title: pH- and salt-dependent molecular combing of DNA: experiments and phenomenological model.
abstract: λ-DNA as well as plasmids can be successfully deposited by molecular combing on hydrophobic surfaces, for pH values ranging from 4 to 10. On polydimethylsiloxane (PDMS) substrates, the deposited DNA molecules are overstretched by about 60-100%. There is a significant influence of sodium ions (NaCl) on the surface density of the deposited DNA, with a maximum near to 100 mM NaCl for a DNA solution (28 ng µl(-1)) at pH 8. The combing process can be described by a micromechanical model including: (i) the adsorption of free moving coiled DNA at the substrate; (ii) the stretching of the coiled DNA by the preceding meniscus; (iii) the relaxation of the deposited DNA to the final length. The sticky ends of λ-DNA cause an adhesion force in the range of about 400 pN which allows a stable overstretching of the DNA by the preceding meniscus. The exposing of hidden hydrophobic bonds of the overstretched DNA leads to a stable deposition on the hydrophobic substrate. The pH-dependent density of deposited DNA as well as the observed influence of sodium ions can be explained by their screening of the negatively charged DNA backbone and sticky ends, respectively. The final DNA length can be derived from a balance of the stored elastic energy of the overstretched molecules and the energy of adhesion.
authors.affiliation: Institut für Werkstoffwissenschaft and Max-Bergmann-Zentrum für Biomaterialien, Technische Universität Dresden, Dresden, Germany. annegret.benke@nano.tu-dresden.de
authors.forename: Annegret
authors.initials: A
authors.lastname: Benke
authors.forename: Michael
authors.initials: M
authors.lastname: Mertig
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Pompe
mesh_terms: D000327:Adsorption; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D004129:Dimethylpolysiloxanes / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D057927:Hydrophobic and Hydrophilic Interactions; D018625:Microscopy, Atomic Force; D008856:Microscopy, Fluorescence; D008958:Models, Molecular; D008967:Molecular Biology / Q000379:methods*; D010957:Plasmids / Q000378:metabolism; D012965:Sodium Chloride / Q000737:chemistry*
chemical_list: D004129:Dimethylpolysiloxanes; D012965:Sodium Chloride; D004247:DNA