相关论文: Quantitative transcription factor binding kinetics…

We investigate the sensitivity of production rates (activities) of the regulatory proteins CI (repressor) and Cro at the right operator (O_R}) of bacteriophage lambda. The DNA binding energies of CI, Cro, and RNA polymerase are perturbed to…

Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…

Transcription factors (TFs) interact with a multitude of binding sites on DNA and partner proteins inside cells. We investigate how nonspecific binding/unbinding to such decoy binding sites affects the magnitude and time-scale of random…

Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…

Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain…

Binding of acridine derivative quinacrine (QA) to chicken erythrocyte DNA was studied by methods of absorption and polarized fluorescent spectroscopy. Measurements were carried out in aqueous buffered solutions (pH 6.9) of different dye…

We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (TF's) with the genomic background (i.e., the genome without…

We develop revised theoretical ideas on the mechanism by which the transcription factor proteins locate their specific binding sites on DNA faster than the three-dimensional (3D) diffusion controlled rate limit. We demonstrate that the…

Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence…

Accurate measurements of kinetic rate constants for interacting biomolecules is crucial for understanding the mechanisms underlying intracellular signalling pathways. The magnitude of binding rates plays a very important molecular…

In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA…

An experimental search for variation in the fundamental coupling constants is strongly motivated by modern high-energy physics theories. Comparison of quasar absorption line spectra with laboratory spectra provides a sensitive probe for…

Genome-wide experiments to map the DNA-binding locations of transcription-associated factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of possible direct target genes. Distinguishing functional from…

Although DNA is often bent in vivo, it is unclear how DNA-bending forces modulate DNA-protein binding affinity. Here, we report how a range of DNA-bending forces modulates the binding of the Integration Host Factor (IHF) protein to various…

Recent observations of destructive quantum interference in single-molecule junctions confirm the role played by quantum effects in the electronic conductance properties of molecular systems. We show here that the destructive interference…

The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…

The possible interaction between the dark components of the Universe (dark matter and dark energy) stands as an attractive alternative to the standard $\Lambda$CDM cosmological model. In this work, we present a novel analysis of three…

Single molecule fluorescence tracking provides information at nm-scale and ms-temporal resolution about the dynamics and interaction of individual molecules in a biological environment. While the dynamic behavior of isolated molecules can…

We describe the application of non-negative matrix factorisation to generate compact reconstructions of quasar spectra from the Sloan Digital Sky Survey (SDSS), with particular reference to broad absorption line quasars (BALQSOs). BAL…

We perform a detailed analysis of a theoretically motivated dark energy quintessence model which interacts with the dark matter sector of the universe. Utilising the current observational datasets from the Cosmic Microwave Background,…