Abstract
A fundamental molecular beacon (MB) consists of a special short nucleic acid strand with a fluorophore-quencher pair attached to its ends. It provides a unique framework that is susceptible to conformational transitions between a hairpin (closed) conformation and an extended (open) conformation. These two conformations are readily discernible because of their differing fluorescence emission characteristics. The broad applicability of the robust MB sensing platform has attracted widespread interest, resulting in extensive research studies ranging from theoretical and bioanalytical chemistry to molecular biology and biomedical applications. In this paper, the principles of MB design and the modes and mechanisms of MB operation are reviewed, including MB modifications based on the utilisation of a thymidine-thymidine mismatch in hybridised MB stem, aptamers, peptides and locked nucleic acid strands in an MB loop, as well as plasmonic quenchers, quantum dots and interactions with graphene and graphene oxide. Specific applications of MBs in the analysis of enzymes, DNA mutation, phosphorylation, methylation and ligation, followed by the detection of pathogens and applications in cancer and other disease diagnostics and therapeutics are also reviewed. Molecular beacon-based sensing platforms are expanding rapidly and offer a promising bioanalytical tool for inexpensive and reliable analysis for research and field diagnostics.
References
Antony, T., Thomas, T., Sigal, L. H., Shirahata, A., & Thomas, T. J. (2001). A molecular beacon strategy for the thermodynamic characterization of triplex DNA: Triplex formation at the promoter region of cyclin D1. Biochemistry, 40, 9387-9395. DOI: 10.1021/bi010397z.10.1021/bi010397zSearch in Google Scholar PubMed
Bi, S., Ji, B., Zhang, Z. P., & Zhu, J. J. (2013). Metal ions triggered ligase activity for rolling circle amplification and its application in molecular logic gate operations. Chemical Science, 4, 1858-1863. DOI: 10.1039/c3sc00043e.10.1039/c3sc00043eSearch in Google Scholar
Buranachai, C., Thavarungkul, P., & Kanatharana, P. (2012). A novel reconfigurable optical biosensor based on DNA aptamers and a DNA molecular beacon. Journal of Fluorescence, 22, 1617-1625. DOI: 10.1007/s10895-012-1105-6.10.1007/s10895-012-1105-6Search in Google Scholar PubMed
Campbell, M. A., & Wengel, J. (2011). Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals. Chemical Society Reviews, 40, 5680-5689. DOI: 10.1039/c1cs15048k.10.1039/c1cs15048kSearch in Google Scholar PubMed
Chang, H. X., Tang, L. H., Wang, Y., Jiang, J. H., & Li, J. H. (2010). Graphene fluorescence resonance energy transfer aptasensor for the thrombin detection. Analytical Chemistry, 82, 2341-2346. DOI: 10.1021/ac9025384.10.1021/ac9025384Search in Google Scholar PubMed
Chen, W., Martinez, G., & Mulchandani, A. (2000). Molecular beacons: a real-time polymerase chain reaction assay for de tecting Salmonella. Analytical Biochemistry, 280, 166-172. DOI: 10.1006/abio.2000.4518.10.1006/abio.2000.4518Search in Google Scholar PubMed
Chen, A. K., Behlke, M. A., & Tsourkas, A. (2008). Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA. Nucleic Acids Research, 36, e69. DOI: 10.1093/nar/gkn331.10.1093/nar/gkn331Search in Google Scholar PubMed PubMed Central
