The α-hemolysin nanopore has attracted much attention as a tool for the single-molecule analysis of DNA due to its potential an ultra-sensitive, specific, and label-free sensing technique. vast majority research with focused on interrogating single-stranded DNA. Nevertheless, structure pore, specifically circa 32.6 cubic nanometer vestibule, is sufficient size short section double-stranded (dsD...

An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. W...

Both Rad51 and Rad52 are required for homologous genetic recombination in Saccharomyces cerevisiae. Rad51 promotes heteroduplex joint formation, a general step in homologous recombination. Rad52 facilitates the binding of Rad51 to replication protein A (RPA)-coated single-stranded DNA. The requirement of RPA can be avoided in vitro, if the single-stranded DNA is short. Using short single-strand...

The formation and maintenance of single-stranded DNA (ssDNA) are essential parts of many processes involving DNA. For example, strand separation of double-stranded DNA (dsDNA) is catalyzed by helicases, and this exposure of the bases on the DNA allows further processing, such as replication, recombination, or repair. Assays of helicase activity and probes for their mechanism are essential for u...

Various helicases and single stranded DNA (ssDNA) binding proteins unfold G-quadruplex (GQ) structures. However, the underlying mechanisms of this activity have only recently come to focus. We report kinetic studies on Bloom (BLM) helicase and human telomeric GQ interactions using single-molecule Förster resonance energy transfer (smFRET). Using partial duplex DNA (pdDNA) constructs with differ...

Recently, Rogers and Crocker (1) proposed a method to predict the interaction between colloids coated with two kinds of ssDNA, A and B. A key step in ref. 1 was to estimate the average number of DNA bonds, 〈N〉, assuming local chemical equilibrium (LCE) between hybridized and unhybridized sticky end concentrations: hNi 1⁄4 Ð dr CAðrÞCBðrÞ exp1⁄2− βΔG0 ρ0 1⁄4 Ð dr1⁄2CAðrÞ−CABðrÞ 1⁄2CBðrÞ−CABðrÞ e...

We investigate the translocation of a single-stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times of the translocation process is calculated, displaying a triple-, double-, or monopeaked behavior, depending on the interconversion rates between the conformations, the applied electric fi...

A new approach for an internally controlled PCR was developed using a custom-synthesized oligonucleotide as the internal control. Three different PCR setups demonstrated the usefulness of this approach: (i) the addition of the respective internal control to samples containing ssDNA virus Parvo B19; (ii) the co-extraction of plasma samples and the respective internal control for the detection of...