Adsorption And Interaction Of Polyelectrolyte(DNA) On Surface&Toehold-Mediated DNA Strand Displacement Reactions

Double-stranded DNA (dsDNA) is a kind of highly negatively charged biopolymer. It is also a kind of stiff polyelectrolyte. dsDNA can interact with multivalent cations and other polyelectrolyte with positive charges such as polyethyleneimine (PEI), forming complexes with different charge conditions. In the present work, the interaction between PEI and DNA on silica surface and the adsorption behaviors of DNA/cation complexes with different charge conditions on silica and amino chip surfaces were studied using dual polarization interferometry (DPI). We determined that when PEI is injected over the PEI-DNA complex bilayer, DNA is stripped off under high PEI concentrations. Our results prove that stripping results from the formation of overcharged DNA/PEI complexes and from the strong electrostatic repulsion between the first PEI layer and the overcharged DNA/PEI complex. Therefore, stripping can be avoided under specific salt conditions because of the charge shielding effect.The adsorption of DNA/Ca2+, DNA/Cu2+, and DNA/Co(NH3)63+complexes on amino and silica chip surface were investigated using dual polarization interferometry. A more compact DNA/cation complex layer formed on the amino chip surface compared with the silica chip surface at the same cation condition. The real-time mass, thickness, and density changes were monitored during the adsorption process. The overall results show that the approaching complexes can cause the conformation rearrangement of pre-adsorbed complexes and the adsorbed complexes affect the deposition pattern of the approaching complexes during the adsorption of DNA/Ca2+and DNA/Cu2+complexes on both chip surfaces. The relatively strong electrostatic repulsion between the approaching and adsorbed complexes results in multiple mass loading rate changes and loose attachment of the following complexes. The weak repulsion between the DNA/Co(NH3)63+complexes cannot induce this kind of rearrangement. Thus, no multiple mass loading rate changes were observed. Meanwhile, the adsorbed DNA/Co(NH3)63+can also affect the deposition pattern of the following complexes because of the geometric resistance.The specificity and predictability of Watson-Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. A kind of DNA hybridization chain reaction (HCR) has recently been designed based on toehold-mediated DNA strand-displacement reactions, which has been used as a new signal amplification technique for DNA and other molecules detection. In the fifth chapter, DNA HCR on a solid-liquid interface was investigated using DPI. The effects of salt concentration and different immobilization positions on HCR efficiency and DNA conformation were also investigated using DPI. With the HCR going on, the formed long dsDNA structure lay on the chip surface, which suppressed the activity of the released single-strand part on DNA hairpin.In the last chapter, we present for the first time a new photocontrolled toehold formation method to generate1:1ratio DNA duplexes for toehold-mediated branch migration reactions. This method is based on the photocleavage of2-nitrobenzyl linker-embedded DNA hairpin precursor structures. Different from previously reported overhanging-toehold systems, light is employed to activate the hidden toehold without addition of any chemicals or formation of waste DNA molecules. More importantly, the amount of released toehold can be easily controlled by fine-tuning the irradiation dose, allowing the rate of the toehold-mediated branch migration reaction to be regulated by changing the initial UV irradiation time. Our system shows potential for the construction of light-responsive dynamic DNA nanostructures and DNA circuits.