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Williams G. A personal appreciation of the career, thus far, of Professor Friedrich Kremer. Colloid Polym Sci 2014. [DOI: 10.1007/s00396-014-3239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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2
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Ueberschär O, Wagner C, Stangner T, Kühne K, Gutsche C, Kremer F. Drag reduction by DNA-grafting for single microspheres in a dilute λ-DNA solution. POLYMER 2011. [DOI: 10.1016/j.polymer.2011.06.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Gutsche C, Elmahdy MM, Kegler K, Semenov I, Stangner T, Otto O, Ueberschär O, Keyser UF, Krueger M, Rauscher M, Weeber R, Harting J, Kim YW, Lobaskin V, Netz RR, Kremer F. Micro-rheology on (polymer-grafted) colloids using optical tweezers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:184114. [PMID: 21508470 DOI: 10.1088/0953-8984/23/18/184114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
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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Affiliation(s)
- C Gutsche
- Institute of Experimental Physics I, Leipzig University, Linnéstrasse 5, D-04103, Leipzig, Germany
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The effective hydrodynamic radius of single DNA-grafted colloids as measured by fast Brownian motion analysis. POLYMER 2011. [DOI: 10.1016/j.polymer.2011.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Liebesny P, Goyal S, Dunlap D, Family F, Finzi L. Determination of the number of proteins bound non-specifically to DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:414104. [PMID: 21386587 PMCID: PMC3653182 DOI: 10.1088/0953-8984/22/41/414104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We have determined the change in the number of proteins bound non-specifically to DNA as a function of applied force using force-extension measurements on tethered DNA. Using magnetic tweezers, single molecules of λ DNA were repeatedly stretched and relaxed in the absence and presence of 170 nM λ repressor protein (CI). CI binds to six specific sites of λ DNA with nanomolar affinity and also binds non-specifically with micromolar affinity. The force versus extension data were analyzed using a recently developed theoretical framework for quantitative determination of protein binding to the DNA. The results indicate that the non-specific binding of CI changes the force-extension relation significantly in comparison to that of naked DNA. The DNA tether used in our experiment would have about 640 bound repressors, if it was completely saturated with bound proteins. We find that as the pulling force on DNA is reduced from 4.81 to 0.13 pN, approximately 138 proteins bind to DNA, which is about 22% of the length of the tethered DNA. Our results show that 0.13 pN is not low enough to cause saturation of DNA by repressor and 4.81 pN is also not high enough to eliminate all the repressors bound to DNA. This demonstrates that the force-extension relation provides an effective approach for estimating the number of proteins bound non-specifically to a DNA molecule.
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Affiliation(s)
- Paul Liebesny
- Department of Physics, Emory University, Atlanta, GA 30322, USA
| | - Sachin Goyal
- Department of Physics, Emory University, Atlanta, GA 30322, USA
| | - David Dunlap
- Department of Cell Biology, Emory University, 615 Michael Street, Atlanta, GA 30322, USA
| | | | - Laura Finzi
- Department of Physics, Emory University, Atlanta, GA 30322, USA
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Wagner C, Olbrich C, Brutzer H, Salomo M, Kleinekathöfer U, Keyser UF, Kremer F. DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations. J Biol Phys 2010; 37:117-31. [PMID: 22210966 DOI: 10.1007/s10867-010-9203-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 09/20/2010] [Indexed: 11/24/2022] Open
Abstract
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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Chaurasiya KR, Paramanathan T, McCauley MJ, Williams MC. Biophysical characterization of DNA binding from single molecule force measurements. Phys Life Rev 2010; 7:299-341. [PMID: 20576476 DOI: 10.1016/j.plrev.2010.06.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 11/25/2022]
Abstract
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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Affiliation(s)
- Kathy R Chaurasiya
- Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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Elmahdy MM, Synytska A, Drechsler A, Gutsche C, Uhlmann P, Stamm M, Kremer F. Forces of Interaction between Poly(2-vinylpyridine) Brushes As Measured by Optical Tweezers. Macromolecules 2009. [DOI: 10.1021/ma901567d] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mahdy M. Elmahdy
- Institute of Experimental Physics I, Leipzig University, Linnéstrasse 5, 04103 Leipzig, Germany
- Department of Physics, Mansoura University, Mansoura 35516, Egypt
| | - Alla Synytska
- Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany
| | - Astrid Drechsler
- Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany
| | - Christof Gutsche
- Institute of Experimental Physics I, Leipzig University, Linnéstrasse 5, 04103 Leipzig, Germany
| | - Petra Uhlmann
- Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany
| | - Manfred Stamm
- Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany
| | - Friedrich Kremer
- Institute of Experimental Physics I, Leipzig University, Linnéstrasse 5, 04103 Leipzig, Germany
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Sensing DNA-coatings of microparticles using micropipettes. Biosens Bioelectron 2009; 24:2423-7. [DOI: 10.1016/j.bios.2008.12.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 12/11/2008] [Accepted: 12/12/2008] [Indexed: 11/22/2022]
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Dominguez-Espinosa G, Synytska A, Drechsler A, Gutsche C, Kegler K, Uhlmann P, Stamm M, Kremer F. Optical tweezers to measure the interaction between poly(acrylic acid) brushes. POLYMER 2008. [DOI: 10.1016/j.polymer.2008.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Rappaport SM, Rabin Y. Model of DNA bending by cooperative binding of proteins. PHYSICAL REVIEW LETTERS 2008; 101:038101. [PMID: 18764298 DOI: 10.1103/physrevlett.101.038101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Indexed: 05/26/2023]
Abstract
We present a model of nonspecific cooperative binding of proteins to DNA in which the binding of isolated proteins generates local bends but binding of proteins at neighboring sites on DNA straightens the polymer. We solve the statistical mechanical problem and calculate the effective persistence length, site occupancy, and cooperativity. Cooperativity leads to nonmonotonic variation of the persistence length with protein concentration, and to an unusual shape of the binding isotherm. The results are in qualitative agreement with recent single molecule experiments on nucleoid protein HU-DNA complexes.
