Regensburg 2010 – scientific programme

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BP: Fachverband Biologische Physik

BP 15: Physics of Cells II

BP 15.5: Talk

Tuesday, March 23, 2010, 15:30–15:45, H43

Does Molecular Crowding affect DNA Hybridization in vivo? — Ingmar Schoen, Hubert Krammer, and •Dieter Braun — Systems Biophysics, Center for Nanoscience, Ludwig Maximilians University, Munich, Germany

Molecules in a cell are subject to significant crowding from their sister molecules. While measurements of anomalous diffusion inside cells point towards a marked effect of molecular crowding, its impact on the rate of reactions is hard to assess.

We have developed a novel technique to image kinetics in living cells using an optical lock-in approach[1]. The reaction time constant is resolved in frequency space with optical resolution under a moderate temperature oscillation and sinusoidal illumination.

DNA hybridization kinetics in living cells is strongly length selective: 16 base pair DNA has a seven-fold faster on-rate as compared to the in vitro situation, whereas 12bp DNA has a five-fold slower on-rate in vivo as compared to in vitro. Evidence points towards a catalytic acceleration for longer DNA and a slowing down by DNA binding proteins.

Above results are not expected from molecular crowding. We assessed molecular crowding with Dextran and Ficoll at high concentrations [20% (w/v)] and find no significant changes in the hybridization kinetics, indicating a minor role of molecular crowding for bi-molecular DNA hybridization.

[1] Schoen, Krammer and Braun, PNAS, in press