• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of biophysjLink to Publisher's site
Biophys J. Apr 1999; 76(4): 1725–1733.
PMCID: PMC1300151

DNA-protein cooperative binding through variable-range elastic coupling.


Cooperativity plays an important role in the action of proteins bound to DNA. A simple mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations, is proposed. These proteins are not in direct physical contact. DNA segments intercalating bound proteins are modeled as a worm-like chain, which is free to deform in two dimensions. The tension-controlled protein-protein interaction is the consequence of two effects produced by the protein binding. The first is the introduction of a bend in the host DNA and the second is the modification of the bending modulus of the DNA in the immediate vicinity of the bound protein. The interaction between two bound proteins may be either attractive or repulsive, depending on their relative orientation on the DNA. Applied tension controls both the strength and the range of protein-protein interactions in this model. Properties of the cooperative interaction are discussed, along with experimental implications.

Full Text

The Full Text of this article is available as a PDF (236K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bednar J, Furrer P, Katritch V, Stasiak AZ, Dubochet J, Stasiak A. Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J Mol Biol. 1995 Dec 8;254(4):579–594. [PubMed]
  • Bensimon A, Simon A, Chiffaudel A, Croquette V, Heslot F, Bensimon D. Alignment and sensitive detection of DNA by a moving interface. Science. 1994 Sep 30;265(5181):2096–2098. [PubMed]
  • Bruinsma R, Goulian M, Pincus P. Self-assembly of membrane junctions. Biophys J. 1994 Aug;67(2):746–750. [PMC free article] [PubMed]
  • Bustamante C, Marko JF, Siggia ED, Smith S. Entropic elasticity of lambda-phage DNA. Science. 1994 Sep 9;265(5178):1599–1600. [PubMed]
  • Cluzel P, Lebrun A, Heller C, Lavery R, Viovy JL, Chatenay D, Caron F. DNA: an extensible molecule. Science. 1996 Feb 9;271(5250):792–794. [PubMed]
  • Hagerman PJ. Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers. 1981 Jul;20(7):1503–1535. [PubMed]
  • Hogan ME, Austin RH. Importance of DNA stiffness in protein-DNA binding specificity. Nature. 1987 Sep 17;329(6136):263–266. [PubMed]
  • Hyre DE, Spicer LD. Thermodynamic evaluation of binding interactions in the methionine repressor system of Escherichia coli using isothermal titration calorimetry. Biochemistry. 1995 Mar 14;34(10):3212–3221. [PubMed]
  • Kam Z, Borochov N, Eisenberg H. Dependence of laser light scattering of DNA on NaCl concentration. Biopolymers. 1981 Dec;20(12):2671–2690. [PubMed]
  • Kim JL, Nikolov DB, Burley SK. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. [PubMed]
  • Bender H, Emrich JG, Eshelman J, Chu MA, Steplewski Z, Biersack HJ, Brady LW. External beam radiation enhances antibody mediated radiocytotoxicity in human glioma cells in vitro. Anticancer Res. 1997 May-Jun;17(3B):1797–1802. [PubMed]
  • Marko JF, Siggia ED. Driving proteins off DNA using applied tension. Biophys J. 1997 Oct;73(4):2173–2178. [PMC free article] [PubMed]
  • Nelson HC. Structure and function of DNA-binding proteins. Curr Opin Genet Dev. 1995 Apr;5(2):180–189. [PubMed]
  • Owen-Hughes T, Workman JL. Experimental analysis of chromatin function in transcription control. Crit Rev Eukaryot Gene Expr. 1994;4(4):403–441. [PubMed]
  • Schleif R. DNA looping. Annu Rev Biochem. 1992;61:199–223. [PubMed]
  • Strick TR, Allemand JF, Bensimon D, Bensimon A, Croquette V. The elasticity of a single supercoiled DNA molecule. Science. 1996 Mar 29;271(5257):1835–1837. [PubMed]
  • Sun LJ, Peterson BR, Verdine GL. Dual role of the nuclear factor of activated T cells insert region in DNA recognition and cooperative contacts to activator protein 1. Proc Natl Acad Sci U S A. 1997 May 13;94(10):4919–4924. [PMC free article] [PubMed]
  • Thoma F, Koller T, Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol. 1979 Nov;83(2 Pt 1):403–427. [PMC free article] [PubMed]
  • Wang JC, Giaever GN. Action at a distance along a DNA. Science. 1988 Apr 15;240(4850):300–304. [PubMed]
  • Werner MH, Gronenborn AM, Clore GM. Intercalation, DNA kinking, and the control of transcription. Science. 1996 Feb 9;271(5250):778–784. [PubMed]
  • Yin H, Wang MD, Svoboda K, Landick R, Block SM, Gelles J. Transcription against an applied force. Science. 1995 Dec 8;270(5242):1653–1657. [PubMed]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Compound
    PubChem Compound links
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...