scholarly journals Kinetic Mechanism of Translocation and dNTP Binding in Individual DNA Polymerase Complexes

2013 ◽  
Vol 135 (24) ◽  
pp. 9149-9155 ◽  
Author(s):  
Kate R. Lieberman ◽  
Joseph M. Dahl ◽  
Ai H. Mai ◽  
Ashley Cox ◽  
Mark Akeson ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Kinetic Mechanism ◽  
Dntp Binding

scholarly journals Kinetic Mechanism of Active Site Assembly and Chemical Catalysis of DNA Polymerase β

Biochemistry ◽  
2011 ◽  
Vol 50 (45) ◽  
pp. 9865-9875 ◽  
Author(s):  
Paul B. Balbo ◽  
Eric Chun-Wei Wang ◽  
Ming-Daw Tsai
Keyword(s):  
Dna Polymerase ◽  
Active Site ◽  
Kinetic Mechanism ◽  
Dna Polymerase Β ◽  
Chemical Catalysis

The Kinetic Mechanism of Formation of the Bacteriophage T4 DNA Polymerase Sliding Clamp

1996 ◽  
Vol 264 (3) ◽  
pp. 440-452 ◽  
Author(s):  
Mark C. Young ◽  
Steven E. Weitzel ◽  
Peter H. von Hippel
Keyword(s):  
Dna Polymerase ◽  
Bacteriophage T4 ◽  
Kinetic Mechanism ◽  
Mechanism Of Formation ◽  
Sliding Clamp

scholarly journals Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment

2013 ◽  
Vol 42 (4) ◽  
pp. 2555-2563 ◽  
Author(s):  
Alfonso Brenlla ◽  
Radoslaw P. Markiewicz ◽  
David Rueda ◽  
Louis J. Romano
Keyword(s):  
Dna Polymerase ◽  
Single Molecule ◽  
Base Pair ◽  
Conformational Dynamics ◽  
Binary Complex ◽  
Translesion Dna Synthesis ◽  
Dna Polymerase Iv ◽  
Y Family ◽  
Dntp Binding ◽  
Base Pair Insertion

Abstract Y-family DNA polymerases play a crucial role in translesion DNA synthesis. Here, we have characterized the binding kinetics and conformational dynamics of the Y-family polymerase Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) using single-molecule fluorescence. We find that in the absence of dNTPs, the binary complex shuttles between two different conformations within ∼1 s. These data are consistent with prior crystal structures in which the nucleotide binding site is either occupied by the terminal base pair (preinsertion conformation) or empty following Dpo4 translocation by 1 base pair (insertion conformation). Most interestingly, on dNTP binding, only the insertion conformation is observed and the correct dNTP stabilizes this complex compared with the binary complex, whereas incorrect dNTPs destabilize it. However, if the n+1 template base is complementary to the incoming dNTP, a structure consistent with a misaligned template conformation is observed, in which the template base at the n position loops out. This structure provides evidence for a Dpo4 mutagenesis pathway involving a transient misalignment mechanism.

Kinetic mechanism of DNA polymerase I (Klenow)

Biochemistry ◽  
1987 ◽  
Vol 26 (25) ◽  
pp. 8410-8417 ◽  
Author(s):  
R. D. Kuchta ◽  
V. Mizrahi ◽  
P. A. Benkovic ◽  
K. A. Johnson ◽  
S. J. Benkovic
Keyword(s):  
Dna Polymerase ◽  
Kinetic Mechanism ◽  
Dna Polymerase I ◽  
Polymerase I
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