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Items: 1 to 50 of 61

1.

Bimodal actions of a naphthyridone/aminopiperidine-based antibacterial that targets gyrase and topoisomerase IV.

Gibson EG, Oviatt AA, Cacho M, Neuman KC, Chan PF, Osheroff N.

Biochemistry. 2019 Oct 16. doi: 10.1021/acs.biochem.9b00805. [Epub ahead of print]

PMID:
31617352
2.

Homology sensing via non-linear amplification of sequence-dependent pausing by RecQ helicase.

Seol Y, Harami GM, Kovács M, Neuman KC.

Elife. 2019 Aug 29;8. pii: e45909. doi: 10.7554/eLife.45909.

3.

Polydopamine encapsulation of fluorescent nanodiamonds for biomedical applications.

Jung HS, Cho KJ, Seol Y, Takagi Y, Dittmore A, Roche PA, Neuman KC.

Adv Funct Mater. 2018 Aug 15;28(33). pii: 1801252. doi: 10.1002/adfm.201801252. Epub 2018 Jun 20.

4.

Direct observation of topoisomerase IA gate dynamics.

Mills M, Tse-Dinh YC, Neuman KC.

Nat Struct Mol Biol. 2018 Dec;25(12):1111-1118. doi: 10.1038/s41594-018-0158-x. Epub 2018 Nov 26.

5.

Kinetic Pathway of Torsional DNA Buckling.

Dittmore A, Silver J, Neuman KC.

J Phys Chem B. 2018 Dec 13;122(49):11561-11570. doi: 10.1021/acs.jpcb.8b07504. Epub 2018 Oct 31.

PMID:
30346755
6.

A minimal threshold of FANCJ helicase activity is required for its response to replication stress or double-strand break repair.

Bharti SK, Sommers JA, Awate S, Bellani MA, Khan I, Bradley L, King GA, Seol Y, Vidhyasagar V, Wu Y, Abe T, Kobayashi K, Shin-Ya K, Kitao H, Wold MS, Branzei D, Neuman KC, Brosh RM Jr.

Nucleic Acids Res. 2018 Jul 6;46(12):6238-6256. doi: 10.1093/nar/gky403.

7.

Defect-facilitated buckling in supercoiled double-helix DNA.

Brahmachari S, Dittmore A, Takagi Y, Neuman KC, Marko JF.

Phys Rev E. 2018 Feb;97(2-1):022416. doi: 10.1103/PhysRevE.97.022416.

8.

RecQ helicase triggers a binding mode change in the SSB-DNA complex to efficiently initiate DNA unwinding.

Mills M, Harami GM, Seol Y, Gyimesi M, Martina M, Kovács ZJ, Kovács M, Neuman KC.

Nucleic Acids Res. 2017 Nov 16;45(20):11878-11890. doi: 10.1093/nar/gkx939.

9.

Supercoiling DNA Locates Mismatches.

Dittmore A, Brahmachari S, Takagi Y, Marko JF, Neuman KC.

Phys Rev Lett. 2017 Oct 6;119(14):147801. doi: 10.1103/PhysRevLett.119.147801. Epub 2017 Oct 3.

10.
11.

Activities of gyrase and topoisomerase IV on positively supercoiled DNA.

Ashley RE, Dittmore A, McPherson SA, Turnbough CL Jr, Neuman KC, Osheroff N.

Nucleic Acids Res. 2017 Sep 19;45(16):9611-9624. doi: 10.1093/nar/gkx649.

12.

Distribution bias and biochemical characterization of TOP1MT single nucleotide variants.

Zhang H, Seol Y, Agama K, Neuman KC, Pommier Y.

Sci Rep. 2017 Aug 17;7(1):8614. doi: 10.1038/s41598-017-09258-2.

13.

Highly Multiplexed, Super-resolution Imaging of T Cells Using madSTORM.

Yi J, Manna A, Barr VA, Hong J, Neuman KC, Samelson LE.

J Vis Exp. 2017 Jun 24;(124). doi: 10.3791/55997.

14.

Brownian ratchet mechanisms of ParA-mediated partitioning.

Hu L, Vecchiarelli AG, Mizuuchi K, Neuman KC, Liu J.

Plasmid. 2017 Jul;92:12-16. doi: 10.1016/j.plasmid.2017.05.002. Epub 2017 May 18. Review. No abstract available.

15.

The dynamic interplay between DNA topoisomerases and DNA topology.

Seol Y, Neuman KC.

Biophys Rev. 2016 Nov;8(Suppl 1):101-111. doi: 10.1007/s12551-016-0240-8. Epub 2016 Nov 14. Review.

16.

Brownian Ratchet Mechanism for Faithful Segregation of Low-Copy-Number Plasmids.

Hu L, Vecchiarelli AG, Mizuuchi K, Neuman KC, Liu J.

Biophys J. 2017 Apr 11;112(7):1489-1502. doi: 10.1016/j.bpj.2017.02.039.

17.

Shuttling along DNA and directed processing of D-loops by RecQ helicase support quality control of homologous recombination.

