scholarly journals A Locked Nucleic Acid Probe Based on Selective Salt-Induced Effect Detects Single Nucleotide Polymorphisms

2015 ◽  
Vol 2015 ◽  
pp. 1-6
Author(s):  
Jing Zhang ◽  
Huizhe Wu ◽  
Qiuchen Chen ◽  
Pengfei Zhao ◽  
Haishan Zhao ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Nucleotide Polymorphisms ◽  
Room Temperature ◽  
Genetic Mutation ◽  
Locked Nucleic Acid ◽  
Nucleotide Polymorphisms ◽  
Buffer Solution ◽  
Single Nucleotide ◽  
Real Time Quantitative Pcr ◽  
Pcr Products

Detection of single based genetic mutation by using oligonucleotide probes is one of the common methods of detecting single nucleotide polymorphisms at known loci. In this paper, we demonstrated a hybridization system which included a buffer solution that produced selective salt-induced effect and a locked nucleic acid modified 12 nt oligonucleotide probe. The hybridization system is suitable for hybridization under room temperature. By using magnetic nanoparticles as carriers for PCR products, the SNPs (MDR1C3435T/A) from 45 volunteers were analyzed, and the results were consistent with the results from pyrophosphoric acid sequencing. The method presented in this paper differs from the traditional method of using molecular beacons to detect SNPs in that it is suitable for research institutions lacking real-time quantitative PCR detecting systems, to detect PCR products at room temperature.

Locked nucleic acid (LNA) induced effect on the hybridization and fluorescence properties of oligodeoxyribonucleotides modified with nucleobase-functionalized DNA monomers

2015 ◽  
Vol 13 (26) ◽  
pp. 7236-7247 ◽  
Author(s):  
Mamta Kaura ◽  
Patrick J. Hrdlicka
Keyword(s):  
Nucleic Acid ◽  
Single Nucleotide Polymorphisms ◽  
Locked Nucleic Acid ◽  
Fluorescence Properties ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Mixmer oligonucleotides modified with LNA and C5-pyrene-functionalized DNA monomers are shown to display interesting fluorescence properties for the discrimination of single nucleotide polymorphisms (SNPs).

MS for Identification of Single Nucleotide Polymorphisms and MS/MS for Discrimination of Isomeric PCR Products

2000 ◽  
Vol 72 (17) ◽  
pp. 4033-4040 ◽  
Author(s):  
Mark T. Krahmer ◽  
James J. Walters ◽  
Karen F. Fox ◽  
Alvin Fox ◽  
Kim E. Creek ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pcr Products

scholarly journals Analysis of Clinically Relevant Single-Nucleotide Polymorphisms by Use of Microelectronic Array Technology

2002 ◽  
Vol 48 (12) ◽  
pp. 2124-2130 ◽  
Author(s):  
Rosa Santacroce ◽  
Antonia Ratti ◽  
Francesco Caroli ◽  
Barbara Foglieni ◽  
Alessandro Ferraris ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Factor Vii ◽  
Restriction Enzyme Digestion ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Ret Protooncogene ◽  
Mismatched Dna ◽  
Specific Pcr ◽  
Pcr Products ◽  
Allele Specific

Abstract Background: Microelectronic DNA chip devices represent an emerging technology for genotyping. We developed methods for detection of single-nucleotide polymorphisms (SNPs) in clinically relevant genes. Methods: Primer pairs, with one containing a 5′-biotin group, were used to PCR-amplify the region encompassing the SNP to be interrogated. After denaturation, the biotinylated strand was electronically targeted to discrete sites on streptavidin-coated gel pads surfaces by use of a Nanogen Molecular Workstation. Allele-specific dye-labeled oligonucleotide reporters were used for detection of wild-type and variant sequences. Methods were developed for SNPs in genes, including factor VII, β-globin, and the RET protooncogene. We genotyped 331 samples for five DNA variations in the factor VII gene, >600 samples from patients with β-thalassemia, and 15 samples for mutations within the RET protooncogene. All samples were previously typed by various methods, including DNA sequence analysis, allele-specific PCR, and/or restriction enzyme digestion of PCR products. Results: Analysis of amplified DNA required 4–6 h. After mismatched DNA was removed, signal-to-noise ratios were >5. More than 940 samples were typed with the microelectronic array platform, and results were totally concordant with results obtained previously by other genotyping methods. Conclusions: The described protocols detect SNPs of clinical interest with results comparable to those of other genotyping methods.

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