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Affiliation(s)
- S M Rappaport
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
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Mukherjee A, Sokunbi AO, Grove A. DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Nucleic Acids Res 2008; 36:3956-68. [PMID: 18515342 PMCID: PMC2475624 DOI: 10.1093/nar/gkn348] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In mesophilic prokaryotes, the DNA-binding protein HU participates in nucleoid organization as well as in regulation of DNA-dependent processes. Little is known about nucleoid organization in thermophilic eubacteria. We show here that HU from the hyperthermophilic eubacterium Thermotoga maritima HU bends DNA and constrains negative DNA supercoils in the presence of topoisomerase I. However, while binding to a single site occludes approximately 35 bp, association of T. maritima HU with DNA of sufficient length to accommodate multiple protomers results in an apparent shorter occluded site size. Such complexes consist of ordered arrays of protomers, as revealed by the periodicity of DNase I cleavage. Association of TmHU with plasmid DNA yields a complex that is remarkably resistant to DNase I-mediated degradation. TmHU is the only member of this protein family capable of occluding a 35 bp nonspecific site in duplex DNA; we propose that this property allows TmHU to form exceedingly stable associations in which DNA flanking the kinks is sandwiched between adjacent proteins. We suggest that T. maritima HU serves an architectural function when associating with a single 35 bp site, but generates a very stable and compact aggregate at higher protein concentrations that organizes and protects the genomic DNA.
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Affiliation(s)
- Anirban Mukherjee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Salomo M, Keyser UF, Struhalla M, Kremer F. Optical tweezers to study single Protein A/Immunoglobulin G interactions at varying conditions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:927-34. [DOI: 10.1007/s00249-008-0310-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 03/05/2008] [Accepted: 03/10/2008] [Indexed: 10/22/2022]
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McCauley MJ, Zimmerman J, Maher LJ, Williams MC. HMGB binding to DNA: single and double box motifs. J Mol Biol 2007; 374:993-1004. [PMID: 17964600 DOI: 10.1016/j.jmb.2007.09.073] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 09/17/2007] [Accepted: 09/22/2007] [Indexed: 11/30/2022]
Abstract
High mobility group (HMG) proteins are nuclear proteins believed to significantly affect DNA interactions by altering nucleic acid flexibility. Group B (HMGB) proteins contain HMG box domains known to bind to the DNA minor groove without sequence specificity, slightly intercalating base pairs and inducing a strong bend in the DNA helical axis. A dual-beam optical tweezers system is used to extend double-stranded DNA (dsDNA) in the absence as well as presence of a single box derivative of human HMGB2 [HMGB2(box A)] and a double box derivative of rat HMGB1 [HMGB1(box A+box B)]. The single box domain is observed to reduce the persistence length of the double helix, generating sharp DNA bends with an average bending angle of 99+/-9 degrees and, at very high concentrations, stabilizing dsDNA against denaturation. The double box protein contains two consecutive HMG box domains joined by a flexible tether. This protein also reduces the DNA persistence length, induces an average bending angle of 77+/-7 degrees , and stabilizes dsDNA at significantly lower concentrations. These results suggest that single and double box proteins increase DNA flexibility and stability, albeit both effects are achieved at much lower protein concentrations for the double box. In addition, at low concentrations, the single box protein can alter DNA flexibility without stabilizing dsDNA, whereas stabilization at higher concentrations is likely achieved through a cooperative binding mode.
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Affiliation(s)
- Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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Kegler K, Salomo M, Kremer F. Forces of interaction between DNA-grafted colloids: an optical tweezer measurement. PHYSICAL REVIEW LETTERS 2007; 98:058304. [PMID: 17358911 DOI: 10.1103/physrevlett.98.058304] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Indexed: 05/14/2023]
Abstract
Optical tweezers are employed to measure the forces of interaction between single DNA-grafted colloids. Parameters to be varied are the length of the DNA, the grafting density, and the ion concentration of the surrounding medium. From the measured force-separation dependence an interaction length at a given force is deduced. It shows in the mushroom regime a scaling with the grafting density which levels off for brushes. For the latter the transition from an osmotic to a salted brush can be traced in detail by varying the ion concentration in accordance with mean field theories.
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Affiliation(s)
- K Kegler
- University of Leipzig, Institute of Experimental Physics I, Linnéstrasse 5, D-04103 Leipzig, Germany
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Salomo M, Keyser UF, Kegler K, Gutsche C, Struhalla M, Immisch C, Hahn U, Kremer F. Kinetics of TmHU binding to DNA as observed by optical tweezers. Microsc Res Tech 2007; 70:938-43. [PMID: 17661366 DOI: 10.1002/jemt.20498] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The kinetics of binding for the histone-like protein TmHU (from Thermotoga maritima) to DNA is analyzed on a single molecule level by use of optical tweezers. For the reaction rate a pronounced concentration-dependence is found with an "all or nothing"-limit which suggests the cooperative nature of the binding-reaction. By analyzing the statistics of mechanically induced dissociation-events of TmHU from DNA multiple reaction sites are observed to become more likely with increasing TmHU concentration. This is interpreted as a hint for a secondary organizational level of the TmHU/DNA complex. The reaction rate of TmHU binding to DNA is remarkably higher than that of the HU protein from Escherichia coli which will be discussed.
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Affiliation(s)
- Mathias Salomo
- Faculty of Experimental Physics 1, University of Leipzig, Linnèstrasse 5, D-04103 Leipzig, Germany.
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