We propose a novel universal methodology, Short Oligonucleotide Tandem Ligation Assay (SOTLA), for SNP genotyping. SOTLA is based on using a tandem of short oligonucleotide (TSO) probes consisting of three fragments: the core oligonucleotide and two flanking oligomers, one of which is immobilized onto a solid support and another one contains the biotin label. TSO is self-associated on a complem...

Molecular beacons are oligonucleotide probes that become fluorescent upon hybridization. We designed molecular beacons to detect a point mutation in the methylenetetrahydrofolate reductase (MTHFR) gene, a mutation that has been related to an increased risk for cardiovascular disease and neural tube defects. The application of molecular beacons enables fast, semiautomated, accurate mutation dete...

The dynamic nature of micellar nanostructures is employed to form a self-assembled Förster resonance energy transfer (FRET) nanoplatform for enhanced sensing DNA. platform consists lipid oligonucleotide FRET probes incorporated into scaffolds, where single recognition events result in fusion and fission DNA mixed micelles, triggering the fluorescence response multiple rather than pair. In compa...

Fluorescent oligonucleotide hybridization probes were used to label bacterial cells for analysis by flow cytometry. The probes, complementary to short sequence elements within the 16S rRNA common to phylogenetically coherent assemblages of microorganisms, were labeled with tetramethylrhodamine and hybridized to suspensions of fixed cells. Flow cytometry was used to resolve individual target and...

Parallel, highly specific analysis methods are required to take advantage of the extensive information about DNA sequence variation and of expressed sequences. We present a scalable laboratory technique suitable to analyze numerous target sequences in multiplexed assays. Sets of padlock probes were applied to analyze single nucleotide variation directly in total genomic DNA or cDNA for parallel...

Fluorescent in situ hybridization (FISH) was carried out using two different oligonucleotide probes speciÞ c for Pseudomonas spp. and Acinetobacter spp. These probes were tested against different organisms and were found to be highly speciÞ c. Sensitivity testing showed that the probes were able to detect as low as 103 CFU/mL. In addition, FISH was carried out directly on positive blood culture...

Synthetic oligonucleotides prepared from known DNA or amino acid sequences can be used as gene probes for detection of DNA and RNA. Short oligonucleotide probes can discriminate between two sequences which differ by only a single nucleotide (1). Biotin is the most frequently used non-radioactive reporter group for labelling of nucleic acids. Enzymatic and/or chemical synthesis have been used to...

By employing in gel competitive reassociation, which distinguishes two DNA preparations, to clone anonymous DNA fragments with altered primary structure, we isolated a clone (BL-1) from a rat DNA which gave an extra, apparently altered, DNA band in a specific tissue (brain) when we used it as a probe for Southern hybridization. The sequence of BL-1 was very similar to a portion of LINE, a highl...

In many areas of molecular biology there is a need to rapidly extract and analyze genetic information; however, current technologies for DNA sequence analysis are slow and labor intensive. We report here how modern photolithographic techniques can be used to facilitate sequence analysis by generating miniaturized arrays of densely packed oligonucleotide probes. These probe arrays, or DNA chips,...

Oligonucleotide microarrays are based on the hybridization of labeled mRNA molecules to short length oligonucleotide probes on a glass surface. Two effects have been shown to affect the raw data: the sequence dependence of the probe hybridization properties and the chemical saturation resulting from surface adsorption processes. We address both issues simultaneously using a physically motivated...