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Berghuis, B.A. (author), Raducanu, Vlad-Stefan (author), Elshenawy, Mohamed M. (author), Jergic, Slobodan (author), Depken, S.M. (author), Dixon, NE (author), Hamdan, Samir M. (author), Dekker, N.H. (author)
Synchronizing the convergence of the two-oppositely moving DNA replication machineries at specific termination sites is a tightly coordinated process in bacteria. In Escherichia coli, a “replication fork trap” – found within a chromosomal region where forks are allowed to enter but not leave – is set by the protein–DNA roadblock Tus–Ter. The...
journal article 2017
document
Berghuis, B.A. (author), Köber, M. (author), van Laar, T. (author), Dekker, N.H. (author)
Recent advances in high-throughput single-molecule magnetic tweezers have paved the way for obtaining information on individual molecules as well as ensemble-averaged behavior in a single assay. Here we describe how to design robust high-throughput magnetic tweezers assays that specifically require application of high forces (>20. pN) for...
journal article 2016
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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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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
document
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
document
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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