Chen, J., Huang, Y., Shi, M., Zhao, S. L., & Zhao, Y. C. (2013). Highly sensitive multiplexed DNA detection using multi-walled carbon nanotube-based multicolor nanobeacon. Talanta, 109, 160-166. DOI: 10.1016/j.talanta.2013.02.003.10.1016/j.talanta.2013.02.003Search in Google Scholar PubMed
Cissell, K. A., Hunt, E. A., & Deo, S. K. (2009). Resonance energy transfer methods of RNA detection. Analytical and Bioanalytical Chemistry, 393, 125-135. DOI: 10.1007/s00216-008-2336-x.10.1007/s00216-008-2336-xSearch in Google Scholar PubMed
Culha, M., Stokes, D. L., Griffin, G. D., & Vo-Dinh, T. (2004). Application of a miniature biochip using the molecular beacon probe in breast cancer gene BRCA1 detection. Biosensors and Bioelectronics, 19, 1007-1012. DOI: 10.1016/j.bios.2003.09.006.10.1016/j.bios.2003.09.006Search in Google Scholar PubMed
Deng, D., Zhang, D. Y., Li, Y., Achilefu, S., & Gu, Y. Q. (2013). Gold nanoparticles based molecular beacons for in vitro and in vivo detection of the matriptase expression on tumor. Biosensors and Bioelectronics, 49, 216-221. DOI: 10.1016/j.bios.2013.05.018.10.1016/j.bios.2013.05.018Search in Google Scholar PubMed
Dong, H. F., Ding, L., Yan, F., Ji, H. X., & Ju, H. X. (2011). The use of polyethylenimine-grafted graphene nanoribbon for cellular delivery of locked nucleic acid modified molecular beacon for recognition of microRNA. Biomaterials, 32, 3875-3882. DOI: 10.1016/j.biomaterials.2011.02.001.10.1016/j.biomaterials.2011.02.001Search in Google Scholar PubMed
Dong, H. F., Hao, K. H., Tian, Y. P., Jin, S., Lu, H. T., Zhou, S. F., & Zhang, X. J. (2014). Label-free and ultra sensitive microRNA detection based on novel molecular beacon binding readout and target recycling amplification. Biosensors and Bioelectronics, 53, 377-383. DOI: 10.1016/j.bios.2013.09.061.10.1016/j.bios.2013.09.061Search in Google Scholar PubMed
Fang, X. H., Li, J. W. J., & Tan, W. H. (2000). Using molecular beacons to probe molecular interactions between lactate dehydrogenase and single-stranded DNA. Analytical Chemistry, 72, 3280-3285. DOI: 10.1021/ac991434j.10.1021/ac991434jSearch in Google Scholar PubMed
Fang, X. H., Jiang, W., Han, X. W., & Zhang, Y. Z. (2013). Molecular beacon based biosensor for the sequence-specific detection of DNA using DNA-capped gold nanoparticlesstreptavidin conjugates for signal amplification. Microchimica Acta, 180, 1271-1277. DOI: 10.1007/s00604-013-1044-1.10.1007/s00604-013-1044-1Search in Google Scholar
Foudeh, A. M., Daoud, J. T., Faucher, S. P., Veres, T., & Tabrizian, M. (2014). Sub-femtomole detection of 16s rRNA from Legionella pneumophila using surface plasmon resonance imaging. Biosensors and Bioelectronics, 52, 129-135. DOI: 10.1016/j.bios.2013.08.032.10.1016/j.bios.2013.08.032Search in Google Scholar PubMed
Gao, Y., Li, Y., Zou, X., Huang, H., & Su, X. G. (2012). Highly sensitive and selective detection of biothiols using graphene oxide-based ”molecular beacon”-like fluorescent probe. Analytica Chimica Acta, 731, 68-74. DOI: 10.1016/j.aca.2012.04.020.10.1016/j.aca.2012.04.020Search in Google Scholar PubMed
