ArticlePloS one2017
DNA mutation motifs in the genes associated with inherited diseases.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
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- Whole exome sequencing in Alopecia Areata identifies rare variants in KRT82.Nature communications · 2022Article
- Design of Oligonucleotides for Allele-Specific Amplification Based on PCR and Isothermal Techniques.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder.NPJ genomic medicine · 2021Article
- Density Functional Theory in the Prediction of Mutagenicity: A Perspective.Chemical research in toxicology · 2021Review
- Importance of base-pair opening for mismatch recognition.Nucleic acids research · 2020Article
- Bending of DNA duplexes with mutation motifs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates.Molecules (Basel, Switzerland) · 2019Article
- iPS-Cell Technology and the Problem of Genetic Instability-Can It Ever Be Safe for Clinical Use?Journal of clinical medicine · 2019Review
- Article
- Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies.American journal of human genetics · 2018Article
- Review of Different Sequence Motif Finding Algorithms.Avicenna journal of medical biotechnologyReview
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mutations in human genes can be responsible for inherited genetic disorders and cancer. Mutations can arise due to environmental factors or spontaneously. It has been shown that certain DNA sequences are more prone to mutate. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected by chance are termed coldspots. Mutation hotspots are usually derived from a mutation spectrum, which reflects particular population where an effect of a common ancestor plays a role. To detect coldspots/hotspots unaffected by population bias, we analysed the presence of germline mutations obtained from HGMD database in the 5-nucleotide segments repeatedly occurring in genes associated with common inherited disorders, in particular, the PAH, LDLR, CFTR, F8, and F9 genes. Statistically significant sequences (mutational motifs) rarely associated with mutations (coldspots) and frequently associated with mutations (hotspots) exhibited characteristic sequence patterns, e.g. coldspots contained purine tract while hotspots showed alternating purine-pyrimidine bases, often with the presence of CpG dinucleotide. Using molecular dynamics simulations and free energy calculations, we analysed the global bending properties of two selected coldspots and two hotspots with a G/T mismatch. We observed that the coldspots were inherently more flexible than the hotspots. We assume that this property might be critical for effective mismatch repair as DNA with a mutation recognized by MutSα protein is noticeably bent.
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