Abstract
Analysis of single-nucleotide polymorphisms (SNPs) is important for diagnosis of infectious and genetic diseases, for environment and population studies, as well as in forensic applications. Herein is a detailed description to design an “operating cooperatively” (OC) sensor for highly specific SNP analysis. OC sensors use two unmodified DNA adaptor strands and a molecular beacon probe to detect a nucleic acid targets with exceptional specificity towards SNPs. Genotyping can be accomplished at room temperature in a homogenous assay. The approach is easily adaptable for any nucleic acid target, and has been successfully used for analysis of targets with complex secondary structures. Additionally, OC sensors are an easy-to-design and cost-effective method for SNP analysis and nucleic acid detection.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Veiga MI, Ferreira PE, Jörnhagen L, Malmberg M, Kone A, Schmidt BA et al (2011) Novel polymorphisms in Plasmodium falciparum ABC transporter genes are associated with major ACT antimalarial drug resistance. PLoS One 6:e20212
Cummings MP, Segal MR (2004) Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis. BMC Bioinformatics 5:137
Zhang L, Liu Y, Song F, Zheng H, Hu L, Lu H et al (2011) Functional SNP in the microRNA-367 binding site in the 3′UTR of the calcium channel ryanodine receptor gene 3 (RYR3) affects breast cancer risk and calcification. Proc Natl Acad Sci USA 108:13653–13658
Lee SH, DeCandia TR, Ripke S, Yang J (2012) Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs. Nat Genet 44:247–250
Sanchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M et al (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27:1713–1724
Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14:303–308
Reed GH, Kent JO, Wittwer CT (2007) High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8:597–608
Gerasimova YV, Hayson A, Ballantyne J, Kolpashchikov DM (2010) A single molecular beacon probe is sufficient for the analysis of multiple nucleic acid sequences. Chembiochem 11:1762–1768
Grimes J, Gerasimova YV, Kolpashchikov DM (2010) Real-time SNP analysis in secondary-structure-folded nucleic acids. Angew Chem Int Ed Engl 49:8950–8953
Kolpashchikov DM (2006) A binary DNA probe for highly specific nucleic acid recognition. J Am Chem Soc 128:10625–10628
Kolpashchikov DM, Gerasimova YV, Khan MS (2011) DNA nanotechnology for nucleic acid analysis: DX motif-based sensor. Chembiochem 12:2564–2567
Nguyen C, Grimes J, Gerasimova YV, Kolpashchikov DM (2011) Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids. Chemistry 17: 13052–13058
Li J, Qi XJ, Du YY, Fu HE, Chen GN, Yang HH (2012) Efficient detection of secondary structure folded nucleic acids related to Alzheimer’s disease based on junction probes. Biosens Bioelectron 36:142–146
Nakayama S, Yan L, Sintim HO (2008) Junction probes—sequence specific detection of nucleic acids via template enhanced hybridization processes. J Am Chem Soc 130:12560–12561
Cornett EM, Campbell EA, Gulenay G, Peterson E, Bhaskar N, Kolpashchikov DM (2012) Molecular logic gates for DNA analysis: detection of rifampin resistance in M. tuberculosis DNA. Angew Chem Int Ed Engl 51:9075–9077
Cornett EM, O’steen MR, Kolpashchikov DM (2013) Operating cooperatively (OC) sensor for highly specific recognition of nucleic acids. PLOS one 8, e55919
Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W et al (2009) Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 48:856–870
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, New York
About this protocol
Cite this protocol
Cornett, E.M., Kolpashchikov, D.M. (2013). SNP Analysis Using a Molecular Beacon-Based Operating Cooperatively (OC) Sensor. In: Kolpashchikov, D., Gerasimova, Y. (eds) Nucleic Acid Detection. Methods in Molecular Biology, vol 1039. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-535-4_6
Download citation
DOI: https://doi.org/10.1007/978-1-62703-535-4_6
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-534-7
Online ISBN: 978-1-62703-535-4
eBook Packages: Springer Protocols