Polymer-monovalent salt-induced DNA compaction studied via single-molecule microfluidic trapping

Abstract

Polymer-monovalent salt-induced single-molecule DNA compaction/condensation in a microfluidic stagnation point flow was studied by analyzing both DNA compaction images and time trajectories. For the whole DNA compaction process we observed three successive steps: Step I, a relaxation process of the stretched DNA that occurs slowly along the whole DNA chain, Step II, nucleus formation and growth, and Step III, corresponding to a rapid compaction of the chain. A memory effect was observed between Steps I and III, and a new (intruder-induced) nucleation mode was observed for the first time. This study extends the use of the microfluidic stagnation point flow, which we have previously used for sequence detection and to measure enzyme kinetics site-specifically.

Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis, and DNA Stretching

“…683 It remains to be seen whether restriction mapping in a cross-slot is a viable method for routine use. For the moment, its main advantages lie in studying the kinetics of an enzymatic reaction 683 or DNA compaction 684 rather than as a high-throughput sizing method.…”

Microfluidic systems for single DNA dynamics

“…Manual control over the stagnation point was used to observe polymer hysteresis, 53 to stretch molecules for DNA sequence detection, 55 and to characterize salt-induced compaction of DNA from a stretched state. 56 For DNA sequence detection, a fluorescently-labelled restriction endonuclease was bound to one of five target sites along λ-DNA, and the positions of the target binding sites were determined to within 1.5 kilobases. 55 Salt-induced compaction was studied by directing two different solutions with variable salt concentrations in the opposing inlet streams.…”

Stretching self-entangled DNA molecules in elongational fields

“…Experiments on single DNA molecules have a rich history in addressing a number of fundamental questions in polymer physics. 25 These devices have also been used to study the transient dynamics of polymer molecules in well-controlled elongational ows/elds, and experiments have revealed surprising congurational diversity 26,27 and hysteresis in the coil-stretch transition. 7 A wide range of microuidic devices have been designed to actively manipulate DNA molecules with hydrodynamic ows or electric elds for analysis 8,9 such as t-junctions, 10 cross-slots, [11][12][13] posts, [14][15][16] contractions, [17][18][19] and nano-scale slits 20,21 and channels.…”