Labeled oligonucleotide

Fuchs, B. M. Wallner, G. Beisker, W. Schwippl, I. Ludwig, W. Amann, R. Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 1998, 64, 4973 1982. 

Dirks RW, van Gijlswijk RP, Tullis RH et al (1990) Simultaneous detection of different mRNA sequences coding for neuropeptide hormones by double in situ hybridization using FITC- and biotin-labeled oligonucleotides. J Flistochem Cytochem 38 467 173... 

Ironically, AP is the enzyme of choice for some applications due to its stability. Since it can withstand the moderately high temperatures associated with hybridization assays better than HRP, AP often is the enzyme of choice for labeling oligonucleotide probes. AP also is capable of maintaining enzymatic activity for extended periods of substrate development. Increased sensitivity can be realized in ELISA procedures by extending the substrate incubation time to hours and sometimes even days. These properties make AP the second most popular choice for antibody-enzyme conjugates (behind HRP), being used in almost 20 percent of all commercial enzyme-linked assays. 

Malicka J, Gryczynski I, Gryczynski Z, Lakowicz JR (2003) Effects of fluorophore-to-silver distance on the emission of cyanine-dye-labeled oligonucleotides. Anal Biochem 315 57-66... 

Moon JH, Deans R, Kruegar E, Hancock LF (2003) Capture and detection of a quencher labeled oligonucleotide by poly(phenylene ethylene) particles. Chem Commun 1 104-105... 

Pu KY, Liu B (2009) Optimizing the cationic conjugated polymer-sensitized fluorescent signal of dye labeled oligonucleotide for biosensor applications. Biosens Bioelectron... 

Availability of a sample isotopically enriched with 15N and 13C offers the NMR spectro-scopist additional tools for overcoming the problems encountered in homonuclear experiments. In an obvious extension of the homonuclear experiments, the carbon or nitrogen dimension can be used to improve the resolution in NOESY spectra. However, recent trends clearly favor the through-bond approach where the presence of a cross peak unambiguously proves the existence of a chemical bond between the nuclei involved. Let us review briefly the experiments available for labeled oligonucleotides. 

Assay for human immunodeficiency virus type 1 (HIV-1) proviral DNA in peripheral blood monuclear cells can be performed by PCR followed by detection of PCR products by electrochemiluminescence-labeled oligonucleotide probe [Tris-bipyridine ruthenium (II) complex]. Since one of the PCR primers is biotin-labeled at the 5 end, facile capture of the PCR product-probe complex can be accomplished on streptavidin-conjugated magnetic particles, prior to analysis in an electrochemiluminescence analyzer (S3). 

K.J. Fountain, M. Gilar, Y. Budman and J.C. Gebler, Purification of dye-labeled oligonucleotides by ion-pair reversed-phase high-performance liquid chromatography. J. Chromatogr.B, 783 (2003) 61-72. 

Tata, AM. 2001. An in situ hybridization protocol to detect rare mRNA expressed in neural tissue using biotin-labelled oligonucleotide probes. Brain Res Prot 6 178-184. 

This technique, described in Section I, involves the construction of short DNA sequences (oligonucleotides) of approximately 20 bp that exactly complement either the mutated sequence or the normal sequence (hence, allele-specific ). The labeled oligonucleotide is then used to probe DNA from the individual in question. This DNA may be placed, for example, on a dot blot. Successful hybridization of the ASO containing the mutation indicates presence of the mutation, whereas hybridization of the normal ASO indicates presence of the normal sequence. Hybridization of both probes would be seen in a heterozygote. Because a different probe must be constructed for each mutation, this technique is practical when a limited number of mutations... 

Gel electrophoresis of P-end-labelled oligonucleotides irradiated with visible light in the presence of RufTAP)] showed that the principal photochemical product is a less electrophoretically-mobile species [96]. This is consistent with the formation of a photo-adduct and it is clear that the yield of this reaction is... 

DNA arrays have been categorized into different formats based upon what is immobilized to the surface (also known as the solid phase, substrate, or chip) and what is captured from the sample solution. Definitions change depending upon the format. For the classic Southern dot blot, the sample was first spotted down on the surface, cross-linked, and then bathed with a radio-labeled oligonucleotide under hybridization (complementary nucleic acid strand base-pairing) conditions to detect the presence of a parhcular sequence within the sample. This was called probing. The oligonucleohde... 

Figure 6.18 ImmunoRCA Assay. Top left A reporter Ab conjugated to an oligonucleotide binds to a test analyte captured on a solid surface by a covalent attachment or by a capture Ab. Top right DNA circle hybridizes to a complementary sequence in the oligonucleotide. Bottom left Resulting complex is washed to remove excess reagents, and the DNA tag is amplified by RCA. Bottom right Amplified product is labeled in situ by hybridization with fluor-labeled oligonucleotides. (From Schweitzer, B. et al, Proc. Natl. Acad. Sci. USA, 97, 10113-10119, 2000. With permission.)...

E. Hedberg, B. Langstrom, Synthesis of 4-([ F]fluoromethyl)phenyl isothiocyanate and its use in labeling oligonucleotides, Acta Chem. Scand. 51 (1997) 1236-1240. 

Lanthanide-labeled oligonucleotide probes are now available commercially (161). Oligonucleotides are synthesized containing free amino groups, which are then labeled with a lanthanide chelate via a Schiff base conjugation [similar to the reaction shown in Fig. 19 but with a monoaldehyde functional group (linker) of a lanthanide complex in place of glutaraldehyde]. b. 

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