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#DNA excision

2 public questions tagged with this topic.

Repair Pathway

Length of DNA removed during prokaryotic NER is approximately

Size of excised patch in nucleotide excision repair defined by positions of UvrC cuts relative to lesion creating specific oligonucleotide length. In Escherichia coli UvrC cuts at 8th phosphodiester bond 5' to lesion and 4th-5th bond 3' to lesion, releasing 12-13 nucleotide fragment bearing bulky adduct, which is removed by UvrD helicase. This short patch is sufficient to eliminate thymine dimers while minimizing resynthesis burden. Eukaryotic NER excises larger 24-32 nucleotide fragment due to larger open complex involving XPB and XPD helicases requiring broader bubble for dual incision by XPF-ERCC1 and XPG.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 5: Length of DNA Excised in Prokaryotic NER

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Gene Tar getting

Which recombinase is used for inversion and excision of DNA fragments in eukaryotes?

Several recombinases perform site-specific DNA rearrangements. RecA mediates homologous recombination, not site specific excision. Flp recognizes FRT sites in yeast system analogous to Cre. Cas9 is RNA guided nuclease, not recombinase. Cre from bacteriophage P1 is widely used in eukaryotes for both deletion when loxP sites are directly repeated and inversion when oppositely oriented. Its ability to function without cofactors, high efficiency in mammalian nuclei, and reversibility control via mutant lox variants makes Cre preferred for conditional knockouts, lineage tracing and chromosome engineering.

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

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