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The physics of protein-DNA interaction networks in the control of gene expression.
J Phys Condens Matter. 2012 May 16;24(19):193102. doi: 10.1088/0953-8984/24/19/193102. Epub 2012 Apr 19.
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Effect of DNA looping on the induction kinetics of the lac operon.
J Theor Biol. 2007 Aug 21;247(4):695-712. doi: 10.1016/j.jtbi.2007.03.030. Epub 2007 Mar 28.
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DNA looping and physical constraints on transcription regulation.
J Mol Biol. 2003 Aug 29;331(5):981-9. doi: 10.1016/s0022-2836(03)00764-2.
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Bacterial repression loops require enhanced DNA flexibility.
J Mol Biol. 2005 Jun 17;349(4):716-30. doi: 10.1016/j.jmb.2005.04.035.
9
Hinge-helix formation and DNA bending in various lac repressor-operator complexes.
EMBO J. 1999 Nov 15;18(22):6472-80. doi: 10.1093/emboj/18.22.6472.
10
Origin of the asymmetrical contact between lac repressor and lac operator DNA.
J Mol Biol. 1993 Oct 5;233(3):389-99. doi: 10.1006/jmbi.1993.1519.

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Designed architectural proteins that tune DNA looping in bacteria.
Nucleic Acids Res. 2021 Oct 11;49(18):10382-10396. doi: 10.1093/nar/gkab759.
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Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression.
Annu Rev Biophys. 2019 May 6;48:121-163. doi: 10.1146/annurev-biophys-052118-115525.
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Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects.
Biophys Rev. 2016 Sep;8(3):197-207. doi: 10.1007/s12551-016-0204-z. Epub 2016 Jun 10.
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Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects.
Biophys Rev. 2016 Nov;8(Suppl 1):123-133. doi: 10.1007/s12551-016-0239-1. Epub 2016 Nov 14.
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Supercoiling Effects on Short-Range DNA Looping in E. coli.
PLoS One. 2016 Oct 26;11(10):e0165306. doi: 10.1371/journal.pone.0165306. eCollection 2016.
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Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system.
BMC Syst Biol. 2016 Jun 30;10(1):43. doi: 10.1186/s12918-016-0290-3.
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Scaling of gene expression with transcription-factor fugacity.
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Comparison of the theoretical and real-world evolutionary potential of a genetic circuit.
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本文引用的文献

1
Bacterial repression loops require enhanced DNA flexibility.
J Mol Biol. 2005 Jun 17;349(4):716-30. doi: 10.1016/j.jmb.2005.04.035.
2
Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation.
Proc Natl Acad Sci U S A. 2005 May 10;102(19):6783-8. doi: 10.1073/pnas.0409387102. Epub 2005 Apr 29.
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Transcriptional regulation by the numbers: applications.
Curr Opin Genet Dev. 2005 Apr;15(2):125-35. doi: 10.1016/j.gde.2005.02.006.
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Transcriptional regulation by the numbers: models.
Curr Opin Genet Dev. 2005 Apr;15(2):116-24. doi: 10.1016/j.gde.2005.02.007.
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Implications of the dependence of the elastic properties of DNA on nucleotide sequence.
Philos Trans A Math Phys Eng Sci. 2004 Jul 15;362(1820):1403-22. doi: 10.1098/rsta.2004.1380.
7
DNA looping and physical constraints on transcription regulation.
J Mol Biol. 2003 Aug 29;331(5):981-9. doi: 10.1016/s0022-2836(03)00764-2.
8
The structure of DNA in the nucleosome core.
Nature. 2003 May 8;423(6936):145-50. doi: 10.1038/nature01595.

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