Gormally, E., Vineis, P., Matullo, G., Veglia, F., Carboux, E., Le Roux, E., Peluso, M., Garte, S., Guarrera, S., Munnia, A., Airoldi, L., Autrup, H., Malaveille, C., Dunning, A., Overvad, K., Tjønneland, A., Lund, E., Clavel-Chapelon, F., Boeing, H., Trichopoulou, A., Palli, D., Krogh, V., Tumino, R., Panico, S., Bueno-de-Mesquita, H. B., Peeters, P. H., Pera, G., Martinez, C., Dorronsoro, M., Barricarte, A., Navarro, C., Ramón Quirós, J., Hallmans, G., Day, N. E., Key, T. J., Saracci, R., Kaaks, R., Riboli, E., & Hainaut, P. (2006). TP53 and KRAS2 mutations in plasma DNA of healthy subjects and subsequent cancer occurrence: a prospective study. Cancer Research, 66, 6871-6876. DOI: 10.1158/0008-5472.can-05-4556. 10.1158/0008-5472.CAN-05-4556Search in Google Scholar PubMed
Han, H. J., Zylstra, J., & Maye, M. M. (2011). Direct attachment of oligonucleotides to quantum dot interfaces. Chemistry of Materials, 23, 4975-4981. DOI: 10.1021/cm2021593.10.1021/cm2021593Search in Google Scholar
He, J. L., Wu, Z. S., Zhang, S. B., Shen, G. L., & Yu, R. Q. (2010). Fluorescence aptasensor based on competitivebinding for human neutrophil elastase detection. Talanta, 80, 1264-1268. DOI: 10.1016/j.talanta.2009.09.019.10.1016/j.talanta.2009.09.019Search in Google Scholar PubMed
He, X. X., Ni, X. Q., Wang, Y. H., Wang, K. M., & Jian, L. X. (2011). Electrochemical detection of nicotinamide adenine dinucleotide based on molecular beacon-like DNA and E. coli DNA ligase. Talanta, 83, 937-942. DOI: 10.1016/j.talanta.2010.10.051.10.1016/j.talanta.2010.10.051Search in Google Scholar
Hepel, M., & Stobiecka, M. (2011). Comparative kinetic model of fluorescence enhancement in selective binding of monochlorobimane to glutathione. Journal of Photochemistry and Photobiology A: Chemistry, 225, 72-80. DOI: 10.1016/j.jphotochem.2011.09.028.10.1016/j.jphotochem.2011.09.028Search in Google Scholar
Hepel, M., Stobiecka, M., Peachey, J., & Miller, J. (2012). Intervention of glutathione in pre-mutagenic catechol-mediated DNA damage in the presence of copper(II) ions. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 735, 1-11. DOI: 10.1016/j.mrfmmm.2012.05.005.10.1016/j.mrfmmm.2012.05.005Search in Google Scholar
Huang, J. H., Zheng, Q. B., Kim, J. K., & Li, Z. G. (2013). A molecular beacon and graphene oxide-based fluorescent biosensor for Cu2+ detection. Biosensors and Bioelectronics, 43, 379-383. DOI: 10.1016/j.bios.2012.12.056.10.1016/j.bios.2012.12.056Search in Google Scholar
Jo, S. M., Kim, Y.W., Jeong, Y. S., Oh, Y. H., Park, K. C., & Kim, H. S. (2013). Rapid detection of exon 2-deleted AIMP2 mutation as a potential biomarker for lung cancer by molecular beacons. Biosensors and Bioelectronics, 46, 142-149. DOI: 10.1016/j.bios.2013.02.037.10.1016/j.bios.2013.02.037Search in Google Scholar
Khandelwal, G., & Bhyravabhotla, J. (2010). A phenomenological model for predicting melting temperatures of DNA sequences. PLoS ONE, 5, e12433: 12431-12439. DOI: 10.1371/ journal.pone.0012433.Search in Google Scholar
Kihara, T., Yoshida, N., Kitagawa, T., Nakamura, C., Nakamura, N., & Miyake, J. (2010). Development of a novel method to detect intrinsic mRNA in a living cell by using a molecular beacon-immobilized nanoneedle. Biosensors and Bioelectronics, 26, 1449-1454. DOI: 10.1016/j.bios.2010.07. 079.Search in Google Scholar
Kim, M. Y., Kim, J., & Hah, S. S. (2012). Poly(A)-targeting molecular beacons: Fluorescence resonance energy transferbased in vitro quantitation and time-dependent imaging in live cells. Analytical Biochemistry, 429, 92-98. DOI: 10.1016/j.ab.2012.07.010.10.1016/j.ab.2012.07.010Search in Google Scholar
