Journal of Industrial and Engineering Chemistry, Vol.88, 78-83, August, 2020
Highly selective detection of single nucleotide polymorphism (SNP) using a dumbbell DNA probe with a gap-filling approach
Single nucleotide polymorphism (SNP) is the most common type of genetic sequence variations and known to associate with the development of various diseases including cancer. Accurate detection of SNP is often necessary to determine the susceptibility of patients to diseases as well as their response to the medical treatments. Molecular inversion probe (MIP) has been widely utilized as an alternative method to detect the SNP as compared to the conventional PCR/genome sequencing method. However, basepairing based detection of SNP fundamentally lacks target specificity toward the single mismatch of bases and often fails to meet the accuracy requirement for SNP detection. In this study, we report the development of new SNP detection method using a dumbbell-probe with a gap-filling approach. Two separate DNA strands are designed to self-assemble to form a dumbbell DNA probe for the selective detection of EGFR 21 point mutation. Unlike the direct binding of MIP to the target sequence, our system has an additional process for the enhancement of sequence specificity through a base matched gapfilling. In the presence of target sequences, the dumbbell-probe undergoes base-pair hybridization to the target sequence followed by sequence specific gap-filling and ligation in single-step. The detection of EGFR 21 point mutation is achieved with a highly specific and selective manner. This simple and robust detection method offers promising future potential in the diagnosis of various genetic mutations.
Keywords:Molecular inversion probe (MIP);Single nucleotide polymorphism (SNP);Dumbbell probe;Gap filling
- Jin J, Wu X, Yin J, Li M, Shen J, Li J, Zhao Y, Zhao Q, Wu J, Wen Q, Cho CH, Yi T, Xiao Qu L, Front. Oncol., 9, 263 (2019)
- Jorge SE, Kobayashi SS, Costa DE, Braz. J. Med. Biol. Res., 47, 929 (2014)
- Li AR, Chitale D, Riely GJ, Pao W, Miller VA, Zakowski MF, Rusch V, Kris MG, Ladanyi M, J. Mol. Diagn., 10, 242 (2008)
- Angulo B, Conde E, Suarez-Gauthier A, Plaza C, Martinez R, Redondo P, Izquierdo E, Rubio-Viqueira B, Paz-Ares L, Hidalgo M, Lopez-Rios F, PLoS ONE, 7, e43842 (2012)
- Gong J, Li YS, Lin T, Feng XY, Chu L, RSC Adv., 8, 27375 (2018)
- Lau HY, Palanisamy R, Trau M, Botella JR, PLOS ONE, 9 (2014)
- Stefan CP, Koehler JW, Minogue TD, Sci. Rep., 6, 25904 (2016)
- Jung IY, Kim JS, Choi BR, Lee K, Lee H, Adv. Healthc. Mater., 6, 2 (2017)
- Cao W, Trends Biotechnol., 22, 38 (2004)
- Rittie L, Perbal B, J. Cell Commun. Signal., 2, 25 (2008)
- Lohman GJ, Bauer RJ, Nichols NM, Mazzola L, Bybee J, Rivizzigno D, Cantin E, Evans TC, Nucleic Acids Res., 44, e14 (2016)
- Jung IY, You JB, Choi BR, Kim JS, Lee HK, Jang B, Jeong HS, Lee K, Im SG, Lee H, Adv. Healthc. Mater., 5, 2168 (2016)
- Lee HY, Jeong H, Jung IY, Jang B, Seo YC, Lee H, Lee H, Adv. Mater., 27(23), 3513 (2015)
- Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA, Fakhrai-Rad H, Ronaghi M, Willis TD, Landegren U, Davis RW, Nat. Biotechnol., 21, 673 (2003)
- Ali MM, Li F, Zhang Z, Zhang K, Kang DK, Ankrum JA, Le XC, Zhao W, Chem. Soc. Rev., 43, 3324 (2014)
- Gu L, Yan W, Liu L, Wang S, Zhang X, Lyu M, Pharmaceuticals (Basel), 11 (2018).
- Johne R, Muller H, Rector A, van Ranst M, Stevens H, Trends Microbiol., 17, 205 (2009)
- Elazezy M, Joosse SA, Comput. Struct. Biotechnol. J., 16, 370 (2018)
- Lim M, Kim CJ, Sunkara V, Kim MH, Cho YJ, Micromachines (Basel), 9 (2018).
- Vendrell JA, Mau-Them FT, Beganton B, Godreuil S, Coopman P, Solassol J, Int. J. Mol. Sci., 18 (2017)
- Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA, J. Comput. Chem., 32, 170 (2011)
- Li XY, Du YC, Zhang YP, Kong DM, Sci. Rep., 7, 6263 (2017)
- Wei H, Tang S, Hu T, Zhao G, Guan Y, Sci. Rep., 6, 29229 (2016)
- Sonobe M, Manabe T, Wada H, Tanaka F, Br. J. Cancer, 93, 355 (2005)
- Lovett ST, EcoSal Plus, 4 (2011)
- Bettegowda C, Sausen M, Leary RJ, et al., Sci. Transl. Med., 6, 224ra224 (2014).
- Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, et al., BMC Bioinform., 12, 231 (2011)