Range of Interaction between DNA-Bending Proteins is Controlled by the Second-Longest Correlation Length for Bending Fluctuations

Zhang, Houyin; Marko, John F.

doi:10.1103/physrevlett.109.248301

Cited by 4 publications

(4 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As we increased the Fis concentration up from zero, we observed a gradual compaction (reduction of extension) of the molecule until 20 nM Fis was reached. This is the expected effect for a DNA-bending protein such as Fis; the added bends introduced by the protein binding to the double helix lead to an effective shortening of its persistence length, and therefore a compaction of it against applied force 34; 35; 36; 37 . In this regime, the degree of compaction can be taken as a proxy for protein binding, since the compaction is monotonically increasing with solution protein concentration and therefore binding.…”

Section: Resultsmentioning

confidence: 91%

DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response

Giuntoli

Linzer

Banigan

et al. 2015

Journal of Molecular Biology

Self Cite

View full text Add to dashboard Cite

The rate of dissociation of a DNA-protein complex is often considered to be a property of that complex, without dependence on other nearby molecules in solution. We study the kinetics of dissociation of the abundant E. coli nucleoid protein Fis from DNA, using a single-molecule mechanics assay. The rate of Fis dissociation from DNA is strongly dependent on the solution concentration of DNA. The off-rate (koff) of Fis from DNA shows an initially linear dependence on solution DNA concentration, characterized by an exchange rate of kex ≈ 9×10−4 s−1 (ng/μl)−1 for 100 mM univalent salt buffer, with a very small off-rate at zero DNA concentration. The off-rate saturates at approximately koff,max ≈ 8×10−3 s−1 for DNA concentrations above ≈ 20 ng/μl. This exchange reaction depends mainly on DNA concentration with little dependence on the length of the DNA molecules in solution or on binding affinity, but does increase with increasing salt concentration. We also show data for the yeast HMGB protein NHP6A showing a similar DNA-concentration-dependent dissociation effect, with faster rates suggesting generally weaker DNA binding by NHP6A relative to Fis. Our results are well-described by a model with an intermediate partially-dissociated state where the protein is susceptible to being captured by a second DNA segment, in the manner of “direct transfer” reactions studied for other DNA-binding proteins. This type of dissociation pathway may be important to protein-DNA binding kinetics in vivo where DNA concentrations are large.

show abstract

Section: Resultsmentioning

confidence: 91%

DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response

Giuntoli

Linzer

Banigan

et al. 2015

Journal of Molecular Biology

Self Cite

View full text Add to dashboard Cite

show abstract

“…(10) predicts. This factor of two difference arises due to rotational symmetry around the force axis [63]. This is an example of a situation where one has a local degree of freedom (the occupation number for protein occupation n i ) whose correlation function decays with a correlation length differing from that controlling the free energy ( i.e ., distinct from the correlation length arising from the two largest eigenvalues of the transfer matrix).…”

Section: Dna-protein Interactionsmentioning

confidence: 99%

Biophysics of protein–DNA interactions and chromosome organization

Marko

2015

Physica A: Statistical Mechanics and its Applications

Self Cite

View full text Add to dashboard Cite

The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed.

show abstract

“…So far, most of the previous theoretical studies have been mainly focused on understanding of the effects of stretching force on protein binding to a torsionally relaxed DNA, proposing several different approaches to investigate this question [42,44,[62][63][64][65][66][67][68][69][70][71][72][73]. Among the proposed methods, the transfer-matrix theory developed based on a discretized semi-flexible polymer chain model of DNA has several unique advantages by providing very fast semi-analytical calculations of equilibrium conformations of DNA that allow one to easily incorporate DNA heterogeneity into the computations [42,64,69,74].…”

Section: Introductionmentioning

confidence: 99%

Transfer-matrix calculations of the effects of tension and torque constraints on DNA–protein interactions

Efremov

Yan

2018

Nucleic Acids Research

View full text Add to dashboard Cite

Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. Although the existing experimental techniques allow to exert these type of mechanical constraints on individual DNA biopolymers, their exact effects in regulation of DNA–protein interactions are still not completely understood due to the lack of systematic theoretical methods able to efficiently interpret complex experimental observations. To fill this gap, we have developed a general theoretical framework based on the transfer-matrix calculations that can be used to accurately describe behaviour of DNA–protein interactions under force and torque constraints. Potential applications of the constructed theoretical approach are demonstrated by predicting how these constraints affect the DNA-binding properties of different types of architectural proteins. Obtained results provide important insights into potential physiological functions of mechanical forces in the chromosomal DNA organization by architectural proteins as well as into single-DNA manipulation studies of DNA–protein interactions.

show abstract

Range of Interaction between DNA-Bending Proteins is Controlled by the Second-Longest Correlation Length for Bending Fluctuations

Cited by 4 publications

References 20 publications

DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response

DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response

Biophysics of protein–DNA interactions and chromosome organization

Transfer-matrix calculations of the effects of tension and torque constraints on DNA–protein interactions

Contact Info

Product

Resources

About