Search Results - "Poon, Gregory M."

Detecting recurrent passenger mutations in melanoma by targeted UV damage sequencing by Selvam, Kathiresan, Sivapragasam, Smitha, Poon, Gregory M. K., Wyrick, John J.

“…Sequencing of melanomas has identified hundreds of recurrent mutations in both coding and non-coding DNA. These include a number of well-characterized…”
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Pharmacologic efficacy of PU.1 inhibition by heterocyclic dications: a mechanistic analysis by Stephens, Dominique C, Kim, Hye Mi, Kumar, Arvind, Farahat, Abdelbasset A, Boykin, David W, Poon, Gregory M

“…Heterocyclic dications are receiving increasing attention as targeted inhibitors of transcription factors. While many dications act as purely competitive…”
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Structure of an RNA G-quadruplex from the West Nile virus genome by Terrell, J. Ross, Le, Thao T., Paul, Ananya, Brinton, Margo A., Wilson, W. David, Poon, Gregory M. K., Germann, Markus W., Siemer, Jessica L.

“…Potential G-quadruplex sites have been identified in the genomes of DNA and RNA viruses and proposed as regulatory elements. The genus Orthoflavivirus contains…”
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ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma by Mao, Peng, Brown, Alexander J., Esaki, Shingo, Lockwood, Svetlana, Poon, Gregory M. K., Smerdon, Michael J., Roberts, Steven A., Wyrick, John J.

“…Recurrent mutations are frequently associated with transcription factor (TF) binding sites (TFBS) in melanoma, but the mechanism driving mutagenesis at TFBS is…”
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Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains by Stephens, Dominique C, Poon, Gregory M K

“…Transactivation by the ETS family of transcription factors, whose members share structurally conserved DNA-binding domains, is variably sensitive to…”
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Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6 by Vo, Tam D, Schneider, Amelia L, Wilson, W David, Poon, Gregory M K

“…Electrostatic protein/DNA interactions arise from the neutralization of the DNA phosphodiester backbone as well as coupled exchanges by charged protein…”
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Distinct Roles for Interfacial Hydration in Site-Specific DNA Recognition by ETS-Family Transcription Factors by Xhani, Suela, Esaki, Shingo, Huang, Kenneth, Erlitzki, Noa, Poon, Gregory M. K

“…The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding…”
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Dissecting Knowledge, Guessing, and Blunder in Multiple Choice Assessments by Abu-Ghazalah, Rashid M., Dubins, David N., Poon, Gregory M.K.

“…Multiple choice results are inherently probabilistic outcomes, as correct responses reflect a combination of knowledge and guessing, while incorrect responses…”
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High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors by Duan, Mingrui, Sivapragasam, Smitha, Antony, Jacob S, Ulibarri, Jenna, Hinz, John M, Poon, Gregory M K, Wyrick, John J, Mao, Peng

“…DNA base damage arises frequently in living cells and needs to be removed by base excision repair (BER) to prevent mutagenesis and genome instability. Both the…”
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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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DNA Binding Regulates the Self-Association of the ETS Domain of PU.1 in a Sequence-Dependent Manner by Poon, Gregory M. K

“…The current paradigm of ETS transcription factors holds that their DNA-binding (ETS) domain binds to a single sequence-specific site with strict 1:1…”
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CTCF puts a new twist on UV damage and repair in skin cancer by Stark, Bastian, Poon, Gregory M. K., Wyrick, John J.

“…Somatic mutations in skin cancers are highly enriched at binding sites for CCCTC-binding factor (CTCF). We have discovered that CTCF binding alters the DNA…”
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Probing the Electrostatics and Pharmacological Modulation of Sequence-Specific Binding by the DNA-Binding Domain of the ETS Family Transcription Factor PU.1: A Binding Affinity and Kinetics Investigation by Munde, Manoj, Poon, Gregory M.K., Wilson, W. David

“…Members of the ETS family of transcription factors regulate a functionally diverse array of genes. All ETS proteins share a structurally conserved but…”
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Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields by Schneider, Amelia L, Albrecht, Amanda V, Huang, Kenneth, Germann, Markus W, Poon, Gregory M K

“…Fixed-charge (non-polarizable) forcefields are accurate and computationally efficient tools for modeling the molecular dynamics of nucleic acid polymers,…”
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DNA mismatches reveal conformational penalties in protein–DNA recognition by Afek, Ariel, Shi, Honglue, Rangadurai, Atul, Sahay, Harshit, Senitzki, Alon, Xhani, Suela, Fang, Mimi, Salinas, Raul, Mielko, Zachery, Pufall, Miles A., Poon, Gregory M. K., Haran, Tali E., Schumacher, Maria A., Al-Hashimi, Hashim M., Gordân, Raluca

“…Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription…”
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Prodrug Applications for Targeted Cancer Therapy by Giang, Irene, Boland, Erin L., Poon, Gregory M. K.

“…Prodrugs are widely used in the targeted delivery of cytotoxic compounds to cancer cells. To date, targeted prodrugs for cancer therapy have achieved great…”
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The Non-continuum Nature of Eukaryotic Transcriptional Regulation by Poon, Gregory M K

“…Eukaryotic transcription factors are versatile mediators of specificity in gene regulation. This versatility is achieved through mutual specification by…”
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PU.1 controls fibroblast polarization and tissue fibrosis by Wohlfahrt, Thomas, Rauber, Simon, Uebe, Steffen, Luber, Markus, Soare, Alina, Ekici, Arif, Weber, Stefanie, Matei, Alexandru-Emil, Chen, Chih-Wei, Maier, Christiane, Karouzakis, Emmanuel, Kiener, Hans P., Pachera, Elena, Dees, Clara, Beyer, Christian, Daniel, Christoph, Gelse, Kolja, Kremer, Andreas E., Naschberger, Elisabeth, Stürzl, Michael, Butter, Falk, Sticherling, Michael, Finotto, Susetta, Kreuter, Alexander, Kaplan, Mark H., Jüngel, Astrid, Gay, Steffen, Nutt, Stephen L., Boykin, David W., Poon, Gregory M. K., Distler, Oliver, Schett, Georg, Distler, Jörg H. W., Ramming, Andreas

“…Fibroblasts are polymorphic cells with pleiotropic roles in organ morphogenesis, tissue homeostasis and immune responses. In fibrotic diseases, fibroblasts…”
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Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors by Vernon, Tyler N, Terrell, J Ross, Albrecht, Amanda V, Germann, Markus W, Wilson, W David, Poon, Gregory M K

“…Nucleobases such as inosine have been extensively utilized to map direct contacts by proteins in the DNA groove. Their deployment as targeted probes of…”
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CTCF binding modulates UV damage formation to promote mutation hot spots in melanoma by Sivapragasam, Smitha, Stark, Bastian, Albrecht, Amanda V, Bohm, Kaitlynne A, Mao, Peng, Emehiser, Raymond G, Roberts, Steven A, Hrdlicka, Patrick J, Poon, Gregory M K, Wyrick, John J

“…Somatic mutations in DNA‐binding sites for CCCTC‐binding factor (CTCF) are significantly elevated in many cancers. Prior analysis has suggested that elevated…”
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