Kostrikis, L. G., Tyagi, S., Mhlanga, M. M., Ho, D. D., & Kramer, F. R. (1998). Molecular beacons. Spectral genotyping of human alleles. Science, 279, 1228-1229. DOI: 10.1126/science.279.5354.1228.10.1126/science.279.5354.1228Search in Google Scholar
Li, J. J., Fang, X. H., Schuster, S. M., & Tan, W. H. (2000a). Molecular beacons: A novel approach to detect protein-DNA interactions. Angewandte Chemie International Edition, 39, 1049-1052. DOI: 10.1002/(sici)1521-3773(20000317)39:6<1049::aid-anie1049>3.0.co;2-2.10.1002/(SICI)1521-3773(20000317)39:6<1049::AID-ANIE1049>3.0.CO;2-2Search in Google Scholar
Li, J. J., Geyer, R., & Tan, W. (2000b). Using molcular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA. Nucleic Acids Research, 28, E52.10.1093/nar/28.11.e52Search in Google Scholar
Li, J., Yan, H. F., Wang, K., Tan, W. H., & Zhou, X. W. (2007). Hairpin fluorescence DNA probe for real-time monitoring of DNA methylation. Analytical Chemistry, 79, 1050-1056. DOI: 10.1021/ac061694i.10.1021/ac061694iSearch in Google Scholar
Li, J., Cao, Z. C., Tang, Z.W.,Wang, K., & Tan, W. H. (2008a). Molecular beacons for protein-DNA interaction studies. In A. Marx, & O. Seitz (Eds.), Molecular beacons: Signalling nucleic acid probes, methods, and protocols (Vol. 429, pp. 209-224). Totowa, NJ, USA: Humana Press. DOI: 10.1007/978-1-60327-040-3 15. Li, X. M., Song, C., Zhao, M. P., & Li, Y. Z. (2008b). Continuous monitoring of restriction endonuclease cleavage activity by universal molecular beacon light quenching coupled with real-time polymerase chain reaction. Analytical Biochemistry, 381, 1-7. DOI: 10.1016/j.ab.2008.06.027.10.1016/j.ab.2008.06.027Search in Google Scholar PubMed
Li, N., & Wong, P. K. (2010). Transfection of molecular beacons in microchannels for single cell gene expression analysis. Bioanalysis, 2, 1689-1699. DOI: 10.4155/bio.10.116.10.4155/bio.10.116Search in Google Scholar PubMed
Li, D., Song, S., & Fan, C. H. (2010). Target-responsive structural switching for nucleic acid-based sensors. Accounts of Chemical Research, 43, 631-641. DOI: 10.1021/ar900245u.10.1021/ar900245uSearch in Google Scholar PubMed
Li, F., Du, Z. F., Yang, L. M., & Tang, B. (2013a). Selective and sensitive turn-on detection of adenosine triphosphate and thrombin based on bifunctional fluorescent oligonucleotide probe. Biosensors and Bioelectronics, 41, 907-910. DOI: 10.1016/j.bios.2012.10.007.10.1016/j.bios.2012.10.007Search in Google Scholar PubMed
Li, M., Zhou, X. J., Guo, S. W., & Wu, N. Q. (2013b). Detection of lead (II) with a ”turn on” fluorescent biosensor based on energy transfer from CdSe/ZnS quantum dots to graphene oxide. Biosensors and Bioelectronics, 43, 69-74. DOI: 10.1016/j.bios.2012.11.039.10.1016/j.bios.2012.11.039Search in Google Scholar PubMed
Li, Z., Wang, Y. J., Liu, Y., Zeng, Y. Y., Huang, A. M., Peng, N. C., Liu, X. L., & Liu, J. F. (2013c). A novel aptasensor for the ultra-sensitive detection of adenosine triphosphate via aptamer/quantum dot based resonance energy transfer. Analyst, 138, 4732-4736. DOI: 10.1039/c3an00449j.10.1039/c3an00449jSearch in Google Scholar PubMed
