Dancing on DNA: Kinetic Aspects of Search Processes on DNA

Tafvizi, Anahita; Mirny, Leonid A.; Oijen, Antoine M. van

doi:10.1002/cphc.201100112

Cited by 126 publications

(145 citation statements)

References 75 publications

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“…2C). One-dimensional diffusion of proteins on both ssDNA and dsDNA is now a well-documented phenomenon, [23][24][25][26][27][28][29][30][31] and we have previously observed 1D diffusion of human Rad51 along dsDNA, 32 supporting the notion that Rad51/RecA monomers within the presynaptic complex might also be capable of sliding at least short distances along ssDNA. The ability of Rad51/RecA to slide just §1-nucleotide would ensure optimal alignment of DNA triplet sequences during the early stages of homology recognition and strand exchange.…”

Section: The Problem Of Protein Registersupporting

confidence: 72%

On the influence of protein-DNA register during homologous recombination

Greene

2016

Cell Cycle

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Homologous recombination enables the exchange of genetic information between related DNA molecules and is a driving force in evolution. Using single-molecule optical microscopy we have recently shown that members of the Rad51/RecA family of recombinases stabilize paired homologous strand of DNA in precise 3-nt increments. Here we discuss an interesting conceptual implication of these results, which is that the recombinases may actively sense and reorganize their alignment register relative to the bound DNA sequences to ensure optimal base triplet pairing interactions during the early stages of recombination.

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Section: The Problem Of Protein Registersupporting

confidence: 72%

On the influence of protein-DNA register during homologous recombination

Greene

2016

Cell Cycle

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“…Taken together, these results exclude FD over distances in the range from ∼10 bp to 3 kbp as a significant pathway for σ 54 RNAP to reach the promoter under the ionic conditions studied here, which are intended to mimic the conditions in live bacteria. They also exclude other mechanisms that use the flanking DNA in this length range (40).…”

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confidence: 99%

RNA polymerase approaches its promoter without long-range sliding along DNA

Friedman

Mumm

Gelles

2013

Proc. Natl. Acad. Sci. U.S.A.

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Sequence-specific DNA binding proteins must quickly bind target sequences, despite the enormously larger amount of nontarget DNA present in cells. RNA polymerases (or associated general transcription factors) are hypothesized to reach promoter sequences by facilitated diffusion (FD). In FD, a protein first binds to nontarget DNA and then reaches the target by a 1D sliding search. We tested whether Escherichia coli σ 54 RNA polymerase reaches a promoter by FD using the colocalization single-molecule spectroscopy (CoSMoS) multiwavelength fluorescence microscopy technique. Experiments directly compared the rates of initial polymerase binding to and dissociation from promoter and nonpromoter DNAs measured in the same sample under identical conditions. Binding to a nonpromoter DNA was much slower than binding to a promoter-containing DNA of the same length, indicating that the detected nonspecific binding events are not on the pathway to promoter binding. Truncating one of the DNA segments flanking the promoter to a length as short as 7 bp or lengthening it to ∼3,000 bp did not alter the promoter-specific binding rate. These results exclude FD over distances corresponding to the length of the promoter or longer from playing any significant role in accelerating promoter search. Instead, the data support a direct binding mechanism, in which σ 54 RNA polymerase reaches the local vicinity of promoters by 3D diffusion through solution, and suggest that binding may be accelerated by atypical structural or dynamic features of promoter DNA. Direct binding explains how polymerase can quickly reach a promoter, despite occupancy of promoter-flanking DNA by bound proteins that would impede FD.1D diffusion | total internal reflection fluorescence | transcription initiation T he binding of a multisubunit RNA polymerase (RNAP) or general transcription factors to a specialized transcription promoter DNA sequence is an essential step in initiating DNA transcription in all organisms (1, 2). Control of this promoter binding step is a key mechanism by which gene expression is regulated (3). To understand how this regulation occurs, it is necessary to understand the process by which the transcription machinery efficiently finds and binds to target sequences embedded in chromosomal DNA, where targets are outnumbered by orders of magnitude excess nontarget DNA.Bacterial transcription is a convenient model system for studying promoter search, because the process can be efficiently reconstituted in vitro from purified components and bacterial RNAP holoenzymes recognize and bind directly to specific promoter DNA sequence motifs (4, 5). For the well-studied Escherichia coli RNAP, the rate at which the enzyme finds its cognate promoters can approach or even possibly exceed limits calculated for simple 3D diffusion of the protein up to the target sequence followed by direct promoter binding (6-8). Although there are uncertainties in calculating the magnitude of this limit because of uncertain contributions from orientation constraints and electr...

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“…The parameters in the model that are most difficult to measure and for which there exists the least data to support are k 1 and k 2 . Indeed, the estimation of k 1 , k 2 values has relied on theoretical models [Tafvizi et al, 2011]. Another parameter for which their exists much uncertainty is the diffusion coefficient, D. Experimentalists have found the diffusion coefficient of soluble proteins in aqueous buffers to be in the range 6 × 10 −12 m 2 min −1 to 6 × 10 −11 m 2 min −1 [Matsuda et al, 2008, Seksek et al, 1997 but this value may depend on factors such as the size of the protein and the cell type.…”

Section: Parameter Valuesmentioning

confidence: 99%

Mean field analysis of a spatial stochastic model of a gene regulatory network

et al. 2014

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A gene regulatory network may be defined as a collection of DNA segments which interact with each other indirectly through their RNA and protein products. Such a network is said to contain a negative feedback loop if its products inhibit gene transcription, and a positive feedback loop if a gene product promotes its own production. Negative feedback loops can create oscillations in mRNA and protein levels while positive feedback loops are primarily responsible for signal amplification. It is often the case in real biological systems that both negative and positive feedback loops operate in parameter regimes that result in low copy numbers of gene products.In this paper we investigate the spatio-temporal dynamics of a single feedback loop in a eukaryotic cell. We first develop a simplified spatial stochastic model of a canonical feedback system (either positive or negative). Using a Gillespie's algorithm, we compute sample trajectories and analyse their corresponding statistics. We then derive a system of equations that describe the spatio-temporal evolution of the stochastic means. Subsequently, we examine the spatially homogeneous case and compare the results of numerical simulations with the spatially explicit case. Finally, using a combination of steady-state analysis and data clustering techniques, we explore model behaviour across a subregion of the parameter space that is difficult to access experimentally and compare the parameter landscape of our spatio-temporal and spatially-homogeneous models.

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Dancing on DNA: Kinetic Aspects of Search Processes on DNA

Cited by 126 publications

References 75 publications

On the influence of protein-DNA register during homologous recombination

On the influence of protein-DNA register during homologous recombination

RNA polymerase approaches its promoter without long-range sliding along DNA

Mean field analysis of a spatial stochastic model of a gene regulatory network

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