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Vlijm, R. (author), Smitshuijzen, J.S.J. (author), Lusser, A. (author), Dekker, C. (author)
While many proteins are involved in the assembly and (re)positioning of nucleosomes, the dynamics of protein-assisted nucleosome formation are not well understood. We study NAP1 (nucleosome assembly protein 1) assisted nucleosome formation at the single-molecule level using magnetic tweezers. This method allows to apply a well-defined stretching...
journal article 2012
document
Vlijm, R. (author), Lee, M. (author), Lipfert, J. (author), Lusser, A. (author), Dekker, C. (author), Dekker, N.H. (author)
DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to maintain DNA accessibility in transcription, replication, and repair. Using freely orbiting magnetic tweezers, which measure the twist and length of single DNA molecules, we monitor the real...
journal article 2015
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Vlijm, R. (author), Lee, M. (author), Ordu, O. (author), Boltengagen, A. (author), Lusser, A. (author), Dekker, N.H. (author), Dekker, C. (author)
Eukaryotic nucleosomes consists of an (H3-H4)2 tetramer and two H2A-H2B dimers, around which 147 bp of DNA are wrapped in 1.7 left-handed helical turns. During chromatin assembly, the (H3-H4)2 tetramer binds first, forming a tetrasome that likely constitutes an important intermediate during ongoing transcription. We recently showed that (H3-H4)2...
journal article 2015
document
Vlijm, R. (author), Torre, J. (author), Dekker, C. (author)
The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a...
journal article 2015
document
Kim, S.H. (author), Vlijm, R. (author), van der Torre, J. (author), Dalal, Y. (author), Dekker, C. (author)
Centromere-specific nucleosomes are a central feature of the kinetochore complex during mitosis, in which microtubules exert pulling and pushing forces upon the centromere. CENP-A nucleosomes have been assumed to be structurally unique, thereby providing resilience under tension relative to their H3 canonical counterparts. Here, we directly test...
journal article 2016
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Vlijm, R. (author), Kim, S.H. (author), De Zwart, P. L. (author), Dalal, Y. (author), Dekker, C. (author)
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness...
journal article 2017
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