Li, B., Li, Z. L., Situ, B., Dai, Z., Liu, Q. L., Wang, Q., Gu, D., & Zheng, L. (2014). Sensitive HIV-1 detection in ahomogeneous solution based on an electrochemical molecular beacon coupled with a nafion-graphene composite film modified screen-printed carbon electrode. Biosensors and Bioelectronics, 52, 330-336. DOI: 10.1016/j.bios.2013.09.016.10.1016/j.bios.2013.09.016Search in Google Scholar PubMed
Liang, Y., Zhang, Z. P., Wei, H. P., Hu, Q. X., Deng, J. Y., Guo, D., Cui, Z. Q., & Zhang, X. E. (2011). Aptamer beacons for visualization of endogenous protein HIV-1 reverse transcriptase in living cells. Biosensors and Bioelectronics, 28, 270-276. DOI: 10.1016/j.bios.2011.07.031.10.1016/j.bios.2011.07.031Search in Google Scholar PubMed
Liu, L. F., Tang, Z. W., Wang, K. M., Tan, W. H., Li, J., Guo, Q. P., Meng, X. X., & Ma, C. B. (2005). Using molecular beacon to monitor activity of E. coli DNA ligase. Analyst, 130, 350-357. DOI: 10.1039/b413959c.10.1039/b413959cSearch in Google Scholar PubMed
Liu, C., Zeng, G. M., Tang, L., Zhang, Y., Li, Y. P., Liu, Y. Y., Li, Z., Wu, M. S., & Luo, J. (2011). Electrochemical detection of Pseudomonas aeruginosa 16S rRNA using a biosensor based on immobilized stem-loop structured probe. Enzyme and Microbial Technology, 49, 266-271. DOI: 10.1016/j.enzmictec.2011.06.011.10.1016/j.enzmictec.2011.06.011Search in Google Scholar PubMed
Liu, X. J., Chen, M. Q., Hou, T., Wang, X. Z., Liu, S. F., & Li, F. (2013). A novel electrochemical biosensor for label-free detection of uracil DNA glycosylase activity based on enzyme-catalyzed removal of uracil bases inducing strand release. Electrochimica Acta, 113, 514-518. DOI: 10.1016/j.electacta.2013.09.131.10.1016/j.electacta.2013.09.131Search in Google Scholar
Liu, J. C., Guan, Z., Lv, Z. Z., Jiang, X. L., Yang, S. M., & Chen, A. L. (2014). Improving sensitivity of gold nanoparticle based fluorescence quenching and colorimetric aptasensor by using water resuspended gold nanoparticle. Biosensors and Bioelectronics, 52, 265-270. DOI: 10.1016/j.bios.2013.08.059.10.1016/j.bios.2013.08.059Search in Google Scholar PubMed
Lo, P. C., Chen, J., Stefflova, K., Warren, M. S., Navab, R., Bandarchi, B., Mullins, S., Tsao, M., Cheng, J. D., & Zheng, G. (2009). Photodynamic molecular beacon triggered by fibroblast activation protein on cancer-associated fibroblasts for diagnosis and treatment of epithelial cancers. Journal of Medicinal Chemistry, 52, 358-368. DOI: 10.1021/jm801052f.10.1021/jm801052fSearch in Google Scholar PubMed PubMed Central
Lu, Y., Li, X. C., Zhang, L., Yu, P., Su, L., & Mao, L. Q. (2008). Aptamer-based electrochemical sensors with aptamer-complementary DNA oigonucleotides as probe. Analytical Chemistry, 80, 1883-1890. DOI: 10.1021/ac7018014. 10.1021/ac7018014Search in Google Scholar PubMed
Lubin, A. A., & Plaxco, K. W. (2010). Folding-based electrochemical biosensors: The case for responsive nucleic acid architectures. Accounts of Chemical Research, 43, 496-505. DOI: 10.1021/ar900165x.10.1021/ar900165xSearch in Google Scholar PubMed PubMed Central
Ma, C. B., Tang, Z. W., Huo, X. Q., Yang, X. H., Li, W., & Tan, W. H. (2008). Real-time monitoring of double-stranded DNA cleavage using molecular beacons. Talanta, 76, 458-461. DOI: 10.1016/j.talanta.2008.03.038.10.1016/j.talanta.2008.03.038Search in Google Scholar PubMed
