Triplex DNA: A New Platform for Polymerase Chain Reaction-based Biosensor

Overview

Journal Sci Rep

Specialty Science

Date 2015 Aug 14

PMID 26268575

Citations 2

Authors

Yubin Li

Xiangmin Miao

Liansheng Ling

Affiliations

Soon will be listed here.

Abstract

Non-specific PCR amplification and DNA contamination usually accompany with PCR process, to overcome these problems, here we establish a sensor for thrombin by sequence-specific recognition of the PCR product with molecular beacon through triplex formation. Probe A and probe B were designed for the sensor, upon addition of thrombin, two probes hybridized to each other and the probe B was extended in the presence of Klenow Fragment polymerase and dNTPs. The PCR amplification occurred with further addition of Taq DNA Polymerase and two primers, the PCR product was recognized by molecular beacon through triplex formation. The fluorescence intensity increased with the logarithm of the concentration of thrombin over the range from 1.0 × 10(-12) M to 1.0 × 10(-7) M, with a detection limit of 261 fM. Moreover, the effect of DNA contamination and non - specific amplification could be ignored completely in the proposed strategy.

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References

Miao X, Xiong C, Wang W, Ling L, Shuai X . Dynamic-light-scattering-based sequence-specific recognition of double-stranded DNA with oligonucleotide-functionalized gold nanoparticles. Chemistry. 2011; 17(40):11230-6. DOI: 10.1002/chem.201003010. View

Xue L, Zhou X, Xing D . Highly sensitive protein detection based on aptamer probe and isothermal nicking enzyme assisted fluorescence signal amplification. Chem Commun (Camb). 2010; 46(39):7373-5. DOI: 10.1039/c0cc02038a. View

Lewis F, Wu Y, Hayes R, Wasielewski M . DNA-mediated electron transfer across synthetic T:A.T triplex structures. Angew Chem Int Ed Engl. 2002; 41(18):3485-7. DOI: 10.1002/1521-3773(20020916)41:18<3485::AID-ANIE3485>3.0.CO;2-9. View

Manzini G, Xodo L, Gasparotto D, Quadrifoglio F, van der Marel G, VAN Boom J . Triple helix formation by oligopurine-oligopyrimidine DNA fragments. Electrophoretic and thermodynamic behavior. J Mol Biol. 1990; 213(4):833-43. DOI: 10.1016/S0022-2836(05)80267-0. View

Lin X, Chen Q, Liu W, Li H, Lin J . A portable microchip for ultrasensitive and high-throughput assay of thrombin by rolling circle amplification and hemin/G-quadruplex system. Biosens Bioelectron. 2014; 56:71-6. DOI: 10.1016/j.bios.2013.12.061. View

Wang J, Ramakrishnan R, Tang Z, Fan W, Kluge A, Dowlati A . Quantifying EGFR alterations in the lung cancer genome with nanofluidic digital PCR arrays. Clin Chem. 2010; 56(4):623-32. DOI: 10.1373/clinchem.2009.134973. View

Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S . High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet. 2011; 43(5):464-9. DOI: 10.1038/ng.804. View

Komatsu M, Kobayashi D, Saito K, Furuya D, Yagihashi A, Araake H . Tumor necrosis factor-alpha in serum of patients with inflammatory bowel disease as measured by a highly sensitive immuno-PCR. Clin Chem. 2001; 47(7):1297-301. View

CLELAND J . UNIVERSITY EXPEDITION TO STUDY THE NATIVES OF CENTRAL AUSTRALIA. Science. 1933; 77(1993):260-1. DOI: 10.1126/science.77.1993.260-a. View

10.

McKenzie F, Faulds K, Graham D . LNA functionalized gold nanoparticles as probes for double stranded DNA through triplex formation. Chem Commun (Camb). 2008; (20):2367-9. DOI: 10.1039/b802163e. View

11.

Kutyavin I, Afonina I, Mills A, Gorn V, Lukhtanov E, Belousov E . 3'-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res. 1999; 28(2):655-61. PMC: 102528. DOI: 10.1093/nar/28.2.655. View

12.

Amodio A, Zhao B, Porchetta A, Idili A, Castronovo M, Fan C . Rational design of pH-controlled DNA strand displacement. J Am Chem Soc. 2014; 136(47):16469-72. DOI: 10.1021/ja508213d. View

13.

Han M, Lytton-Jean A, Mirkin C . A gold nanoparticle based approach for screening triplex DNA binders. J Am Chem Soc. 2006; 128(15):4954-5. PMC: 3200552. DOI: 10.1021/ja0606475. View

14.

Kuang H, Ma W, Xu L, Wang L, Xu C . Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications. Acc Chem Res. 2013; 46(11):2341-54. DOI: 10.1021/ar300206m. View

15.

Yuan Y, Yuan R, Chai Y, Zhuo Y, Ye X, Gan X . Hemin/G-quadruplex simultaneously acts as NADH oxidase and HRP-mimicking DNAzyme for simple, sensitive pseudobienzyme electrochemical detection of thrombin. Chem Commun (Camb). 2012; 48(38):4621-3. DOI: 10.1039/c2cc31423a. View

16.

Rottiers V, Naar A . MicroRNAs in metabolism and metabolic disorders. Nat Rev Mol Cell Biol. 2012; 13(4):239-50. PMC: 4021399. DOI: 10.1038/nrm3313. View

17.

Furuya D, Kaneko R, Yagihashi A, Endoh T, Yajima T, Kobayashi D . Immuno-PCR assay for homodimeric osteoprotegerin. Clin Chem. 2001; 47(8):1475-7. View

18.

Li T, Ackermann D, Hall A, Famulok M . Input-dependent induction of oligonucleotide structural motifs for performing molecular logic. J Am Chem Soc. 2012; 134(7):3508-16. PMC: 3284195. DOI: 10.1021/ja2108883. View

19.

Idili A, Vallee-Belisle A, Ricci F . Programmable pH-triggered DNA nanoswitches. J Am Chem Soc. 2014; 136(16):5836-9. DOI: 10.1021/ja500619w. View

20.

Zhang H, Zhao Q, Li X, Le X . Ultrasensitive assays for proteins. Analyst. 2007; 132(8):724-37. DOI: 10.1039/b704256f. View