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Fluorescent analysis of translesion DNA synthesis by using a novel, non-natural nucleotide analogue.
Lee I, Berdis A. Lee I, et al. Chembiochem. 2006 Dec;7(12):1990-7. doi: 10.1002/cbic.200600128. Chembiochem. 2006. PMID: 17091513
The replication of damaged DNA is a promutagenic process that can lead to disease development. This report evaluates the dynamics of nucleotide incorporation opposite an abasic site, a commonly formed DNA lesion, by using two fluorescent nucleotide analogues, 2-amin …
The replication of damaged DNA is a promutagenic process that can lead to disease development. This report evaluates the dynamics of …
Adenosine triphosphate-dependent degradation of a fluorescent lambda N substrate mimic by Lon protease.
Lee I, Berdis AJ. Lee I, et al. Anal Biochem. 2001 Apr 1;291(1):74-83. doi: 10.1006/abio.2001.4988. Anal Biochem. 2001. PMID: 11262158
Escherichia coli Lon exhibits a varying degree of energy requirement toward hydrolysis of different substrates. Efficient degradation of protein substrates requires the binding and hydrolysis of ATP such that the intrinsic ATPase of Lon is enhanced during protein degradati …
Escherichia coli Lon exhibits a varying degree of energy requirement toward hydrolysis of different substrates. Efficient degradation …
Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase.
Berdis AJ. Berdis AJ. Biochemistry. 2001 Jun 19;40(24):7180-91. doi: 10.1021/bi0101594. Biochemistry. 2001. PMID: 11401565
The mechanism and dynamics of translesion DNA synthesis were evaluated using primer/templates containing a tetrahydrofuran moiety designed to mimic an abasic site. ...Extension beyond an A:abasic mispair is approximately 20-fold and 100-fold faster than extension be …
The mechanism and dynamics of translesion DNA synthesis were evaluated using primer/templates containing a tetrahydrofuran moiety des …
Molecular mechanism of sequence-specific termination of lentiviral replication.
Berdis AJ, Stetor SR, LeGrice SF, Barkley MD. Berdis AJ, et al. Biochemistry. 2001 Oct 9;40(40):12140-9. doi: 10.1021/bi010354i. Biochemistry. 2001. PMID: 11580289
However, termination products accumulate due to a substantial increase in the rate of nonproductive enzyme-nucleic acid complex formation after incorporation of four to five adenosines of a T(6)-tract within the CTS. ...These results have allowed us to develop a
However, termination products accumulate due to a substantial increase in the rate of nonproductive enzyme-nucleic acid complex forma …
Manganese substantially alters the dynamics of translesion DNA synthesis.
Hays H, Berdis AJ. Hays H, et al. Biochemistry. 2002 Apr 16;41(15):4771-8. doi: 10.1021/bi0120648. Biochemistry. 2002. PMID: 11939771
At the molecular level, the enhancement in translesion DNA synthesis reflects a substantial increase in the rate of the conformational change preceding phosphoryl transfer for all dNTPs that were tested. This is best illustrated by the biphasic pre-steady-state time course …
At the molecular level, the enhancement in translesion DNA synthesis reflects a substantial increase in the rate of the conformationa …
Evaluating the effects of enhanced processivity and metal ions on translesion DNA replication catalyzed by the bacteriophage T4 DNA polymerase.
Reineks EZ, Berdis AJ. Reineks EZ, et al. J Mol Biol. 2003 May 16;328(5):1027-45. doi: 10.1016/s0022-2836(03)00370-x. J Mol Biol. 2003. PMID: 12729739
The effect of enhancing the processivity of the T4 DNA polymerase, gp43, on translesion DNA replication was evaluated using a defined in vitro assay system. ...Specifically, the exonuclease-deficient replicase dissociates at a rate constant, k(off), of 1.1s(-1) whil …
The effect of enhancing the processivity of the T4 DNA polymerase, gp43, on translesion DNA replication was evaluated using a defined …
Evaluating the contribution of base stacking during translesion DNA replication.
Reineks EZ, Berdis AJ. Reineks EZ, et al. Biochemistry. 2004 Jan 20;43(2):393-404. doi: 10.1021/bi034948s. Biochemistry. 2004. PMID: 14717593
Despite the nontemplating nature of the abasic site, dAMP is often preferentially inserted opposite the lesion, a phenomenon commonly referred to as the "A-rule". ...Pre-steady-state kinetic measurements yield a kpol value of 126 s(-1) and a Kd value o …
Despite the nontemplating nature of the abasic site, dAMP is often preferentially inserted opposite the lesion, a phenomenon commonly …
Evaluating the contributions of desolvation and base-stacking during translesion DNA synthesis.
Zhang X, Lee I, Berdis AJ. Zhang X, et al. Org Biomol Chem. 2004 Jun 21;2(12):1703-11. doi: 10.1039/b401732c. Epub 2004 May 19. Org Biomol Chem. 2004. PMID: 15188037
DNA polymerases catalyze the insertion of a nucleoside triphosphate into the growing polymer chain using the template strand as a guide. ...Reineks and A. J. Berdis, Biochemistry, 2004, 43, 393-404). The catalytic enhancement was proposed to reflect in …
DNA polymerases catalyze the insertion of a nucleoside triphosphate into the growing polymer chain using the template strand as a
Monitoring the timing of ATP hydrolysis with activation of peptide cleavage in Escherichia coli Lon by transient kinetics.
Vineyard D, Patterson-Ward J, Berdis AJ, Lee I. Vineyard D, et al. Biochemistry. 2005 Feb 8;44(5):1671-82. doi: 10.1021/bi048618z. Biochemistry. 2005. PMID: 15683251
Using rapid quench-flow and fluorescence stopped-flow spectroscopy techniques, we demonstrated that ATP hydrolysis occurs before peptide cleavage, with the former reaction displaying a burst and the latter displaying a lag in product production. The detection of bur …
Using rapid quench-flow and fluorescence stopped-flow spectroscopy techniques, we demonstrated that ATP hydrolysis occurs before peptide cle …
Attenuation of DNA replication by HIV-1 reverse transcriptase near the central termination sequence.
Ignatov ME, Berdis AJ, Le Grice SF, Barkley MD. Ignatov ME, et al. Biochemistry. 2005 Apr 12;44(14):5346-56. doi: 10.1021/bi048000p. Biochemistry. 2005. PMID: 15807528
Previous pre-steady-state kinetic studies of equine infectious anemia virus-1 (EIAV) reverse transcriptase (RT) showed two effects of DNA substrates containing the central termination sequence (CTS) on the polymerization reaction: reduction of burst amplitude in single nucleotide …
Previous pre-steady-state kinetic studies of equine infectious anemia virus-1 (EIAV) reverse transcriptase (RT) showed two effects of DNA su …
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