CRISPRdigger: detecting CRISPRs with better direct repeat annotations [PDF]
Scientific Reports, 2016 AbstractClustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems’ fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common
Ruiquan Ge +6 more
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Role of direct repeat and stem-loop motifs in mtDNA deletions: cause or coincidence? [PDF]
PLoS ONE, 2012 Deletion mutations within mitochondrial DNA (mtDNA) have been implicated in degenerative and aging related conditions, such as sarcopenia and neuro-degeneration. While the precise molecular mechanism of deletion formation in mtDNA is still not completely
Lakshmi Narayanan Lakshmanan +3 more
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Recombineering in Streptococcus mutans Using Direct Repeat-Mediated Cloning-Independent Markerless Mutagenesis (DR-CIMM) [PDF]
Frontiers in Cellular and Infection Microbiology, 2017 Studies of the dental caries pathogen Streptococcus mutans have benefitted tremendously from its sophisticated genetic system. As part of our own efforts to further improve upon the S. mutans genetic toolbox, we previously reported the development of the
Shan Zhang +5 more
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Preferential Deletion Events in the Direct Repeat Locus of Mycobacterium tuberculosis [PDF]
Journal of Clinical Microbiology, 2011 ABSTRACT The “Harlingen” IS 6110 restriction fragment length polymorphism (RFLP) cluster has linked over 100 tuberculosis cases in The Netherlands since 1993. Four Mycobacterium tuberculosis isolates that were epidemiologically linked to this cluster had different spoligotype ...
Schurch, AC +5 more
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Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats [PDF]
Bioinformatics and Biology InsightsGenomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for understanding the evolution and adaptation of a given organism.
Ruslan Kalendar, Ulykbek Kairov
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Are mutagenic non D-loop direct repeat motifs in mitochondrial DNA under a negative selection pressure? [PDF]
Nucleic Acids Res, 2015 Lakshmi Narayanan Lakshmanan +3 more
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Biomedicines, 2022 Huntington’s Disease (HD) is an autosomal dominant disease that results in severe neurodegeneration with no cure. HD is caused by the expanded CAG trinucleotide repeat (TNR) on the Huntingtin gene (HTT). Although the somatic and germline expansion of the
In K. Cho +3 more
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Instability of large direct repeats in retrovirus vectors [PDF]
Journal of Virology, 1987 Retrovirus vectors were constructed with large (0.85- to 1.3-kilobase-pair) direct repeats in their genomes. Deletions involving the direct repeats occurred at a high frequency. Deletions occurred both when the direct repeats were in tandem and when they were separated by additional sequences. These deletions occurred during virus replication.
Michael Emerman +2 more
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CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes
BMC Bioinformatics, 2022 Background Clustered regularly interspaced short palindromic repeats (CRISPR) and their spacers are important components of prokaryotic CRISPR-Cas systems.
Lei Sun +5 more
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Somatic and germinal recombination of a direct repeat in Arabidopsis. [PDF]
Genetics, 1992 Abstract Homologous recombination between a pair of directly repeated transgenes was studied in Arabidopsis. The test construct included two different internal, non-overlapping deletion alleles of npt (neomycin phosphotransferase) flanking an active HPT (hygromycin phosphotransferase) gene.
Ethan R. Signer, Farhah F. Assaad
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