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Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study

Zhuo Song, Yang Cao, David C. Samuels, Dennis R. Livesay
2011 PLoS Computational Biology  
Pausing of pol-c might increase the chance of deletion and depletion of mitochondrial DNA.  ...  A467T variant showed at most a doubling in the length of the pauses compared to the wild-type.  ...  Results We modeled three types of pol c, the wild type and two mutants (the human pathogenic variation A467T and the completely Author Summary As a polymerase copies a DNA strand, it may briefly pause  ... 
doi:10.1371/journal.pcbi.1002287 pmid:22125488 pmcid:PMC3219627 fatcat:s3lbj6xuwjanvbdom5bfubfjii

Analysis of mutational spectra by denaturing capillary electrophoresis

Per O Ekstrøm, Konstantin Khrapko, Xiao-Cheng Li-Sucholeiki, Ian W Hunter, William G Thilly
2008 Nature Protocols  
DCE has been used to define quantitative point mutational spectra for study a wide variety of genetic phenomena: errors of DNA polymerases, mutations induced in human cells by chemicals and irradiation  ...  Numbers and kinds of point mutant within DNA from cells, tissues and human population may be discovered for nearly any 75-250bp DNA sequence.  ...  Wild type DNA was amplified with Taq DNA polymerase, which has been shown to induce mutants at about 10 −5 /base pair/ doubling 49 .  ... 
doi:10.1038/nprot.2008.79 pmid:18600220 pmcid:PMC2742298 fatcat:avvvcsekujep7kabj4zdel3rcm

General sessions (1A-01 – 3E-11)

2012 Genes & Genetic Systems  
Buckwheat exhibits self-incompatibility and breeding between individuals with the same type of flowers fails.  ...  This heterostylous self-incompatible trait is governed by a single genetic locus or gene complex, i.e., S-locus, and the genotypes of plants with short and long style flowers are S/s and s/s, respectively  ...  The one of the PolB-like proteins from C. subterraneum indeed behaves like a typical B-family DNA polymerase, i.e. seems to be primarily a DNA replication polymerase, based on its processivity rates and  ... 
doi:10.1266/ggs.87.397 fatcat:ab6vtx5e2ncdjlggsn4nguxyha


2004 Biochimica et Biophysica Acta - Bioenergetics  
Genetic studies reveal mutations in the mitochondrial DNA-dependent DNA polymerase gamma (POLG) gene.  ...  POLG1 encodes the catalytic alpha subunit of polymerase gamma and is the only polymerase known to be involved in mtDNA replication.  ...  the type I error.  ... 
doi:10.1016/j.bbabio.2004.05.001 fatcat:ocvsmh3qvfg6xkhvkr64vfzkfe

DNA polymerases: Mechanistic insight from biochemical and biophysical studies

Emmanuelle Delagoutte
2012 Frontiers in Bioscience  
Replicative and repair DNA polymerases and 8-oxoguanine lesion 4. Nucleotide incorporation reaction of TLS DNA polymerases 4.1. Domain organization of the Y family of DNA polymerases 4.2.  ...  References ABSTRACT In vivo the DNA polymerases are responsible for replicative and repair DNA synthesis.  ...  Introducing the notion of dynamic processivity Recent measurements of DNA polymerase processivity using wild type and specific mutant DNA polymerases in the context of a full replisome led us to revisit  ... 
doi:10.2741/3941 pmid:22201758 fatcat:3oyz33bpnnbola5fovs5ab4rxu

Cellular responses to environmental DNA damage

1991 Mutation Research/DNA Repair  
mutant population and DGGE was used to separate wild type DNA sequences from mutant sequences.  ...  In past studies, when an amber mutation at position 128 was suppressed with the incorporation of a serine residue, the resulting mutant enzyme had wild type D NA binding and normal glycosylic bond scisoion  ...  Ml3mp2 single-stranded DNA was used as a template for in vitro DNA synthesis by wild-type and the above two The replicated molecule (RF) was introduced into the competent cells of E. coil $90C (routs +  ... 
doi:10.1016/0921-8777(91)90055-t fatcat:wbtywgadgfbydbto7zbsybdqgu

The Universally Conserved Prokaryotic GTPases

N. Verstraeten, M. Fauvart, W. Versees, J. Michiels
2011 Microbiology and Molecular Biology Reviews  
Moreover, E. coli obg mutant cells have a higher DNA content than do wild-type cells, and Obg was suggested previously to regulate the total DNA content within E. coli cells (202) .  ...  A first observation hinting at a possible role for Obg in DNA replication came from studies with a heat-sensitive B. subtilis obg mutant.  ...  A C. glutamicum ⌬hflX strain has the same cell morphology and growth behavior as those of the wild type (78) . Role in ribosome assembly.  ... 
doi:10.1128/mmbr.00009-11 pmid:21885683 pmcid:PMC3165542 fatcat:lgjrr5v3izbstdnktcbnzzzebe

Dissecting Highly Mutagenic Processing of Complex Clustered DNA Damage in Yeast Saccharomyces cerevisiae

Stanislav G. Kozmin, Gregory Eot-Houllier, Anne Reynaud-Angelin, Didier Gasparutto, Evelyne Sage
2021 Cells  
in wild-type, BER, and translesion synthesis-deficient cells.  ...  Clusters of DNA damage, also called multiply damaged sites (MDS), are a signature of ionizing radiation exposure.  ...  E.S. is very thankful to late Betsy Sutherland, to Lynn Harrison, and Susan Wallace for their warm encouragement and support for our studies on the processing of clustered DNA damage and their outcome.  ... 
doi:10.3390/cells10092309 pmid:34571958 pmcid:PMC8471780 fatcat:vquktuys7vevpk25mg7l2dgpji

