AI Article Synopsis

  • A deletion occurred in a pUC19 plasmid containing Streptomyces DNA, likely due to a recombination process that doesn't involve the RecA protein.
  • The deletion affected both an unknown part of the inserted genomic DNA and a section of the plasmid's multiple cloning site.
  • A 13 bp GC-rich sequence, similar to an established hotspot for spontaneous deletions, was discovered at the site of the deletion.

Article Abstract

A spontaneous deletion probably caused by rec A independent recombination between short-direct repeat sequences was observed in pUC19 plasmid carrying a piece of Streptomyces genomic DNA after culturing in liquid medium. The deletion removed an unknown portion of the cloned DNA and the BamHI-EcoRI part of the multiple cloning site with an additional flanking 111 bp from the vector. At the junction a 13 bp GC-rich DNA sequence highly homologous to a known spontaneous deletion hotspot was found.

Download full-text PDF

Source

Publication Analysis

Top Keywords

cloned dna
8
spontaneous deletion
8
short gc-rich
4
gc-rich sequence
4
sequence involved
4
deletion
4
involved deletion
4
deletion formation
4
formation cloned
4
dna
4

Similar Publications

We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into repetitive sequences, up to 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell.

View Article and Find Full Text PDF

Kaposi Sarcoma (KS) is a frequently aggressive malignancy caused by Kaposi sarcoma herpesvirus (KSHV/HHV-8). People with immunodeficiencies, including HIV, are at increased risk for developing KS, but our understanding of the contributions of the cellular genome to KS pathogenesis remains limited. To determine if there are cellular genetic alterations in KS that might provide biological or therapeutic insights, we performed whole exome sequencing on 78 KS tumors and matched normal control skin from 59 adults with KS (46 with HIV-associated KS and 13 with HIV-negative KS) receiving treatment at the Uganda Cancer Institute in Kampala, Uganda.

View Article and Find Full Text PDF

Measuring XNA polymerase fidelity in a hydrogel particle format.

Nucleic Acids Res

January 2025

Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, United States.

Growth in the development of engineered polymerases for synthetic biology has led to renewed interest in assays that can measure the fidelity of polymerases that are capable of synthesizing artificial genetic polymers (XNAs). Conventional approaches require purifying the XNA intermediate of a replication cycle (DNA → XNA → DNA) by denaturing polyacrylamide gel electrophoresis, which is a slow, costly, and inefficient process that requires a large-scale transcription reaction and careful extraction of the XNA strand from the gel slice. In an effort to streamline the assay, we developed a purification-free approach in which the XNA transcription and reverse transcription steps occur inside the matrix of a hydrogel-coated magnetic particle.

View Article and Find Full Text PDF

Tumour hypoxia in driving genomic instability and tumour evolution.

Nat Rev Cancer

January 2025

Translational Oncogenomics Laboratory, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK.

Intratumour hypoxia is a feature of all heterogenous solid tumours. Increased levels or subregions of tumour hypoxia are associated with an adverse clinical prognosis, particularly when this co-occurs with genomic instability. Experimental evidence points to the acquisition of DNA and chromosomal alterations in proliferating hypoxic cells secondary to inhibition of DNA repair pathways such as homologous recombination, base excision repair and mismatch repair.

View Article and Find Full Text PDF

ABC-type salt tolerance transporter genes are abundant and mutually shared among the microorganisms of the hypersaline Sambhar Lake.

Extremophiles

January 2025

Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India.

To fish-out novel salt-tolerance genes, metagenomic DNA of moderately saline sediments of India's largest hypersaline Sambhar Lake was cloned in fosmid. Two functionally-picked clones helped the Escherichia coli host to tolerate 0.6 M NaCl.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!