We show that Escherichia coli DinB polymerase, which creates single-base deletions, prefers to extend slipped DNA substrates with the skipped base at the -4 position. A DinB(Y79L) variant, which extends these substrates less efficiently in vitro, allows the proofreading function of polymerase III to reverse their formation in vivo.
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http://dx.doi.org/10.1128/JB.00005-11 | DOI Listing |
Forensic Sci Int Genet
December 2024
Forensic & National Security Sciences Institute, Syracuse University, Syracuse, NY, USA. Electronic address:
Short tandem repeat analysis is a robust and reliable DNA analysis technique that aids in source identification of a biological sample. However, the interpretation, particularly when DNA mixtures are present at low levels, can be complicated by the presence of PCR artifacts most commonly referred to as stutter. The presence of stutter products can increase the difficulty of interpretation in DNA mixtures as well as low-level DNA samples down to a single cell.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA.
Human mitochondrial RNA polymerase (POLRMT) and protein factors TFAM and TFB2M assemble on mitochondrial DNA promoters to initiate promoter-specific transcription. We present cryo-EM structures of two initiation complexes, IC3 and slipped-IC3, with fully resolved transcription bubbles containing RNA transcripts starting from +1 and -1 positions, respectively. These structures reveal the mechanisms of promoter melting, start site selection, and slippage synthesis.
View Article and Find Full Text PDFBiomolecules
October 2024
Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
Dynamic mutations in some human genes containing trinucleotide repeats are associated with severe neurodegenerative and neuromuscular disorders-known as Trinucleotide (or Triplet) Repeat Expansion Diseases (TREDs)-which arise when the repeat number of triplets expands beyond a critical threshold. While the mechanisms causing the DNA triplet expansion are complex and remain largely unknown, it is now recognized that the expandable repeats lead to the formation of nucleotide configurations with atypical structural characteristics that play a crucial role in TREDs. These nonstandard nucleic acid forms include single-stranded hairpins, Z-DNA, triplex structures, G-quartets and slipped-stranded duplexes.
View Article and Find Full Text PDFLife (Basel)
July 2024
College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China.
MicroPubl Biol
February 2024
Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States.
The gene of the fission yeast supports both positive and negative selection; consequently, this gene is widely employed as a powerful tool to study diverse biological processes. Here we report the DNA sequences of two functionally null alleles, and . The allele has a four bp duplication of bp +63 to +66 (5'-CAAG-3') within the ORF and the allele has a nonsynonymous substitution (G to A) at bp +679.
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