Ma, C. B., & Yeung, E. S. (2010). Highly sensitive detection of DNA phosphorylation by counting single nanoparticles. Analytical and Bioanalytical Chemistry, 397, 2279-2284. DOI: 10.1007/s00216-010-3801-x.10.1007/s00216-010-3801-xSearch in Google Scholar PubMed
Ma, C. B. (2012). Highly sensitive detection of alkaline phosphatase using molecular beacon probes based on enzymatic polymerization. Molecular and Cellular Probes, 26, 113-115. DOI: 10.1016/j.mcp.2012.03.005.10.1016/j.mcp.2012.03.005Search in Google Scholar PubMed
Majlessi, M., Nelson, N. C., & Becker, M. M. (1998). Advantages of 2’-O-methyl oligoribonucleotide probes for detecting RNA targets. Nucleic Acids Research, 26, 2224-2229. DOI: 10.1093/nar/26.9.2224.10.1093/nar/26.9.2224Search in Google Scholar PubMed PubMed Central
Maxwell, D. J., Taylor, J. R., & Nie, S. (2002). Self-assembled nanoparticle probes for recognition and detection of biomolecules. Journal of the American Chemical Society, 124, 9606-9612. DOI: 10.1021/ja025814p.10.1021/ja025814pSearch in Google Scholar PubMed
Medley, C. D., Drake, T. J., Tomasini, J. M., Rogers, R. J., & Tan, W. H. (2005). Simultaneous monitoring of the expression of multiple genes inside of single breast carcinoma cells. Analytical Chemistry, 77, 4713-4718. DOI: 10.1021/ac050881y.10.1021/ac050881ySearch in Google Scholar PubMed
Nguyen, B., & Wilson, W. D. (2009). The effects of hairpin loops on ligand-DNA interactions. The Journal of Physical Chemistry B, 113, 14329-14335. DOI: 10.1021/jp904830m.10.1021/jp904830mSearch in Google Scholar PubMed PubMed Central
Pande, V., & Nilsson, L. (2008). Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Acids Research, 36, 1508-1516. DOI: 10.1093/nar/gkm1182.10.1093/nar/gkm1182Search in Google Scholar PubMed PubMed Central
Peng, X. H., Cao, Z. H., Xia, J. T., Carlson, G. W., Lewis, M. M., Wood, W. C., & Yang, L. (2005). Real-time detection of gene expression in cancer cells using molecular beacon imaging: New strategies for cancer research. Cancer Research, 65, 1909-1917. DOI: 10.1158/0008-5472.can-04-3196.10.1158/0008-5472.CAN-04-3196Search in Google Scholar PubMed
Petersen, K., Vogel, U., Rockenbauer, E., Nielsen, K. V., Kølvraa, S., Bolund, L., & Nexø, B. (2004). Short PNA molecular beacons for real-time PCR allelic discrimination of single nucleotide polymorphisms. Molecular and Cellular Probes, 18, 117-122. DOI: 10.1016/j.mcp.2003.10.003.10.1016/j.mcp.2003.10.003Search in Google Scholar PubMed
Piao, Y. X., Liu, F., & Seo, T. S. (2012). A novel molecular beacon bearing a graphite nanoparticle as a nanoquencher for in situ mRNA detection in cancer cells. ACS Applied Materials & Interfaces, 4, 6785-6789. DOI: 10.1021/am301976r.10.1021/am301976rSearch in Google Scholar PubMed
Piatek, A. S., Tyagi, S., Pol, A. C., Telenti, A., Miller, L. P., Kramer, F. R., & Alland, D. (1998). Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nature Biotechnology, 16, 359-363. DOI: 10.1038/nbt0498-359.10.1038/nbt0498-359Search in Google Scholar PubMed
Rai, V., Nyine, Y. T., Hapuarachchi, H. C., Yap, H., Ng, L. C., & Toh, C. S. (2012). Electrochemically amplified molecular beacon biosensor for ultrasensitive DNA sequence-specific detection of Legionella sp. Biosensors and Bioelectronics, 32, 133-140. DOI: 10.1016/j.bios.2011.11.046.10.1016/j.bios.2011.11.046Search in Google Scholar PubMed