Harami GM, Seol Y, In J, Ferencziová V, Martina M, Gyimesi M, Sarlós K, Kovács ZJ, Nagy NT, Sun Y, Vellai T, Neuman KC, Kovács M.

Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):E466-E475. doi: 10.1073/pnas.1615439114. Epub 2017 Jan 9.

18.

The Dynamic Interplay Between DNA Topoisomerases and DNA Topology.

Seol Y, Neuman KC.

Biophys Rev. 2016 Sep;8(3):221-231. Epub 2016 Jul 2.

19.

madSTORM: a superresolution technique for large-scale multiplexing at single-molecule accuracy.

Yi J, Manna A, Barr VA, Hong J, Neuman KC, Samelson LE.

Mol Biol Cell. 2016 Nov 7;27(22):3591-3600. Epub 2016 Oct 5.

20.

Internal strain drives spontaneous periodic buckling in collagen and regulates remodeling.

Dittmore A, Silver J, Sarkar SK, Marmer B, Goldberg GI, Neuman KC.

Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):8436-41. doi: 10.1073/pnas.1523228113. Epub 2016 Jul 11.

21.

Single molecule measurements of DNA helicase activity with magnetic tweezers and t-test based step-finding analysis.

Seol Y, Strub MP, Neuman KC.

Methods. 2016 Aug 1;105:119-27. doi: 10.1016/j.ymeth.2016.04.030. Epub 2016 Apr 27.

22.

Membrane-bound MinDE complex acts as a toggle switch that drives Min oscillation coupled to cytoplasmic depletion of MinD.

Vecchiarelli AG, Li M, Mizuuchi M, Hwang LC, Seol Y, Neuman KC, Mizuuchi K.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):E1479-88. doi: 10.1073/pnas.1600644113. Epub 2016 Feb 16.

23.

A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting.

Herbert KM, Sarkar SK, Mills M, Delgado De la Herran HC, Neuman KC, Steitz JA.

RNA. 2016 Feb;22(2):175-83. doi: 10.1261/rna.054684.115. Epub 2015 Dec 18.

24.

Directed and persistent movement arises from mechanochemistry of the ParA/ParB system.

Hu L, Vecchiarelli AG, Mizuuchi K, Neuman KC, Liu J.

Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):E7055-64. doi: 10.1073/pnas.1505147112. Epub 2015 Dec 8.

25.

Single-Molecule Supercoil Relaxation Assay as a Screening Tool to Determine the Mechanism and Efficacy of Human Topoisomerase IB Inhibitors.

Seol Y, Zhang H, Agama K, Lorence N, Pommier Y, Neuman KC.

Mol Cancer Ther. 2015 Nov;14(11):2552-9. doi: 10.1158/1535-7163.MCT-15-0454. Epub 2015 Sep 8.

26.
27.

A moving ParA gradient on the nucleoid directs subcellular cargo transport via a chemophoresis force.

Vecchiarelli AG, Seol Y, Neuman KC, Mizuuchi K.

Bioarchitecture. 2014;4(4-5):154-9. doi: 10.4161/19490992.2014.987581.

28.

A robust assay to measure DNA topology-dependent protein binding affinity.

Litwin TR, Solà M, Holt IJ, Neuman KC.

Nucleic Acids Res. 2015 Apr 20;43(7):e43. doi: 10.1093/nar/gku1381. Epub 2014 Dec 30.

29.

Role of the water-metal ion bridge in mediating interactions between quinolones and Escherichia coli topoisomerase IV.

Aldred KJ, Breland EJ, Vlčková V, Strub MP, Neuman KC, Kerns RJ, Osheroff N.

Biochemistry. 2014 Sep 2;53(34):5558-67. doi: 10.1021/bi500682e. Epub 2014 Aug 21.

30.

Poisoning of mitochondrial topoisomerase I by lamellarin D.

Khiati S, Seol Y, Agama K, Dalla Rosa I, Agrawal S, Fesen K, Zhang H, Neuman KC, Pommier Y.

Mol Pharmacol. 2014 Aug;86(2):193-9. doi: 10.1124/mol.114.092833. Epub 2014 Jun 2.

31.

Wide-field in vivo background free imaging by selective magnetic modulation of nanodiamond fluorescence.

Sarkar SK, Bumb A, Wu X, Sochacki KA, Kellman P, Brechbiel MW, Neuman KC.

Biomed Opt Express. 2014 Mar 14;5(4):1190-202. doi: 10.1364/BOE.5.001190. eCollection 2014 Apr 1.

32.

A propagating ATPase gradient drives transport of surface-confined cellular cargo.

Vecchiarelli AG, Neuman KC, Mizuuchi K.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4880-5. doi: 10.1073/pnas.1401025111. Epub 2014 Feb 24.

33.

The tail that wags the dog: topoisomerase IV ParC C-terminal domain controls strand passage activity through multipartite topology-dependent interactions with DNA.

Neuman KC.

J Mol Biol. 2013 Sep 9;425(17):3025-8. doi: 10.1016/j.jmb.2013.07.004. Epub 2013 Jul 11. No abstract available.

34.

