 5
MismatcheddATP:dA 1 0 6 Ā± 9 f 2 7 9 Ā± 8 3 f 0 . 3 8 Ā± 0 . 0 3 (34)
AbasicdATP:Sp[0] 2 0 9 Ā± 3 3 h 7 5 Ā± 3 7 h 2 . 8 Ā± 0 . 4 4 (4.6)
Exo- polMatcheddTTP:dA 1 9 9 Ā± 2 6 i 4 . 8 Ā± 2 . 1 i 4 1 . 5 Ā± 5 . 4
MismatcheddATP:dA 8 . 7 Ā± 0 . 5 j 1 3 1 Ā± 2 4 j 0 . 0 7 Ā± 0 . 0 0 4 (600)
WTMatcheddATP:dT 2 6 1 Ā± 2 6 f (estimated)NDND
pol/UL42dTTP:dA 1 3 7 Ā± 2 1 f 6 . 4 + 2 . 8 f 2 1 . 4 Ā± 3 . 3
MismatcheddATP:dA 3 7 Ā± 4 f 2 2 9 + 8 9 f 0 . 1 6 Ā± 0 . 0 2 (130)
Exo- MatcheddGTP:dC 6 4 0 Ā± 6 0 g (estimated) 8 Ā± 2 g 8 0 Ā± 7 . 5
pol/UL42Chain termACV-TP:dC 1 0 . 1 Ā± 0 . 8 g 6 Ā± 1 g 1 . 7 Ā± 0 . 3 (48)
a Refers to incoming dNTP for incorporation opposite the templating residue (N) indicated. b Rate constant at unlimiting incoming dNTP concentration determined by the equation š‘˜ o b s = š‘˜ p o l [ d N T P ] / ( [ d N T P ] + š¾ d ) . c Apparent ground-state dissociation constant of dNTP determined according to the function indicated above. d Efficiency for incorporation of dNTP was calculated as š‘˜ p o l / š¾ d (dNTP). Relative discrimination was estimated by dividing the efficiency for formation of a matched terminus by that for formation of mismatched, abasic, or chain terminator (acyclovir triphosphater, ACV-TP) primer/template interface. Number shown in parentheses is inverse of relative discrimination for formation of that terminus. e Not Done (ND). f From [64]. g From [78]. h From [79]. i From [75]. j From [80]