Related Experiment Video

Updated: Jul 22, 2026

Steady-state, Pre-steady-state, and Single-turnover Kinetic Measurement for DNA Glycosylase Activity
14:27

Steady-state, Pre-steady-state, and Single-turnover Kinetic Measurement for DNA Glycosylase Activity

Published on: August 19, 2013

Characterization of a catalytically slow AP lyase activity in DNA polymerase gamma and other family A DNA polymerases

K G Pinz1, D F Bogenhagen

  • 1Department of Pharmacological Sciences State University of New York at Stony Brook, Stony Brook, New York 11794-8651, USA.

The Journal of Biological Chemistry
|April 25, 2000
PubMed

Insights

Mitochondrial DNA polymerase gamma and other family A DNA polymerases can remove 5'-deoxyribose phosphate (dRP) groups during DNA repair. This dRP lyase activity is limited by stable enzyme-dRP intermediates, suggesting a role in low-frequency AP site repair.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Apurinic/apyrimidinic (AP) sites are common DNA lesions.
  • Base excision repair (BER) pathways address AP sites.
  • DNA polymerase gamma (pol gamma) is involved in mitochondrial DNA maintenance.

Purpose of the Study:

  • To investigate the dRP lyase activity of DNA pol gamma.
  • To determine if other DNA polymerases share this dRP lyase function.
  • To elucidate the mechanism and limitations of the dRP lyase reaction.

Main Methods:

  • Enzymatic assays to measure dRP lyase activity.
  • Site-directed mutagenesis and protein cross-linking with NaBH(4).
  • Comparative analysis of DNA polymerases from family A.

Main Results:

  • DNA pol gamma exhibits significant dRP lyase activity.
  • Escherichia coli DNA pol I and Klenow fragment also possess dRP lyase activity.
  • The reaction involves stable enzyme-DNA and enzyme-dRP intermediates.

Conclusions:

  • Family A DNA polymerases, including pol gamma, function as dRP lyases.
  • Stable enzyme-dRP intermediates limit the catalytic rate, impacting their role in AP site repair.
  • This activity may be significant for repairing infrequent AP sites in DNA.

More Related Videos

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis07:38

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis

Published on: October 6, 2017

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Related Concept Videos

Proofreading01:43

Proofreading

Synthesis of new DNA molecules starts when DNA polymerase links nucleotides together in a sequence that is complementary to the template DNA strand. DNA polymerase has a higher affinity for the correct base to ensure fidelity in DNA replication. The DNA polymerase furthermore proofreads during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.Errors during Replication Are Corrected by the DNA Polymerase EnzymeGenomic DNA is synthesized in...
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
The Replisome03:01

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Proofreading01:31

Proofreading

Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore,  it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase Enzyme
Replication in Eukaryotes01:29

Replication in Eukaryotes

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
Many Proteins Orchestrate Replication at the Origin
Eukaryotic replication follows many of the same...