Atomic force microscopic study of low temperature induced disassembly of RecA-dsDNA filaments.

The assembly and disassembly of RecA-DNA nucleoprotein filaments on double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) are important steps for homologous recombination and DNA repair. The assembly and disassembly of the nucleoprotein filaments are sensitive to the reaction conditions. In this work, we investigated different morphologies of the formed nucleoprotein filaments at low temperature under different solution conditions by atomic force microscopy (AFM). We found that low temperature and long keeping time could induce the incomplete disassembly of the formed nucleoprotein filaments. In addition, when the formed filaments were kept at -20 degrees C for 20 h with 1,4-dithiothreitol (DTT), the integrated filaments disassembled. It was similar to the case under the same condition without anything added. However, when glycerol was used as a substitute for DTT, there was no obvious disassembly at the same condition. Oppositely, when the formed filaments were kept at 4 degrees C for 20 h, the disassembly with additional DTT was not as obvious as the case at -20 degrees C for 20 h, whereas the case with additional glycerol disassembled. The experiments indicated the effect of cold denaturation on the interaction of DNA and RecA. Meanwhile, the study of these phenomena can supply guidelines for the property and stability of RecA as well as the relevant roles of influencing factors to RecA and DNA in further theoretical studies.

Self-assembly of lambda-DNA networks/Ag nanoparticles: hybrid architecture and active-SERS substrate.

In this article, highly rough and stable surface enhanced Raman scattering (SERS)-active substrates had been fabricated by a facile layer-by-layer technique. Unique lambda-DNA networks and CTAB capped silver nanoparticles (AgNP) were alternatively self-assembled on the charged mica surface until a desirable number of bilayers were reached. The as-prepared hybrid architectures were characterized by UV-vis spectroscopy, tapping mode atomic force microscopy (AFM) and confocal Raman microscopy, respectively. Linear increases of the maximum absorbance of DNA band with the number of bilayers present a common LBL assembly feature. The red-shift of surface plasmon of silver nanoparticles within the hybrid films was mainly due to the aggregation effect. With the increase of number of bilayers, the surface coverage of nanoparticles on the substrate became larger, as well as the rising of total amount of nanoparticles and the surface roughness of hybrid films. These rough metallic hybrid architectures could be utilized as SERS-active substrates. A significant enhanced Raman scattering effect of the adsorbed analytes, e.g., methylene blue (MB), on these hybrid films was easily exploited by the confocal Raman microscopy. The enhancement factor depended on the surface coverage of nanoparticles and number of bilayers of lambda-DNA/AgNP.

Effects of bridge ions, DNA species, and developing temperature on flat-lying DNA monolayers.

Recently, we have successfully constructed flat-lying DNA monolayers on a mica surface (J. Phys. Chem. B 2006, 110, 10792-10798). In this work, the effects of various factors including bridge ions, DNA species, and developing temperature on the configuration of DNA monolayers have been investigated by atomic force microscopy (AFM) in detail. AFM results show that the species of bridge ions and developing temperature play a crucial role during the formation process. For example, the divalent cation Zn2+ resulted in many DNA chains stuck side by side in the monolayers due to the strong interactions between it and DNA's bases or the mica surface. Most DNA chain's conglutinations disappeared when the developing temperature was higher than 40 degrees C. Cd2+ and Ca2+ produced more compact DNA monolayers with some obvious aggregations, especially for the DNA monolayers constructed by using Ca2+ as the bridge ion. Co2+ produced well-ordered, flat-lying DNA monolayers similar to that of Mg2+. Furthermore, it was found that the flat-lying DNA monolayers could still form on a mica surface when plasmid DNA pBR 322 and linear DNA pBR 322/Pst I were used as the DNA source. Whereas, it was hard to form DNA monolayers on a (3-aminopropyl)triethoxysilane-mica surface because the strong interactions between DNA and substrate prevented the lateral movement of DNA molecules. These results suggested that the appropriate interactions between divalent cations and DNA or mica surface were important for the formation of flat-lying DNA monolayers. The obtained information is a necessary supplement to our previous studies on the formation kinetics of such monolayers and may be useful for practical application of the monolayers and further theoretical studies.