EBEC Short Reports Volume 13

2004 Biochimica et Biophysica Acta - Bioenergetics  
The cytochrome c machinery in B. subtilis is of the so called System II type which is also present in plants.  ...  We have found that a wide range of different structures, only vaguely resembling fatty acids, are able to initiate UCP1-dependent (re)activation of mitochondrial thermogenesis.  ...  Both single mutants have 50% of wild-type ATPase activity. The reduced double mutant has 30% of wild-type ATPase activity.  ... 
doi:10.1016/j.bbabio.2004.06.002 fatcat:kwzzktmrzbfnlk54eebael35rm

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution

Hye Ran Koh, Rahul Roy, Maria Sorokina, Guo-Qing Tang, Divya Nandakumar, Smita S. Patel, Taekjip Ha
2018 Molecular Cell  
We provide a comprehensive analysis of transcription in real-time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription  ...  They distinguish productive and failed transcription, and show that a majority of productive transcription occurs without abortive initiation, and most of the abortive RNAs result from multiple rounds  ...  Acknowledgments This work was supported by NIH grants (GM118086, GM 122569) and by the Korea Research Foundation Grant (KRF-2006-612-C0020).  ... 
doi:10.1016/j.molcel.2018.04.018 pmid:29775583 pmcid:PMC5983381 fatcat:xaheo7r6szcehn2hbd7e732t7a

1 Keynote address by Nobel Laureate Phillip A. Sharp the 21st century opened with a revolution in RNA biology

Phillip A. Sharp
2015 Journal of Biomolecular Structure and Dynamics  
The discoveries of RNA interference and the evolutionary conservation of microRNAs at the turn of the century heralded a revolution in RNA Biology and the development of important innovations.  ...  Long non-coding RNAs regulate the expression of genes through both cis and trans mechanisms and provide organization to the nucleus.  ...  PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation. Molecular Carcinogenesis. (Epub ahead of print).  ... 
doi:10.1080/07391102.2015.1032624 fatcat:w7iil7k3ize77bjkthcyi52ohy

Meeting report: 32nd International Conference on Antiviral Research

Enzo Tramontano, Bart Tarbet, Jessica R. Spengler, Katherine Seley-Radtke, Chris Meier, Robert Jordan, Zlatko Janeba, Brian Gowen, Brian Gentry, José A. Esté, Mike Bray, Graciela Andrei (+1 others)
2019 Antiviral Research  
It provides a general review of the meeting and awardees, summarizing the presentations, and their main conclusions from the perspective of researchers active in many different areas of antiviral research  ...  This report gives an overview of the conference on behalf of the Society.  ...  Acknowledgements We thank all of the speakers, presenters, participants, organizers, and sponsors of the 32nd ICAR for their contributions to such a successful meeting.  ... 
doi:10.1016/j.antiviral.2019.104550 pmid:31302149 pmcid:PMC7105345 fatcat:27w3m6jfybghdlrrkanjlhzzpy

Abstracts of the 29th Annual Symposium of The Protein Society

2015 Protein Science  
Nuclear magnetic resonance (NMR) is a powerful biophysical method for studying protein-ligand interactions in solution and elucidating the mechanism of action of potential inhibitors.  ...  Finally, 19F-NMR was used to study solvent exposure of the complex and its dynamics in solution through relaxation dispersion of the 19F-nucleus at different temperatures.  ...  Inside the membrane, the relaxosome identifies the single strand for transfer in a plasmid DNA, relaxes and unwinds it, whereas the transferosome is involved in pilus formation (Type IV secretion system  ... 
doi:10.1002/pro.2823 pmid:26452528 pmcid:PMC4632850 fatcat:ejmksoqj3zbsrkabl4jyp7emgi

The 28th Annual Symposium of The Protein Society: Program & Abstracts

2014 Protein Science  
DNA replication system in the yeast Saccharomyces cerevisiae. 1 This system consists of an orthogonal DNA plasmid-DNA polymerase pair wherein the orthogonal DNA polymerase stably and specifically replicates  ...  Computational models and experiments differentiated the structure and behaviour of the wild type from the mutant -differences which may underpin the impaired mechanosensing ability of the mutant found  ...  The catalytic and three-dimensional differences between al the analyzed mutants are reported, and their roll in the dimeric wild type nature of this enzyme discussed.  ... 
doi:10.1002/pro.2504 pmid:25043257 pmcid:PMC4116645 fatcat:yjhug3aif5futn3icovvrkgebm

The effects of extremely low frequency magnetic fields on mutation induction in mice

James W. Wilson, Jackie Haines, Zenon Sienkiewicz, Yuri E. Dubrova
2015 Mutation research  
I would like to take this opportunity to express my utmost gratitude to my supervisor Professor Yuri Dubrova, for all his advice, guidance, and support throughout my time in the laboratory and the completion  ...  of this thesis.  ...  It was therefore theorised that ESTR mutations arise through a replication or repair based process involving DNA polymerase slippage during DNA replication, or through DNA polymerase pausing to repair  ... 
doi:10.1016/j.mrfmmm.2015.01.014 pmid:25769183 fatcat:fhcdhlbiazghtervmdre4vubyy
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