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Dulin, D. (author), Arnold, Jamie J. (author), van Laar, T. (author), Oh, Hyung Suk (author), Lee, Cheri (author), Perkins, Angela L. (author), Harki, Daniel A. (author), Depken, S.M. (author), Cameron, Craig E. (author), Dekker, N.H. (author)
RNA viruses pose a threat to public health that is exacerbated by the dearth of antiviral therapeutics. The RNA-dependent RNA polymerase (RdRp) holds promise as a broad-spectrum, therapeutic target because of the conserved nature of the nucleotide-substrate-binding and catalytic sites. Conventional, quantitative, kinetic analysis of antiviral...
journal article 2017
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Kriegel, Franziska (author), Ermann, Niklas (author), Forbes, R.J.G. (author), Dulin, D. (author), Dekker, N.H. (author), Lipfert, J. (author)
The mechanical properties of DNA fundamentally constrain and enable the storage and transmission of genetic information and its use in DNA nanotechnology. Many properties of DNA depend on the ionic environment due to its highly charged backbone. In particular, both theoretical analyses and direct singlemolecule experiments have shown its...
journal article 2017
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Vtyurina, N. (author), Dulin, D. (author), Docter, M.W. (author), Meyer, A.S. (author), Dekker, N.H. (author), Abbondanzieri, E. (author)
In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA binding protein from starved cells) becomes highly up-regulated and can massively...
journal article 2016
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Van Oene, M.M. (author), Dickinson, L.E. (author), Pedaci, F. (author), Köber, M. (author), Dulin, D. (author), Lipfert, J. (author), Dekker, N.H. (author)
Superparamagnetic beads are widely used in biochemistry and single-molecule biophysics, but the nature of the anisotropy that enables the application of torques remains controversial. To quantitatively investigate the torques experienced by superparamagnetic particles, we use a biological motor to rotate beads in a magnetic field and demonstrate...
journal article 2015
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Dulin, D. (author), Vilfan, I.D. (author), Berghuis, B.A. (author), Hage, S. (author), Bamford, D.H. (author), Poranen, M.M. (author), Depken, S.M. (author), Dekker, N.H. (author)
RNA viruses have specific mutation rates that balance the conflicting needs of an evolutionary response to host antiviral defenses and avoidance of the error catastrophe. While most mutations are known to originate in replication errors, difficulties of capturing the underlying dynamics have left the mechanochemical basis of viral mutagenesis...
journal article 2015
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Dulin, D. (author), Berghuis, B.A. (author), Depken, S.M. (author), Dekker, N.H. (author)
Single-molecule experiments provide a unique means for real-time observation of the activity of individual biomolecular machines. Through such techniques, insights into the mechanics of for example, polymerases, helicases, and packaging motors have been gleaned. Here we describe the recent advances in single-molecule force spectroscopy...
journal article 2015
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Berghuis, B.A. (author), Dulin, D. (author), Xu, Zhi Qiang (author), van Laar, T. (author), Cross, B. (author), Janissen, R. (author), Jergic, Slobodan (author), Dixon, Nicholas E. (author), Depken, S.M. (author), Dekker, N.H. (author)
The bidirectional replication of a circular chromosome by many bacteria necessitates proper termination to avoid the head-on collision of the opposing replisomes. In Escherichia coli, replisome progression beyond the termination site is prevented by Tus proteins bound to asymmetric Ter sites. Structural evidence indicates that strand...
journal article 2015
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Janissen, R. (author), Berghuis, B.A. (author), Dulin, D. (author), Wink, M. (author), Van Laar, T. (author), Dekker, N.H. (author)
Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequently, however, the...
journal article 2014
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Dulin, D. (author), Lipfert, J. (author), Moolman, M.C. (author), Dekker, N.H. (author)
To understand genomic processes such as transcription, translation or splicing, we need to be able to study their spatial and temporal organization at the molecular level. Single-molecule approaches provide this opportunity, allowing researchers to monitor molecular conformations, interactions or diffusion quantitatively and in real time in...
journal article 2013
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