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Related Concept Videos

Mismatch Repair01:20

Mismatch Repair

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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Proofreading01:31

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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.
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Translesion DNA Polymerases02:10

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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.
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Phase II Reactions: Methylation Reactions01:17

Phase II Reactions: Methylation Reactions

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Methylation is a phase II biotransformation process involving the attachment of a methyl group to a substrate. Enzymes known as methyltransferases orchestrate this reaction.
The mechanism of methylation unfolds in two stages. The first stage sees a methyltransferase enzyme facilitating the transfer of a methyl group from S-adenosylmethionine (SAM) to the substrate, forming S-adenosylhomocysteine (SAH). The second stage involves further metabolism of SAH into homocysteine, which can be recycled...
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DNA Base Pairing02:27

DNA Base Pairing

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Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
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Base Excision Repair01:54

Base Excision Repair

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One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
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Updated: Jun 16, 2025

DNAzyme-dependent Analysis of rRNA 2’-O-Methylation
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Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement.

Chongzheng Wen1, Guangyuan Wang2, Lin Yang1

  • 1Division of Biological Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, PR China.

Journal of Molecular Biology
|August 15, 2024
PubMed
Summary
This summary is machine-generated.

Modified DNA with C2'-methoxy (C2'-OMe) enhances nuclease resistance. Crystal structures reveal how evolved DNA polymerase SFM4-3 recognizes C2'-OMe-GTP, uncovering its molecular mechanism and enabling improved enzyme variants.

Keywords:
C2′-modified nucleotidesDNA polymeraseDNA replicationcrystal structuremutation

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An Engineered Split-TET2 Enzyme for Chemical-inducible DNA Hydroxymethylation and Epigenetic Remodeling
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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • DNA modification with C2 '-methoxy (C2 '-OMe) enhances resistance to nucleases, improving the stability of aptamers and DNA nanomaterials.
  • Engineered DNA polymerases can incorporate C2 '-OMe modified nucleoside monophosphates (C2 '-OMe-NMPs), but the mechanism of C2 '-OMe nucleoside triphosphate (C2 '-OMe-NTP) recognition is unclear.

Purpose of the Study:

  • To elucidate the molecular mechanism of C2 '-OMe-NTP recognition by an evolved DNA polymerase.
  • To present crystal structures of the evolved Stoffel fragment of Taq DNA polymerase SFM4-3 processing C2 '-OMe-GTP.
  • To identify structural basis for improved enzyme variants.

Main Methods:

  • X-ray crystallography
  • Directed evolution
  • Biochemical assays

Main Results:

  • Crystal structures of SFM4-3 processing C2 '-OMe-GTP in various states were determined.
  • The structural basis for C2 '-methoxy recognition by SFM4-3 was revealed.
  • A new SFM4-3 variant with enhanced catalytic rate and inhibitor resistance was engineered.
  • A novel pre-insertion conformation provided insights into the polymerase catalytic mechanism.

Conclusions:

  • The study reveals the structural mechanism of C2 '-OMe-NTP recognition by an engineered DNA polymerase.
  • Structural insights facilitated the development of improved DNA polymerase variants.
  • The findings advance the understanding of DNA polymerase catalytic mechanisms.