Kinetics of TmHU binding to DNA as observed by optical tweezers

Salomo, M.; Keyser, Ulrich F.; Kegler, K.; Gutsche, Christof; Struhalla, Marc; Immisch, Claudia; Hahn, Ulrich; Kremer, Friedrich

doi:10.1002/jemt.20498

Cited by 7 publications

(10 citation statements)

References 21 publications

(21 reference statements)

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“…6). Large rupture events obtained when stretching the TmHU/DNA complex give only indirect indications concerning the existence of such clusters [30]. This is also consistent with the structure observed by AFM measurements at 100 μg/ml (Fig.…”

Section: Discussionsupporting

confidence: 89%

“…In the SMD simulation on DNA with a specific sequence we observe that a one-sided unbinding of DNA and protein causes a lengthening of the end-to-end distance of the DNA of at least 2 nm. With this finding it is possible to assign the experimentally observed disruption events of 2-3 nm from recent experiments [30]. Due to the high forces the unbinding process during the simulation is a combination of an unwinding of the DNA tails and a detaching from the protein.…”

Section: Discussionmentioning

confidence: 70%

“…We observed a shortening of the contour length accompanied by a steep force increase up to ∼30 pN where the reaction was inhibited. Investigating the effects of varying protein concentration yielded information about the kinetics of the reaction [30]. As a further refinement, our set-up is now furnished with a force feedback loop, allowing us to keep the force constant during the experiment.…”

Section: Introductionmentioning

confidence: 99%

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DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations

et al. 2010

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The compaction of DNA by the HU protein from Thermotoga maritima (TmHU) is analysed on a single-molecule level by the usage of an optical tweezers-assisted force clamp. The condensation reaction is investigated at forces between 2 and 40 pN applied to the ends of the DNA as well as in dependence on the TmHU concentration. At 2 and 5 pN, the DNA compaction down to 30% of the initial end-to-end distance takes place in two regimes. Increasing the force changes the progression of the reaction until almost nothing is observed at 40 pN. Based on the results of steered molecular dynamics simulations, the first regime of the length reduction is assigned to a primary level of DNA compaction by TmHU. The second one is supposed to correspond to the formation of higher levels of structural organisation. These findings are supported by results obtained by atomic force microscopy.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 70%

Section: Introductionmentioning

confidence: 99%

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DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations

et al. 2010

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“…Cooperative binding has been implicated as a way that HU may stabilize DNA. In this mode DNA is compacted in a histone-like manner [158-159]. Increases in the concentration of HU with respect to the concentrations of IHF have also been shown to inhibit the binding of the latter, as the cooperative binding mechanism apparently excludes IHF binding [156].…”

Section: Double-stranded Dna Binding Proteinsmentioning

confidence: 99%

Biophysical characterization of DNA binding from single molecule force measurements

Chaurasiya

Paramanathan

McCauley

et al. 2010

Physics of Life Reviews

166

153

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Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.

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“…By using strongly focused laser light a dielectric particle is trapped in a focal point. The unique possibility to hold and manipulate the single particle under study in a suitable medium and to measure the forces acting on it without mechanical contact enables one to carry out exciting novel experiments in micro-rheology and materials research [11,[19][20][21][22][23][24][25][26][27][28][29][30][31]].…”

Section: Introductionmentioning

confidence: 99%

Micro-rheology on (polymer-grafted) colloids using optical tweezers

Gutsche¹,

Elmahdy²,

Kegler³

et al. 2011

J. Phys.: Condens. Matter

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Optical tweezers are experimental tools with extraordinary resolution in positioning (± 1 nm) a micron-sized colloid and in the measurement of forces (± 50 fN) acting on it-without any mechanical contact. This enables one to carry out a multitude of novel experiments in nano- and microfluidics, of which the following will be presented in this review: (i) forces within single pairs of colloids in media of varying concentration and valency of the surrounding ionic solution, (ii) measurements of the electrophoretic mobility of single colloids in different solvents (concentration, valency of the ionic solution and pH), (iii) similar experiments as in (i) with DNA-grafted colloids, (iv) the nonlinear response of single DNA-grafted colloids in shear flow and (v) the drag force on single colloids pulled through a polymer solution. The experiments will be described in detail and their analysis discussed.

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Kinetics of TmHU binding to DNA as observed by optical tweezers

Cited by 7 publications

References 21 publications

DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations

DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations

Biophysical characterization of DNA binding from single molecule force measurements

Micro-rheology on (polymer-grafted) colloids using optical tweezers

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