We investigate by means of molecular dynamics simulations stretch-induced stepwise translocation of single-stranded DNA (ssDNA) through graphene nanopores. The intrinsic stepwise DNA motion, found to be largely independent of size and shape of the graphene nanopore, is brought about through alternating conformational changes between spontaneous adhesion of DNA bases to the rim of the graphene n...

We have investigated the structure of single-stranded (ss) DNA self-assembled monolayers (SAMs) on gold by combining peak force tapping, Kelvin probe and phase contrast atomic force microscopy (AFM) techniques. The adhesion, surface potential and phase shift signals show heterogeneities in the DNA film structure at two levels: microscale and nanoscale; which cannot be clearly discerned in the t...

Replication protein A (RPA) is a eukaryotic single-stranded DNA (ssDNA) binding protein that plays critical roles in most aspects of genome maintenance, including replication, recombination and repair. RPA binds ssDNA with high affinity, destabilizes DNA secondary structure and facilitates binding of other proteins to ssDNA. However, RPA must be removed from or redistributed along ssDNA during ...

Slow kinetics of homopyrimidine PNA binding to single stranded DNA and RNA targets is manifested in significant hysteresis in thermal UV absorption experiments. We have compared temperatures of dissociation (Tdis) and reassociation (Tass) for triplexes formed by DNA and single or bis PNAs with K50 derived from gel mobility experiments. Results indicated there was no correlation between Tdis and...

On linear single-stranded DNA, RecA filaments assemble and disassemble in the 5' to 3' direction. Monomers (or other units) associate at one end and dissociate from the other. ATP hydrolysis occurs throughout the filament. Dissociation can result when ATP is hydrolyzed by the monomer at the disassembly end. We have developed a comprehensive model for the end-dependent filament disassembly proce...

Escherichia coli single-stranded DNA (ssDNA) binding protein (SSB) is the defining bacterial member of ssDNA binding proteins essential for DNA maintenance. SSB binds ssDNA with a variable footprint of ∼30-70 nucleotides, reflecting partial or full wrapping of ssDNA around a tetramer of SSB. We directly imaged single molecules of SSB-coated ssDNA using total internal reflection fluorescence (TI...

Single-walled carbon nanotubes (SWNTs) were effectively dispersed and functionalized by wrapping with single-stranded DNA (ssDNA). The ssDNA-SWNTs attach strongly on glass substrate and easily form a uniform film, making it possible for electrochemical analysis and sensing. The film was fabricated into a working electrode, which exhibited good electrochemical voltammetric properties, such as fl...

Abstract Thermophilic Argonaute proteins (Agos) have been shown to utilize small DNA guides for cleaving complementary in vitro, which shows great potential nucleic acid detection. In this study, we explored mesophilic Agos the detection of molecule by cooperating with allosteric transcription factors (aTFs). Two from bacteria, Paenibacillus borealis ( Pb Ago) and Brevibacillus laterosporus Bl ...

Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein that serves to protect ssDNA from degradation and annealing, and as a template for recruitment of many downstream factors in virtually all DNA transactions in cell. During many of these transactions, DNA is tethered and is likely subject to force. Previous studies of RPA's binding behavior on ssDN...