5’ nuclease assay

Latif S, Bauer-Sardina I, Ranade K, Livak KJ, Kwok PY. Fluorescence polarization in homogeneous nucleic acid analysis II 5 -nuclease assay. Genome Res 2001 11 436 140. 

Happich D, Schwaab R, Hanfland P, Hoernschemeyer D. AUelic discrimination of factor V leiden using a 5 nuclease assay. Thromb Haemost 1999 82 1294-6. 

The fluorogenic 5 nuclease assay, which utilises the 5 nuclease activity inherent as a secondary function of Taq DNA polymerase to cleave a gene-specific probe, thereby releasing a fluorescent molecule for detection. 

Livak, K. J., Allelic discrimination using fluorogenic probes and the 5 nuclease assay. Genet Anal, 1999. 14(5-6) p. 143-9. 

T. Schlaurman, R. de Boer, R. Patty, M. Kooistra-Smid, and A. van Zwet Comparative evalnation of in-honse manual, and commercial semi-automated and automated DNA extraction platforms in the sample preparation of human stool specimens for a Salmonella enterica 5 -nuclease assay. Journal of Microbiological Methods 71, 238-245 (2007)... 

Allele-specific expression levels can be assessed in two ways. Expression of mRNA and cDNA with different alleles at heterozygote SNPs is assessed using oligonucleotides and TaqMan/real-time PCR 5 nuclease assays (ABI, Foster City, CA) or the primer extension method (SnapShot, ABI, Foster City, CA and MALDI TOF, Sequenome). 

Fic. 4. Dependence of Kem and Km on pH for the cleavage of the synthetic substrate nitrophcnyl-pdTp by staphylococcal nuclease. Assays were performed in 0.05 M borate buffer, 0.015 M CaCh. 

According to this method, DNA is treated with SI nuclease after hybridization and then precipitated. SI nuclease digests single-stranded DNA but not double-stranded DNA. The rigor of enzyme treatment can have a dramatic effect on the effective criterion, and it is important to establish strict control in SI nuclease assays. 

Becker, S., Boger, P., Oehlmann, R., and Ernst, A. (2000). PCR bias in ecological analysis A case study for quantitative Taq nuclease assays in analyses of microbial communities. Appl. Environ. Microbiol. 66, 4945—4953. 

DNA-modified gold nanoparticles have been used as drug delivery vectors for doxorubicin as well as for oligonucleotides. " An electrochemical method is reported for the detection of DNA methylation in an assay for methyltransferase activity," and various assays are described for nuclease assays." " Multimerised siRNA crosslinked by gold... 

It should be pointed out that when using ethidium bromide the sensitivity of the assays varies depending on the physical state of the nucleic acids (see Table I). Ethidium does not discriminate between RNA and DNA, although dyes are available which bind DNA exclusively, so the relative amounts of each may be determined by taking two sets of measurements. Alternatively, nucleases (DNA-ase or RNA-ase) can be used to exclusively remove one or the other in a mixture. Nucleic acids from different sources (see Table II) also show a variation in sensitivity, and the fluorescence assay lacks the selectivity of the hybridization technique. Nevertheless, for rapid screening or quality-control applications the fluorescence assay is still the method of choice. 

Plitnik, L.M., et al., Cytokine profiling for chemical sensitizers Application of the ribo-nuclease protection assay and effect of dose. Toxicol. Appl. Pharmacol., 179, 145, 2002. 

On the basis of Scheme 5, we recently realized label-free sequence-specific DNA detection with SNP selectivity with the aid of SI nuclease [59]. In this assay, IBr and TO are chosen as the energy donor and acceptor, respectively. 

Scheme 14 Schematic representations of the assay for nucleases and protease detection based on the complex of ACP, DNA-TR and peptide-H...

Antibiotic Mg complex induced alteration in the ultrastructural changes in the native and HI depleted chromatin were monitored by thermal melting analysis, polyacrylamide gel mobility assay, dynamic light scattering experiments and transmission electron microscopic studies. Micrococcal nuclease digestion is the biochemical probe to assess the accessibility of the antibiotic Mg + complexes to nucleosomal DNA. 

It is obvious that the single-molecule approaches can reveal features of the dynamics of chromatin assembly and its force dependence that could not be observed using the standard biochemical assays to study assembly following changes in superhelicity in closed circular DNA molecules, looking at changes in protection against enzymes like micrococcal nuclease, or the accessibility of restriction enzymes. 

Martel, R.R., Botros, I.W., Rounseville, M.R, Hinton, J.R, Staples, R.R., Morales, D.A., Farmer, J.B., and Seligmann, B.E., Multiplexed screening assay for mRNA combining nuclease protection with luminescent array detection. Assay Drug Dev. TechnoL, 1, 61-72, 2002. 

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