Measuring Sequence-Dependent DNA Looping Kinetics
نویسندگان
چکیده
منابع مشابه
DNA looping kinetics analyzed using diffusive hidden Markov model.
Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via an approximately micrometer-length polymer, to infer the behavior of the invisible polymer. Currently, this method is used to measure rate constants of DNA loop formation and breakdown mediated by repressor protein that binds to the DNA. We report a new techni...
متن کاملDNA looping by Ku and the DNA-dependent protein kinase.
The DNA-dependent protein kinase (DNA-PK) is required for DNA double-strand break (DSB) repair and immunoglobulin gene rearrangement and may play a role in the regulation of transcription. The DNA-PK holoenzyme is composed of three polypeptide subunits: the DNA binding Ku70/86 heterodimer and an approximately 460-kDa catalytic subunit (DNA-PKcs). DNA-PK has been hypothesized to assemble at DNA ...
متن کاملDNA looping.
DNA looping is widely used in nature. It is well documented in the regulation of prokaryotic and eukaryotic gene expression, DNA replication, and site-specific DNA recombination. Undoubtedly looping also functions in other protein-DNA transactions such as repair and chromosome segregation. While the underlying physical chemistry of DNA looping is common to all systems, the precise biochemical d...
متن کاملSequence Dependence of Transcription Factor-Mediated DNA Looping: Supplementary Material
S1 Modeling the Looping Probability. 2 S1.1 Tuning the simple titration curve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 S1.2 The case of multiple looped states. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 S1.3 Effect of an “inactive fraction” of repressor. . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 S1.4 Effect of the presence of dimers...
متن کاملSequence dependence of transcription factor-mediated DNA looping
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes and DNA looping in transcriptional regulation in both prokaryotes and eukaryotes. These kinds of regulatory problems are now becoming amenable to systematic quantitati...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2012
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2011.11.1522