We have developed an approach for simultaneous detection of individual endogenous protein modifications and mRNA molecules in single cells in situ. For this purpose we combined two methods previously developed in our lab: in situ proximity ligation assay for the detection of individual protein interactions and -modifications and in situ detection of single mRNA molecules using padlock probes. A...

Nucleic acid-based biochemical assays are crucial to modern biology. Key applications, such as detection of bacterial, viral and fungal pathogens, require detailed knowledge of assay sensitivity and specificity to obtain reliable results. Improved methods to predict assay performance are needed for exploiting the exponentially growing amount of DNA sequence data and for reducing the experimenta...

The current arsenal of molecular tools for site-directed cleavage of single-stranded DNA (ssDNA) is limited. Here, we describe a method for targeted DNA cleavage that requires only the presence of an A nucleotide at the target position. The procedure involves hybridization of a complementary oligonucleotide probe to the target sequence. The probe is designed to create a deliberate G:A mismatch ...

genomic information, there is a need for improved DNA literacy. Despite the availability of computer programs to evaluate DNA and RNA sequences, the human eye can still play a vital role in sequence analysis for patterns and motifs. We describe a set of fonts that represent DNA sequences in an intuitive manner, suitable for teaching and for visual inspection of strand complementarity, conserved...

The molecular inversion probe (MIP) assay technology was originally developed for single nucleotide polymorphism (SNP) genotyping, but has subsequently been used for identifying other types of genetic variation including focal insertions and deletions, larger copy number alterations (CNAs), loss of heterozygosity (LOH), and most recently, for somatic mutation detection. The assay requires as li...

Gene expression - a key feature for modulating cell fate-is regulated in part by histone modifications, which modulate accessibility of the chromatin to transcription factors. Until now, protein-DNA interactions (PDIs) have mostly been studied in bulk without retrieving spatial information from the sample or with poor sequence resolution. New tools are needed to reveal proteins interacting with...

conclusions it seems that smoking cannot increase the prevalence of high risk hpv 16, 18 in saliva samples. results there were no high-risk types of virus in patients and no significant differences between the groups (p = 1). patients and methods a hundred healthy adult subjects were selected from zahedan dental school for this pilot study. dna was isolated from saliva samples and screened for ...

Recent advances in endoscopic therapeutics allow conditions such as fistulas of the digestive system to be treated endoscopically. These cases were recently managed with surgery. The Padlock® system includes a nitinol clip that was recently introduced for endoscopic therapy. There are few reports with regard to its use in the daily clinical practice. We report a case of a colonic fistula that w...