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Items: 1 to 20 of 93

1.
Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo
Kiyoto Kamagata, Yuji Itoh, Cheng Tan, Eriko Mano, Yining Wu, Sridhar Mandali, Shoji Takada, Reid C Johnson
Nucleic Acids Res. 2021 Sep 7; 49(15): 8642–8664. Published online 2021 Aug 5. doi: 10.1093/nar/gkab658
PMCID:
PMC8421229
AbstractArticlePDF–6.0M
2.
The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA
Kiyoto Kamagata, Kana Ouchi, Cheng Tan, Eriko Mano, Sridhar Mandali, Yining Wu, Shoji Takada, Satoshi Takahashi, Reid C Johnson
Nucleic Acids Res. 2020 Nov 4; 48(19): 10820–10831. Published online 2020 Sep 30. doi: 10.1093/nar/gkaa799
PMCID:
PMC7641734
AbstractArticlePDF–4.8M
3.
Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A
Manas Kumar Sarangi, Viktoriya Zvoda, Molly Nelson Holte, Nicole A Becker, Justin P Peters, L James Maher, III, Anjum Ansari
Nucleic Acids Res. 2019 Apr 8; 47(6): 2871–2883. Published online 2019 Jan 30. doi: 10.1093/nar/gkz022
PMCID:
PMC6451137
AbstractArticlePDF–1.6M
4.
Facilitated dissociation of transcription factors from single DNA binding sites
Ramsey I. Kamar, Edward J. Banigan, Aykut Erbas, Rebecca D. Giuntoli, Monica Olvera de la Cruz, Reid C. Johnson, John F. Marko
Proc Natl Acad Sci U S A. 2017 Apr 18; 114(16): E3251–E3257. Published online 2017 Mar 31. doi: 10.1073/pnas.1701884114
PMCID:
PMC5402408
AbstractArticlePDF–1.3M
5.
DNA-segment-facilitated dissociation of Fis and NHP6A from DNA detected via single-molecule mechanical response
Rebecca D. Giuntoli, Nora B. Linzer, Edward J. Banigan, Charles E. Sing, Monica Olvera de la Cruz, John S. Graham, Reid C. Johnson, John F. Marko
J Mol Biol. Author manuscript; available in PMC 2016 Sep 25.
Published in final edited form as: J Mol Biol. 2015 Sep 25; 427(19): 3123–3136. Published online 2015 Jul 26. doi: 10.1016/j.jmb.2015.07.015
PMCID:
PMC4579036
AbstractArticlePDF–1.2M
6.
High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli
Nicole A. Becker, L. James Maher, III
Proc Natl Acad Sci U S A. 2015 Jun 9; 112(23): 7177–7182. Published online 2015 May 26. doi: 10.1073/pnas.1500412112
PMCID:
PMC4466710
AbstractArticlePDF–1.7M
7.
Single-molecule FRET analysis of DNA binding and bending by yeast HMGB protein Nhp6A
Julie E. Coats, Yuyen Lin, Emily Rueter, L. James Maher, III, Ivan Rasnik
Nucleic Acids Res. 2013 Jan; 41(2): 1372–1381. Published online 2012 Dec 5. doi: 10.1093/nar/gks1208
PMCID:
PMC3554232
AbstractArticlePDF–706K
8.
Basic N-terminus of yeast Nhp6A regulates the mechanism of its DNA flexibility enhancement
Jingyun Zhang, Micah J. McCauley, L. James Maher, III, Mark C. Williams, N. E. Israeloff
J Mol Biol. Author manuscript; available in PMC 2013 Feb 10.
Published in final edited form as: J Mol Biol. 2012 Feb 10; 416(1): 10–20. Published online 2011 Dec 13. doi: 10.1016/j.jmb.2011.12.004
PMCID:
PMC3280093
AbstractArticlePDF–4.0M
9.
Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins
Luke Czapla, Justin P. Peters, Emily M. Rueter, Wilma K. Olson, L. James Maher, III
J Mol Biol. Author manuscript; available in PMC 2012 Jun 3.
Published in final edited form as: J Mol Biol. 2011 Jun 3; 409(2): 278–289. Published online 2011 Apr 1. doi: 10.1016/j.jmb.2011.03.050
PMCID:
PMC3095720
AbstractArticlePDF–2.6M
10.
Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA
John S. Graham, Reid C. Johnson, John F. Marko
Nucleic Acids Res. 2011 Mar; 39(6): 2249–2259. Published online 2010 Nov 20. doi: 10.1093/nar/gkq1140
PMCID:
PMC3064784
AbstractArticlePDF–2.8M
11.
Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription
Noah L. Dowell, Adam S. Sperling, Michael J. Mason, Reid C. Johnson
Genes Dev. 2010 Sep 15; 24(18): 2031–2042. doi: 10.1101/gad.1948910
PMCID:
PMC2939365
AbstractArticlePDF–1.1M
12.
Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding.
F H Allain, Y M Yen, J E Masse, P Schultze, T Dieckmann, R C Johnson, J Feigon
EMBO J. 1999 May 4; 18(9): 2563–2579. doi: 10.1093/emboj/18.9.2563
PMCID:
PMC1171337
SummaryPDF–1.0M
13.
Single and double box HMGB proteins differentially destabilize nucleosomes
Micah J McCauley, Ran Huo, Nicole Becker, Molly Nelson Holte, Uma M Muthurajan, Ioulia Rouzina, Karolin Luger, L James Maher, III, Nathan E Israeloff, Mark C Williams
Nucleic Acids Res. 2019 Jan 25; 47(2): 666–678. Published online 2018 Nov 16. doi: 10.1093/nar/gky1119
PMCID:
PMC6344895
AbstractArticlePDF–4.1M
14.
Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility
Micah J. McCauley, Emily M. Rueter, Ioulia Rouzina, L. James Maher, III, Mark C. Williams
Nucleic Acids Res. 2013 Jan; 41(1): 167–181. Published online 2012 Nov 7. doi: 10.1093/nar/gks1031
PMCID:
PMC3592474
AbstractArticlePDF–3.2M
15.
Nhp6: A Small but Powerful Effector of Chromatin Structure in Saccharomyces cerevisiae
David J. Stillman
Biochim Biophys Acta. Author manuscript; available in PMC 2011 Jan 1.
Published in final edited form as: Biochim Biophys Acta. 2010 Jan–Feb; 1799(1-2): 175. doi: 10.1016/j.bbagrm.2009.11.010
PMCID:
PMC2818483
AbstractArticlePDF–780K
16.
Enhancement of DNA flexibility in vitro and in vivo by HMGB box A proteins carrying box B residues
Nadia Sebastian, Emily M. Bystry, Nicole A. Becker, L. James Maher, III
Biochemistry. Author manuscript; available in PMC 2010 Mar 17.
Published in final edited form as: Biochemistry. 2009 Mar 17; 48(10): 2125–2134. doi: 10.1021/bi802269f
PMCID:
PMC2668924
AbstractArticlePDF–2.0M
17.
A Novel Upstream RNA Polymerase III Promoter Element Becomes Essential When the Chromatin Structure of the Yeast U6 RNA Gene Is Altered
Michael P. Martin, Valerie L. Gerlach, David A. Brow
Mol Cell Biol. 2001 Oct; 21(19): 6429–6439. doi: 10.1128/MCB.21.19.6429-6439.2001
PMCID:
PMC99790
AbstractArticlePDF–1.5M
18.
Role of Nhp6 and Hmo1 in SWI/SNF occupancy and nucleosome landscape at gene regulatory regions
Matias I. Hepp, Michaela Smolle, Cristian Gidi, Roberto Amigo, Nicole Valenzuela, Axel Arriagada, Alejandro Maureira, Madelaine M. Gogol, Marcela Torrejón, Jerry L. Workman, José L. Gutiérrez
Biochim Biophys Acta. Author manuscript; available in PMC 2018 Apr 24.
Published in final edited form as: Biochim Biophys Acta. 2017 Mar; 1860(3): 316–326. Published online 2017 Jan 9. doi: 10.1016/j.bbagrm.2017.01.002
PMCID:
PMC5913752
AbstractArticlePDF–2.3M
19.
Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae
Christos Andreadis, Christoforos Nikolaou, George S. Fragiadakis, Georgia Tsiliki, Despina Alexandraki
Nucleic Acids Res. 2014 Nov 10; 42(20): 12650–12667. Published online 2014 Oct 9. doi: 10.1093/nar/gku915
PMCID:
PMC4227768
AbstractArticlePDF–699K
20.
Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output
Barbara Celona, Assaf Weiner, Francesca Di Felice, Francesco M. Mancuso, Elisa Cesarini, Riccardo L. Rossi, Lorna Gregory, Dilair Baban, Grazisa Rossetti, Paolo Grianti, Massimiliano Pagani, Tiziana Bonaldi, Jiannis Ragoussis, Nir Friedman, Giorgio Camilloni, Marco E. Bianchi, Alessandra Agresti
PLoS Biol. 2011 Jun; 9(6): e1001086. Published online 2011 Jun 28. doi: 10.1371/journal.pbio.1001086
PMCID:
PMC3125158
AbstractArticlePDF–977K

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