The development of novel DNA sequencing methods is one of the ongoing challenges in various fields of research seeking to address the demand for sequence information. However, many of these techniques rely on some kind of labeling or amplification steps. Here we investigate the intrinsic properties of tip-enhanced Raman scattering (TERS) towards the development of a novel, label-free, direct se...

Center for Environmental Health Sciences and Division of Toxicology, Whitaker College of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 The efficacy of PCR is measured by its specificity, efficiency (i.e. yield), and fidelity. A highly specific PCR will generate one and only one amplification product that is the intended target sequence. Mo...

Dissociation of disulfide is normally mandatory prior to disulfide peptide sequencing via electrospray ionization collision induced dissociation mass spectrometry (ESI-CID-MS). Herein, a facile method for directly sequencing intact disulfide peptides was proposed. The basic principles involved were electrolyte-enhanced corona discharge in ESI and the following oxidative cleavage reaction.

OBJECTIVES HIV drug resistance is a major concern as the emergence of resistant strains of virus results in failure of first-line therapies with an associated increase in the cost of subsequent regimens. Genotypic resistance is currently assessed by direct sequencing and cannot detect resistant species below 20%. Real-time PCR amplification was assessed for its ability to detect the signature m...

BACKGROUND A sensitive, phenotypic reverse transcriptase (RT)-based drug susceptibility assay for the detection of etravirine (ETR) resistance in patient isolates was developed and compared with the results from direct sequencing and ultra-deep pyrosequencing (UDPS). METHODS Samples were obtained from 15 patients with antiretroviral therapy (ART) failure and from five non-nucleoside reverse t...

The rate of mutation refers to the probability that a unit length of DNA (generally a base pair) mutates with time. Fluctuation analysis or mutant accumulation assays applied to phenotypic changes measure mutation rates of cells. However, only a few phenotypic changes indicative of mutations are known thus limiting the analysis to those rare genes. Direct sequencing overcomes the limitations im...

In mammalian genomes a sixth base, 5-hydroxymethylcytosine ((hm)C), is generated by enzymatic oxidation of 5-methylcytosine ((m)C). This discovery has raised fundamental questions about the functional relevance of (hm)C in mammalian genomes. Due to their very similar chemical structure, discrimination of the rare (hm)C against the far more abundant (m)C is technically challenging and to date no...

Three distinct genotypes were identified amongst 50 measles virus (MV) strains characterized in the UK between 1992 and 1995 by direct sequencing of the RT-PCR products amplified from clinical specimens. All three genotypes were related to viruses previously reported in the United States or in continental Europe. Phylogenetic analyses of 255 and 152 nucleotide sequences from the N and M genes, ...

Extended-spectrum beta-lactamases (ESBLs) are widespread in hospital settings worldwide. The present investigation was undertaken to assess the distribution and prevalence of ESBLs belonging to the TEM and SHV families in 448 ESBL-producing clinical isolates of Enterobacteriaceae collected from 10 different Italian hospitals. The natures of TEM and SHV determinants were identified by direct seq...

OBJECTIVE To study the circulation, distribution, and genomic diversity of HPVs in common warts in Beijing area of China. METHODS Forty eight patients with pathologically diagnosed common warts were screened for the presence of HPV with HPV type-specific PCR and direct sequencing analysis. The genomic diversity of HPVs prevalent in Chinese patients was analyzed based on LCR. RESULTS Forty o...