title: Using dual-polarization interferometry to study surface-initiated DNA hybridization chain reactions in real time.
abstract: In this study we used dual-polarization interferometry to investigate DNA hybridization chain reactions (HCRs) at solid-liquid interfaces. We monitored the effects of variations in mass, thickness, and density of the immobilized initiator on the subsequent HCRs at various salt concentrations. At low salt concentrations, the single-stranded DNA (ssDNA) initiator was attached uniformly to the chip surface. At high salt concentrations, it lay on the surface at the onset of the immobilization process, but the approaching ssDNA forced the pre-immobilized ssDNA strands to extend into solution as a result of increased electrostatic repulsion between the pre-adsorbed and approaching ssDNA chains. Injection of a mixture of H1 and H2 increased the mass and thickness of the films initially, but thereafter the thickness decreased. These changes indicate that the long double-stranded DNA that formed lay on the surface, rather than extended into the solution, thereby suppressing the subsequent initiation activity of the released single-strand parts of H1 and H2. Increasing the salt concentration increased the HCR efficiency and reaction rate. The HCR efficiency of the initiator ssDNA immobilized on its 5' end was higher than that immobilized on its 3' end, suggesting that the released single-strand parts of H1 and H2 close to the chip surface decreased the initiation activity relative to those of the ones extending into solution.
authors.affiliation: CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, PR China.
authors.forename: Fujian
authors.initials: F
authors.lastname: Huang
authors.forename: Pingping
authors.initials: P
authors.lastname: Xu
authors.forename: Haojun
authors.initials: H
authors.lastname: Liang
mesh_terms: D015374:Biosensing Techniques / Q000379:methods; D004277:DNA, Single-Stranded / Q000032:analysis*; D007368:Interferometry / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D012492:Salts / Q000737:chemistry
chemical_list: D004277:DNA, Single-Stranded; D012492:Salts
keywords: DNA hybridization chain reaction; Dual-polarization interferometry; HCR efficiency; Immobilization position; Salt condition; Solid–liquid interface