Riccelli, P. V., Mandell, K. E., & Benight, A. S. (2002). Melting studies of dangling-ended DNA hairpins: Effects of end length, loop sequence and biotinylation of loop bases. Nucleic Acids Research, 30, 4088-4093. DOI: 10.1093/nar/gkf514.10.1093/nar/gkf514Search in Google Scholar PubMed PubMed Central
Rosa, J., Conde, J., de la Fuente, J., Lima, J. C., & Baptista, P. V. (2012). Gold-nanobeacons for real-time monitoring of RNA synthesis. Biosensors and Bioelectronics, 36, 161-167. DOI: 10.1016/j.bios.2012.04.006. 10.1016/j.bios.2012.04.006Search in Google Scholar PubMed
SantaLucia, J., Jr. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences of the United States of America, 95, 1460-1465. DOI: 10.1073/pnas.95.4.1460.10.1073/pnas.95.4.1460Search in Google Scholar PubMed PubMed Central
Seitz, O. (2000). Solid-phase synthesis of doubly labeled peptide nucleic acids as probes for the real-time detection of hybridization. Angewandte Chemie International Edition, 39, 3249-3252. DOI: 10.1002/1521-3773(20000915)39:18<3249:: aid-anie3249>3.0.co;2-m.Search in Google Scholar
Sokol, D. L., Zhang, X. L., Lu, P. Z., & Gewitz, A. M. (1998). Real time detection of DNA RNA hybridization in living cells. Proceedings of the National Academy of Sciences of the United States of America, 95, 11538-11543. DOI: 10.1073/pnas.95.20.11538.10.1073/pnas.95.20.11538Search in Google Scholar PubMed PubMed Central
Stobiecka, M., Deeb, J., & Hepel, M. (2009). Molecularlytemplated polymer matrix films for biorecognition processes: sensors for evaluating oxidative stress and redox buffering capacity. ECS Transactions, 19, 15-32. DOI: 10.1149/1.3253474.10.1149/1.3253474Search in Google Scholar
Stobiecka, M., Coopersmith, K., & Hepel, M. (2010a). Resonance elastic light scattering (RELS) spectroscopy of fast non-langmuirian ligand-exchange in glutathione-induced gold nanoparticle assembly. Journal of Colloid and Interface Science, 350, 168-177. DOI: 10.1016/j.jcis.2010.06.010.10.1016/j.jcis.2010.06.010Search in Google Scholar PubMed
Stobiecka, M., Deeb, J., & Hepel, M. (2010b). Ligand exchange effects in gold nanoparticle assembly induced by oxidative stress biomarkers: Homocysteine and cysteine. Biophysical Chemistry, 146, 98-107. DOI: 10.1016/j.bpc.2009.11.001.10.1016/j.bpc.2009.11.001Search in Google Scholar PubMed
Stobiecka, M., & Hepel, M. (2011a). Effect of buried potential barrier in label-less electrochemical immunodetection of glutathione and glutathione-capped gold nanoparticles. Biosensors and Bioelectronics, 26, 3524-3530. DOI: 10.1016/j.bios.2011.01.038.10.1016/j.bios.2011.01.038Search in Google Scholar PubMed
Stobiecka, M., & Hepel, M. (2011b). Multimodal coupling of optical transitions and plasmonic oscillations in rhodamine B modified gold nanoparticles. Physical Chemistry Chemical Physics, 13, 1131-1139. DOI: 10.1039/c0cp00553c.10.1039/C0CP00553CSearch in Google Scholar
Stobiecka, M., Molinero, A. A., ChałlTyagi, S., & Kramer, F. R. (1996). Molecular beacons: Probes that fluoresce upon hybridization. Nature Biotechnology, 14, 303-308. DOI: 10.1038/nbt0396-303.10.1038/nbt0396-303Search in Google Scholar PubMed
Stobiecka, M. (2014). Novel plasmonic field-enhanced nanoassay for trace detection of proteins. Biosensors and Bioelectronics, 55, 379-385. DOI: 10.1016/j.bios.2013.11.073.10.1016/j.bios.2013.11.073Search in Google Scholar PubMed
