Methods of stretching DNA molecules using flow fields.
Using fluorescence microscopy, we compare the degree of adsorption and stretching of DNA onto surfaces achieved by published stretching methods that use fluid flow: molecular combing, spin-stretching, and air-blowing. Molecular combing uses a receding meniscus to stretch out and deposit the DNA onto a hydrophobic surface. In spin-stretching, we find that the effect of radial hydrodynamic flow created by the centrifugal force of the rotating disk is minimal and that the DNA is stretched out on a hydrophobic substrate by the moving meniscus. In air-blowing, a jet of gas pushes liquid across a substrate, depositing stretched DNA molecules along the way. In our study, DNA molecules either combed or spin-stretched onto hydrophobic surfaces stretch to a greater degree than those that are air-blown; fewer are deposited at pH 8.0 than at lower pH, apparently because at pH 8.0 DNA adhesion occurs primarily only at the DNA extremities and so avoids trapped regions of incompletely stretched DNA, with the side effect that more molecules avoid adhesion altogether. We find by high-speed video microscopy that there is complex droplet deformation and motion during air-blowing, which complicates the deposition and stretching process, leading to radial alignment. Our results are a first step toward understanding and optimizing the various proposed methods of DNA stretching and anchoring onto surfaces, which is important in studying their interactions with proteins.
Kim
Ji Hoon
JH
Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, USA.
Shi
Wei-Xian
WX
Larson
Ronald G
RG
D000327:Adsorption; D000388:Air; D001703:Biophysics / Q000379:methods; D002448:Cell Adhesion; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D007091:Image Processing, Computer-Assisted; D008856:Microscopy, Fluorescence / Q000379:methods; D018715:Microscopy, Video; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000737:chemistry; D013499:Surface Properties
D011506:Proteins; D004247:DNA