Single nucleotide polymorphism detection

Hameed AAA, Jean N, Stephen O, Andy PM (2008) Improved single nucleotide polymorphisms detection using conjugated polymer/surfactant system and peptide nucleic acid. Biosens Bioelectron 23 1466-1472... 

Wang YS, Liu B (2007) Label-free single nucleotide polymorphism detection using a cationic tetrahedralfluorene and silica nanoparticles. Anal Chem 79 7214-7220... 

Kohler O, Jarikote DV, Seitz O. Forced Intercalation Probes (FIT Probes) Thiazole orange as a fluorescent base in peptide nucleic 39. acids for homogeneous single-nucleotide-polymorphism detection. ChemBioChem. 2005 6 69-77. 

Inouye M, Ikeda R, Takase M, Tsuii T, Chiba J (2005) Single-nucleotide polymorphism detection with wire-like DNA probes that display quasi on-ofF digital action. Proc Natl Acad SciUS A102 11606-11610... 

Maruyama, K. Takeyama, H. Nemoto, E. Tanaka, T. Yoda, K Matsunaga, T. (2004), Single nucleotide polymorphism detection in aldehyde dehydrogenase 2 (ALDH2) gene using bacterial magnetic particles based on dissociation curve analysis. 

S. Purushothaman, C. Toumazou, C.-P. On, Protons and single nucleotide polymorphism detection a simple use for the Ion Sensitive Field Effect Transistor, Sensors and Actuators B Chemical 114 (2006) 964-968. 

Cancer diagnostics often needs a discrimination of genomic mutations in DNA sequences or special NA structures (miRNA) which can cause various diseases including cancer. SERS technique is very promising for mutation and single nucleotide polymorphisms detection because of the possibility of spatial multiplexing at array format linked with a portable biosensor device. Mahajan and co-workers reported such SERS-based approach using Au substrates prepared by... 

Considerable amounts of quenching of the acridone emissions by guanine in the DNA occurred when guanine was close to acridone, which can be applied as a quencher-free probe (no additional quencher is required) for the detection of a special sequence of DNA. The DNA bearing acridone at the C5 position of inner thymidine could distinguish the opposite T-T base mismatch, while enhancement of discrimination ability is needed for the practical use of single nucleotide polymorphism (SNP) typing. 

Chen, X. and Kwok, P. Y. (1999). Homogeneous genotyping assays for single nucleotide polymorphisms with fluorescence resonance energy transfer detection. Genet. Anal. 14, 157-63. 

T. Sakata and Y. Miyahara, Potentiometric detection of single nucleotide polymorphism by using a genetic field-effect transistor. ChemPhysChem. 6, 703-710 (2005). 

Biomolecular MS and in particular MALDI-TOF-MS (see Sections 2.1.22 and 2.2.1) permit the routine analysis of oligonucleotides up to 70-mers, intact nucleic acids, and the direct detection of DNA products with no primer labels with an increase in analysis speed and mass accuracy especially in contrast to traditional DNA separation techniques such as slab gels or capillary electrophoresis. Applications focus on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Precise and accurate gene expression measurements show relative and absolute numbers of target molecules determined independently of the number of PCR cycles. DNA methylation can be studied quantitatively. 

Li K, Liu B (2009) Conjugated polyelectrolyte amplified thiazole orange emission for label free sequence specific DNA detection with single nucleotide polymorphism selectivity. Anal Chem 81 4099-4105... 

Fig. 1. Errors arising from the incorrect annotation of protein B from genomic data. The correct annotation lies above the dotted line, and incorrect cases lie below the dotted line. Objects colored in red indicate errors. Similar shading of objects implies homology. Other possible errors that are not represented are the incorrect interpretation of single nucleotide polymorphisms (SNPs) of a gene as different genes, and incomplete detection of splice variants.

Primdahl H, Wikman FP, von der Maase H et al. Allelic imbalances in human bladder cancer genome-wide detection with high-density single-nucleotide polymorphism arrays. J Natl Cancer Inst 2002 94 216-223. 

Nannya Y, Sanada M, Nakazaki K et al. A robust algorithm for copy number detection using high-density oligonucleotide single-nucleotide polymorphism genotyping arrays. Cancer Res 2005 65 6071-6079. 

Hoque MO, Lee J, Begum S et al. High-throughput molecular analysis of urine sediment for the detection of bladder eaneer by high-density single-nucleotide polymorphism array. Cancer Res 2003 63 5723-5726. 

Lips EH, Dierssen JW, van Eijk R et al. Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single-nucleotide polymorphism arrays. Cancer 2005 65 10188-10191. 

A. Majumdar, and A. P. Alivisatos. Room-Temperature Single-Nucleotide Polymorphism and Multiallele DNA Detection Using Fluorescent Nanocrystals and Microarrays, Anal. Chem. 2003, 75, 4766. 

---