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Items: 1 to 20 of 114

1.

Sequence dependence of transcription factor-mediated DNA looping.

Johnson S, Lindén M, Phillips R.

Nucleic Acids Res. 2012 Sep;40(16):7728-38. doi: 10.1093/nar/gks473.

2.

Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping.

Johnson S, Chen YJ, Phillips R.

PLoS One. 2013 Oct 11;8(10):e75799. doi: 10.1371/journal.pone.0075799.

3.

Concentration and length dependence of DNA looping in transcriptional regulation.

Han L, Garcia HG, Blumberg S, Towles KB, Beausang JF, Nelson PC, Phillips R.

PLoS One. 2009 May 25;4(5):e5621. doi: 10.1371/journal.pone.0005621.

4.

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation.

Boedicker JQ, Garcia HG, Johnson S, Phillips R.

Phys Biol. 2013 Dec;10(6):066005. doi: 10.1088/1478-3975/10/6/066005.

5.

Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping.

Zhang Y, McEwen AE, Crothers DM, Levene SD.

PLoS One. 2006 Dec 27;1:e136.

6.

What controls DNA looping?

Perez PJ, Clauvelin N, Grosner MA, Colasanti AV, Olson WK.

Int J Mol Sci. 2014 Aug 27;15(9):15090-108. doi: 10.3390/ijms150915090.

7.

Statistical-mechanical theory of DNA looping.

Zhang Y, McEwen AE, Crothers DM, Levene SD.

Biophys J. 2006 Mar 15;90(6):1903-12.

8.

FRET studies of a landscape of Lac repressor-mediated DNA loops.

Haeusler AR, Goodson KA, Lillian TD, Wang X, Goyal S, Perkins NC, Kahn JD.

Nucleic Acids Res. 2012 May;40(10):4432-45. doi: 10.1093/nar/gks019.

9.

Quantitative methods for measuring DNA flexibility in vitro and in vivo.

Peters JP, Becker NA, Rueter EM, Bajzer Z, Kahn JD, Maher LJ 3rd.

Methods Enzymol. 2011;488:287-335. doi: 10.1016/B978-0-12-381268-1.00012-4.

10.
11.

Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation.

Swigon D, Coleman BD, Olson WK.

Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9879-84.

12.

Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion.

Vanzi F, Broggio C, Sacconi L, Pavone FS.

Nucleic Acids Res. 2006 Jul 11;34(12):3409-20.

13.

Tetramer opening in LacI-mediated DNA looping.

Rutkauskas D, Zhan H, Matthews KS, Pavone FS, Vanzi F.

Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16627-32. doi: 10.1073/pnas.0904617106.

14.

DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays.

Hirsh AD, Lillian TD, Lionberger TA, Perkins NC.

Biophys J. 2011 Aug 3;101(3):718-26. doi: 10.1016/j.bpj.2011.06.040.

15.

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors.

Priest DG, Cui L, Kumar S, Dunlap DD, Dodd IB, Shearwin KE.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):349-54. doi: 10.1073/pnas.1317817111.

16.

Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.

Mulligan PJ, Chen YJ, Phillips R, Spakowitz AJ.

Biophys J. 2015 Aug 4;109(3):618-29. doi: 10.1016/j.bpj.2015.06.054.

17.

Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells.

Priest DG, Kumar S, Yan Y, Dunlap DD, Dodd IB, Shearwin KE.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):E4449-57. doi: 10.1073/pnas.1410764111.

18.

Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances.

Ringrose L, Chabanis S, Angrand PO, Woodroofe C, Stewart AF.

EMBO J. 1999 Dec 1;18(23):6630-41.

19.

Modulation of DNA loop lifetimes by the free energy of loop formation.

Chen YJ, Johnson S, Mulligan P, Spakowitz AJ, Phillips R.

Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17396-401. doi: 10.1073/pnas.1415685111.

20.

Lac repressor mediated DNA looping: Monte Carlo simulation of constrained DNA molecules complemented with current experimental results.

Biton YY, Kumar S, Dunlap D, Swigon D.

PLoS One. 2014 May 6;9(5):e92475. doi: 10.1371/journal.pone.0092475.

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