Robert M. Yarrington
University of Utah
PromoterMolecular biologyGeneticsTranscription factorBiology
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Publications 5
#1Robert M. Yarrington (UofU: University of Utah)H-Index: 7
#2Sarah M. Richardson (DOE: United States Department of Energy)H-Index: 12
Last. Jef D. BoekeH-Index: 91
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Extensive mutagenesis via massive recoding of retrotransposon Ty1 produced a synthetic codon-optimized retrotransposon (CO-Ty1). CO-Ty1 is defective for retrotransposition, suggesting a sequence capable of down-regulating retrotransposition. We mapped this sequence to a critical ∼20-bp region within CO-Ty1 reverse transcriptase (RT) and confirmed that it reduced Ty1 transposition, protein, and RNA levels. Repression was not Ty1 specific; when introduced immediately downstream of the green fluore...
10 CitationsSource
#1Sarah M. Richardson (JHUSOM: Johns Hopkins University School of Medicine)H-Index: 12
#2Paul W. Nunley (JHUSOM: Johns Hopkins University School of Medicine)H-Index: 1
Last. Joel S. Bader (JHUSOM: Johns Hopkins University School of Medicine)H-Index: 50
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GeneDesign is a set of web applications that provides public access to a nucleotide manipulation pipeline for synthetic biology. The server is public and freely accessible, and the source is available for download under the New BSD License. Since GeneDesign was published and made publicly available 3 years ago, we have made its code base more efficient, added several algorithms and modules, updated the restriction enzyme library, added batch processing capabilities, and added several command lin...
48 CitationsSource
#1M. Sulek (McMaster University)H-Index: 1
#2Robert M. Yarrington (JHUSOM: Johns Hopkins University School of Medicine)H-Index: 7
Last. Murray S. Junop (McMaster University)H-Index: 25
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Abstract A predominant pathway implicated in repair of DNA double-strand breaks (DSBs) is the evolutionarily conserved non-homologous end-joining (NHEJ) pathway. Among the major constituents of this pathway in Saccharomyces cerevisiae is Nej1p, for which a biochemical function has yet to be determined. In this work we demonstrate that Nej1p exhibits a DNA binding activity ( K D ∼ 1.8 μM) comparable to Lif1p. Although binding is enhanced with larger substrates (>300 bp), short ∼20 bp substrates c...
11 CitationsSource
#1Robert M. Yarrington (Johns Hopkins University)H-Index: 7
#2Jichao Chen (Johns Hopkins University)H-Index: 1
Last. Jef D. Boeke (Johns Hopkins University)H-Index: 91
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Ty1 reverse transcriptase/RNase H (RT/RH) is exquisitely sensitive to manganese concentrations. Elevated intracellular free Mn2+ inhibits Ty1 retrotransposition and in vitro Ty1 RT-polymerizing activity. Furthermore, Mn2+ inhibition is not limited to the Ty1 RT, as this ion similarly inhibits the activities of both avian myeloblastosis virus and human immunodeficiency virus type 1 RTs. To further characterize Mn2+ inhibition, we generated RT/RH suppressor mutants capable of increased Ty1 transpo...
8 CitationsSource
#1Sarah M. Richardson (Johns Hopkins University)H-Index: 12
#2Sarah J. WheelanH-Index: 29
Last. Jef D. BoekeH-Index: 91
view all 4 authors...
Modern molecular biology has brought many new tools to the geneticist as well as an exponentially expanding database of genomes and new genes for study. Of particular use in the analysis of these genes is the synthetic gene, a nucleotide sequence designed to the specifications of the investigator. Typically, synthetic genes encode the same product as the gene of interest, but the synthetic nucleotide sequence for that protein may contain modifications affecting expression or base composition. Ot...
109 CitationsSource