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Related Concept Videos

Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Nucleic Acids02:43

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Nucleic acids02:43

Nucleic acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, 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
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...

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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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DNA adduct structure-function relationships: comparing solution with polymerase structures.

Suse Broyde1, Lihua Wang, Ling Zhang

  • 1Department of Biology, New York University, New York NY 10003, USA. broyde@nyu.edu

Chemical Research in Toxicology
|December 7, 2007
PubMed
Summary

Nuclear Magnetic Resonance (NMR) reveals DNA adduct structures, crucial for understanding mutation risks and repair. These solution structures often mirror those found within DNA polymerases, influencing lesion processing.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Toxicology

Background:

  • Nearly two decades of NMR studies have elucidated DNA duplexes damaged by polycyclic aromatic hydrocarbons and amines.
  • High-resolution structures reveal broad structural themes for these DNA adducts.
  • These structures are hypothesized to be relevant to adduct biochemical processing, mutational properties, and repair susceptibility.

Purpose of the Study:

  • To compare NMR solution structures of DNA adducts with their structures within DNA polymerases.
  • To assess the relevance of solution structures to biochemical processing of DNA lesions.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy for determining DNA duplex solution structures.
  • Analysis of existing crystal structures of DNA adducts within DNA polymerases.

Main Results:

  • Broad structural themes have been uncovered for DNA adducts in solution.
  • NMR solution structural themes for polycyclic aromatic adducts are frequently observed in polymerase crystal structures.
  • Polymerase interactions can influence adduct conformation, but intrinsic solution preferences are often maintained.

Conclusions:

  • Solution structures of DNA adducts provide insights into their behavior within DNA polymerases.
  • Adduct conformations favored in solution likely play a significant role in DNA lesion processing, including mutagenicity and repair.