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Making contacts on a nucleic acid polymer

Making contacts on a nucleic acid polymer,10.1016/S0968-0004(01)01978-8,Trends in Biochemical Sciences,Karsten Rippe

Making contacts on a nucleic acid polymer   (Citations: 62)
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The interaction of proteins bound at distant sites on a nucleic acid chain plays an important role in many molecular biological processes. Contact between the proteins is established by looping of the intervening polymer, which can comprise either double- or single-stranded DNA or RNA, or interphase or metaphase chromatin. The effectiveness of this process, as well as the optimal separation distance, is highly dependent on the flexibility and conformation of the linker. This article reviews how the probability of looping-mediated interactions is calculated for different nucleic acid polymers. In addition, the application of the equations to the analysis of experimental data is illustrated.
Journal: Trends in Biochemical Sciences - TRENDS BIOCHEM SCI , vol. 26, no. 12, pp. 733-740, 2001
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    • ...In both cases the Brownian motion of the protein will be restricted, increasing the local concentration of the protein at target site by an amount given by the J-factor, see review by ...

    Sebastian Bernhardssonet al. Protein Localization with Flexible DNA or RNA

    • ...The dynamics of chromatin has been successfully modeled in yeast [11,24] using a Freely Jointed Chain/ Kratky-Porod worm-like chain model [26]...
    • ...We used the Freely Jointed Chain/Kratky-Porod wormlike chain model [26]...
    • ...For the following analyses, we used a value L = 9.6 nm/kb [26] estimated from a packing ratio of 6 nucleosomes per 11 nm of chromatin in solution at physiological salt concentrations, corresponding to a nucleosome repeat length of about 190 bp, as found in mammalian cell lines...
    • ...The b term in Equation 1 corresponds to the number n of Kuhn’s statistical segments [26], which is directly related to the average spatial distance between the sites 〈R〉 in nm and the length of the statistical segment S as given in Equation 3:...

    Franck Courtet al. Modulated contact frequencies at gene-rich loci support a statistical ...

    • ...For example, charge interactions acting between bound transcription factors (Rippe 2001) will undoubtedly contribute with the depletion attraction to looping...

    Kieran Finanet al. Non-specific (entropic) forces as major determinants of the structure ...

    • ... Analyses of the regulatory regions of the H19 and β-globin gene loci by using 4C and 5...

    Anita Göndöret al. Chromosome crosstalk in three dimensions

    • ...The persistence length P was calculated according to Eq. 3 from the meansquared end-to-end distance using the Kratky-Porod model (see Rippe (39) and references therein):...
    • ...The persistence length P of the chromatin fiber displayed large variations with values between 22 and 390 nm (Tables 1‐3).Thiscorrelateswiththerangeof30‐220nmdetermined experimentally as reviewed by Rippe (39)...

    Nick Kepperet al. Nucleosome Geometry and Internucleosomal Interactions Control the Chro...

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