Search Results - "Bashkin, James"

Oligonucleotides containing abasic threoninol-terpyridine residues as potential artificial ribonucleases by Putnam, William C., Bashkin, James K.

“…Artificial ribonucleases, also known as synthetic ribozymes, were synthesized with an internal, stereochemically-pure, abasic threoninol backbone-residue to…”
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Size matters: DNA binding site kinetics as a function of polyamide size by Niederschulte, Jacquelyn, Song, Yang, Bashkin, James K., Dupureur, Cynthia M.

“…Hairpin polyamides (PAs) are remarkable minor groove-binding DNA ligands that demonstrate high affinity and sequence selectivity. Following extensive studies…”
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DNA damage repair genes controlling human papillomavirus (HPV) episome levels under conditions of stability and extreme instability by Edwards, Terri G, Vidmar, Thomas J, Koeller, Kevin, Bashkin, James K, Fisher, Chris

“…DNA damage response (DDR) genes and pathways controlling the stability of HPV episomal DNA are reported here. We set out to understand the mechanism by which a…”
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Human Papillomavirus Episome Stability Is Reduced by Aphidicolin and Controlled by DNA Damage Response Pathways by Edwards, Terri G, Helmus, Michael J, Koeller, Kevin, Bashkin, James K, Fisher, Chris

“…Article Usage Stats Services JVI Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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DNA binding site kinetics of a large antiviral polyamide by Niederschulte, Jacquelyn, Song, Yang, Park, Andrew H., Bashkin, James K., Dupureur, Cynthia M.

“…Polyamides (PAs) are powerful DNA ligands that can bind the minor groove of DNA with high affinity and specificity. While the characterization of PA-DNA…”
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Thermodynamics and site stoichiometry of DNA binding by a large antiviral hairpin polyamide by Song, Yang, Niederschulte, Jacquelyn, Bales, Kristin N., Bashkin, James K., Dupureur, Cynthia M.

“…PA1 (dIm-PyPyβPyPyPy-γ-PyPyβPyPyPyPyβ-Ta) is a large (14-ring) hairpin polyamide that was designed to recognize the DNA sequence 5’-W2GW7-3’, where W is either…”
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DNA binding thermodynamics and site stoichiometry as a function of polyamide size by Song, Yang, Niederschulte, Jacquelyn, Bales, Kristin N., Park, Andrew H., Bashkin, James K., Dupureur, Cynthia M.

“…The interactions of 6–8 ring hairpin polyamides (PAs) with the minor groove of DNA have been investigated extensively. More recent studies of large antiviral…”
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Modulating DNA by polyamides to regulate transcription factor PU.1-DNA binding interactions by Liu, Beibei, Bashkin, James K., Poon, Gregory M.K., Wang, Shuo, Wang, Siming, Wilson, W. David

“…Hairpin polyamides are synthetic small molecules that bind DNA minor groove sequence-selectively and, in many sequences, induce widening of the minor groove…”
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A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid by Gumpper, Ryan H, Li, Weike, Castañeda, Carlos H, Scuderi, M José, Bashkin, James K, Luo, Ming

“…Polyamides have been shown to bind double-stranded DNA by complementing the curvature of the minor groove and forming various hydrogen bonds with DNA. Several…”
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Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors by He, Gaofei, Tolic, Ana, Bashkin, James K, Poon, Gregory M K

“…The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve…”
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Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis by He, Gaofei, Vasilieva, Elena, Bashkin, James K., Dupureur, Cynthia M.

“…The mapping of DNA footprints and affinity cleavage sites for small DNA ligands is affected by the choice of sequencing chemistry and end label, and the…”
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What is the antiviral potential of pyrrole-imidazole polyamides? by He, Gaofei, Bashkin, James K

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Correlation of Local Effects of DNA Sequence and Position of β‑Alanine Inserts with Polyamide–DNA Complex Binding Affinities and Kinetics by Wang, Shuo, Nanjunda, Rupesh, Aston, Karl, Bashkin, James K, Wilson, W. David

“…To improve our understanding of the effects of β-alanine (β) substitution and the number of heterocycles on DNA binding affinity and selectivity, we…”
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β-Alanine and N-terminal cationic substituents affect polyamide-DNA binding by Liu, Beibei, Wang, Shuo, Aston, Karl, Koeller, Kevin J, Kermani, Shahrzad Fanny Hakami, Castañeda, Carlos H, Scuderi, M José, Luo, Rensheng, Bashkin, James K, Wilson, W David

“…Minor-groove binding hairpin polyamides (PAs) bind specific DNA sequences. Synthetic modifications can improve PA-DNA binding affinity and include flexible…”
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Interactions of two large antiviral polyamides with the long control region of HPV16 by Vasilieva, Elena, Niederschulte, Jacquelyn, Song, Yang, Harris, George Davis, Koeller, Kevin J., Liao, Puhong, Bashkin, James K., Dupureur, Cynthia M.

“…PA1 and PA25 are large hairpin polyamides that are effective in nearly eliminating HPV16 episomes (DNA) in cell culture, and PA25 has broad spectrum activity…”
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Different thermodynamic signatures for DNA minor groove binding with changes in salt concentration and temperature by Wang, Shuo, Kumar, Arvind, Aston, Karl, Nguyen, Binh, Bashkin, James K, Boykin, David W, Wilson, W David

“…The effects of salt concentration and temperature on the thermodynamics of DNA minor groove binding have quite different signatures: binding enthalpy is salt…”
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Binding studies of a large antiviral polyamide to a natural HPV sequence by He, Gaofei, Vasilieva, Elena, Harris, George Davis, Koeller, Kevin J., Bashkin, James K., Dupureur, Cynthia M.

“…PA1 is a large hairpin polyamide (dImPyPy-β-PyPyPy-γ-PyPy-β-PyPyPyPy-β-Ta; Py = pyrrole, Im = imidazole, β = beta alanine) that targets the sequence…”
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Modulation of DNA-polyamide interaction by β-alanine substitutions: a study of positional effects on binding affinity, kinetics and thermodynamics by Wang, Shuo, Aston, Karl, Koeller, Kevin J, Harris, Jr, G Davis, Rath, Nigam P, Bashkin, James K, Wilson, W David

“…Hairpin polyamides (PAs) are an important class of sequence-specific DNA minor groove binders, and frequently employ a flexible motif, β-alanine (β), to reduce…”
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Inorganic Mimics of Ribonucleases and Ribozymes:  From Random Cleavage to Sequence-Specific Chemistry to Catalytic Antisense Drugs by Trawick, Bobby N, Daniher, Andrew T, Bashkin, James K

“…Trawick et al describe the evolution of ribozyme mimics from early, nonspecific, ill-defined catalysts that were derived from "free metal ions in buffer" to…”
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Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA by Joachimiak, Andrzej, Zhang, Rong-guang, Pappas, Terina, Brace, Jennifer L, Miller, Paula C, Oulmassov, Tim, Molyneaux, John M, Anderson, John C, Bashkin, James K, Winans, Stephen C

“…Many proteobacteria are able to monitor their population densities through the release of pheromones known as N-acylhomoserine lactones. At high population…”
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