SnapShot: single-molecule fluorescence.

Sarkar SK, Bumb A, Mills M, Neuman KC.

Cell. 2013 Jun 6;153(6):1408-1408.e1. doi: 10.1016/j.cell.2013.05.024. No abstract available.

35.

SnapShot: force spectroscopy and single-molecule manipulation.

Seol Y, Neuman KC.

Cell. 2013 May 23;153(5):1168-1168.e1. doi: 10.1016/j.cell.2013.04.047. No abstract available.

36.

Silica encapsulation of fluorescent nanodiamonds for colloidal stability and facile surface functionalization.

Bumb A, Sarkar SK, Billington N, Brechbiel MW, Neuman KC.

J Am Chem Soc. 2013 May 29;135(21):7815-8. doi: 10.1021/ja4016815. Epub 2013 Apr 22.

37.

Chiral discrimination and writhe-dependent relaxation mechanism of human topoisomerase IIα.

Seol Y, Gentry AC, Osheroff N, Neuman KC.

J Biol Chem. 2013 May 10;288(19):13695-703. doi: 10.1074/jbc.M112.444745. Epub 2013 Mar 18.

38.

Comparison of DNA decatenation by Escherichia coli topoisomerase IV and topoisomerase III: implications for non-equilibrium topology simplification.

Seol Y, Hardin AH, Strub MP, Charvin G, Neuman KC.

Nucleic Acids Res. 2013 Apr;41(8):4640-9. doi: 10.1093/nar/gkt136. Epub 2013 Mar 4.

39.

A kinetic clutch governs religation by type IB topoisomerases and determines camptothecin sensitivity.

Seol Y, Zhang H, Pommier Y, Neuman KC.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16125-30. doi: 10.1073/pnas.1206480109. Epub 2012 Sep 18.

40.

Single-molecule tracking of collagenase on native type I collagen fibrils reveals degradation mechanism.

Sarkar SK, Marmer B, Goldberg G, Neuman KC.

Curr Biol. 2012 Jun 19;22(12):1047-56. doi: 10.1016/j.cub.2012.04.012. Epub 2012 May 10.

41.

Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis.

He J, Cooper HM, Reyes A, Di Re M, Sembongi H, Litwin TR, Gao J, Neuman KC, Fearnley IM, Spinazzola A, Walker JE, Holt IJ.

Nucleic Acids Res. 2012 Jul;40(13):6109-21. doi: 10.1093/nar/gks266. Epub 2012 Mar 26.

42.

Quantitative characterization of fluorophores in multi-component nanoprobes by single-molecule fluorescence.

Bumb A, Sarkar SK, Wu XS, Brechbiel MW, Neuman KC.

Biomed Opt Express. 2011 Oct 1;2(10):2761-9. doi: 10.1364/BOE.2.002761. Epub 2011 Sep 12.

43.

Magnetic tweezers for single-molecule manipulation.

Seol Y, Neuman KC.

Methods Mol Biol. 2011;783:265-93. doi: 10.1007/978-1-61779-282-3_15.

PMID:
21909894
44.

Single-molecule measurements of topoisomerase activity with magnetic tweezers.

Seol Y, Neuman KC.

Methods Mol Biol. 2011;778:229-41. doi: 10.1007/978-1-61779-261-8_15.

PMID:
21809210
45.

Direct measurement of DNA bending by type IIA topoisomerases: implications for non-equilibrium topology simplification.

Hardin AH, Sarkar SK, Seol Y, Liou GF, Osheroff N, Neuman KC.

Nucleic Acids Res. 2011 Jul;39(13):5729-43. doi: 10.1093/nar/gkr109. Epub 2011 Mar 17.

46.

Use of divalent metal ions in the DNA cleavage reaction of topoisomerase IV.

Pitts SL, Liou GF, Mitchenall LA, Burgin AB, Maxwell A, Neuman KC, Osheroff N.

Nucleic Acids Res. 2011 Jun;39(11):4808-17. doi: 10.1093/nar/gkr018. Epub 2011 Feb 7.

47.

Evolutionary twist on topoisomerases: conversion of gyrase to topoisomerase IV.

Neuman KC.

Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22363-4. doi: 10.1073/pnas.1016041108. Epub 2010 Dec 17. No abstract available.

48.

Single-molecule measurements of DNA topology and topoisomerases.

Neuman KC.

J Biol Chem. 2010 Jun 18;285(25):18967-71. doi: 10.1074/jbc.R109.092437. Epub 2010 Apr 9. Review.

49.

Mechanisms of chiral discrimination by topoisomerase IV.

Neuman KC, Charvin G, Bensimon D, Croquette V.

Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):6986-91. doi: 10.1073/pnas.0900574106. Epub 2009 Apr 9.

50.

Mutational analysis of the helicase-like domain of Thermotoga maritima reverse gyrase.

Bouthier de la Tour C, Amrani L, Cossard R, Neuman KC, Serre MC, Duguet M.

J Biol Chem. 2008 Oct 10;283(41):27395-402. doi: 10.1074/jbc.M800867200. Epub 2008 Jul 8.

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