Swathi, R. S., & Sebastian, K. L. (2008). Resonance energy transfer from a dye molecule to graphene. Journal of Chemical Physics, 129, 054703. DOI: 10.1063/1.2956498.10.1063/1.2956498Search in Google Scholar PubMed
Swathi, R. S., & Sebastian, K. L. (2009). Long range resonance energy transfer from a dye molecule to graphene has (distance)−4 dependence. Journal of Chemical Physics, 130, 086101. DOI: 10.1063/1.3077292.10.1063/1.3077292Search in Google Scholar PubMed
Tan, W. B., Wang, K., & Drake, T. J. (2004). Molecular beacons. Current Opinion in Chemical Biology, 8, 547-553.10.1016/j.cbpa.2004.08.010Search in Google Scholar PubMed
Tang, Z.W.,Wang, K. M.,Tan,W.H., Li, J., Liu, L. F.,Guo,Q. P., Meng, X. X., Ma, C. B., & Huang, S. S. (2003). Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons. Nucleic Acids Research, 31, e148. DOI: 10.1093/nar/gng146.10.1093/nar/gng146Search in Google Scholar PubMed PubMed Central
Tang, Z. W., Wang, K., Tan, W. H., Ma, C. B., Li, J., Liu, L. F., Guo, Q. P., & Meng, X. X. (2005). Real-time investigation of nucleic acids phosphorylation process using molecular beacons. Nucleic Acids Research, 33, e97. DOI: 10.1093/nar/gni096. 10.1093/nar/gni096Search in Google Scholar PubMed PubMed Central
Vicens, M. C., Sen, A., Vanderlaan, A., Drake, T. J., & Tan, W. H. (2005). Investigation of molecular beacon aptamerbased bioassay for platelet-derived growth factor detection. Chembiochem, 6, 900-907. DOI: 10.1002/cbic.200400308.10.1002/cbic.200400308Search in Google Scholar PubMed
Vogelstein, B., & Kinzler, K. W. (1999). Digital PCR. Proceedings of the National Academy of Sciences of the United States of America, 96, 9236-9241. DOI: 10.1073/pnas.96.16. 9236.Search in Google Scholar
Wang, K. M., Tang, Z. W., Yang, C. Y. J., Kim, Y. M., Fang, X. H., Li,W., Wu, Y.R.,Medley, C.D.,Cao, Z.H., Li, J., Colon, P., Lin, H., & Tan, W. H. (2009). Molecular engineering of DNA: Molecular beacons. Angewandte Chemie International Edition, 48, 856-870. DOI: 10.1002/anie.200800370.10.1002/anie.200800370Search in Google Scholar PubMed PubMed Central
Wang, X. Y., He, P. G., & Fang, Y. Z. (2010). A solidstate electrochemiluminescence biosensing switch for detection of DNA hybridization based on ferrocene-labeled molecular beacon. Journal of Luminescence, 130, 1481-1484. DOI: 10.1016/j.jlumin.2010.03.016.10.1016/j.jlumin.2010.03.016Search in Google Scholar
Wang, D. Z., Chen, G. J.,Wang, H. M., Tang, W., Pan,W., Li, N., & Liu, F. (2013a). A reusable quartz crystal microbalance biosensor for highly specific detection of single-base DNA mutation. Biosensors and Bioelectronics, 48, 276-280. DOI: 10.1016/j.bios.2013.04.035.10.1016/j.bios.2013.04.035Search in Google Scholar PubMed
Wang, D. C., Hu, L. H., Zhou, H. M., Abdel-Halim, E. S., Zhu, J. J. (2013b). Molecular beacon structure mediated rolling circle amplification for ultrasensitive electrochemical detection of microRNA based on quantum dots tagging. Electrochemistry Communications, 33, 80-83. DOI: 10.1016/j.elecom.2013.04.030.10.1016/j.elecom.2013.04.030Search in Google Scholar
Wood, R. J., McKelvie, J. C., Maynard-Smith, M. D., & Roach, P. L. (2010). A real-time assay for CpG-specific cytosine-C5 methyltransferase activity. Nucleic Acids Research, 38, e107. DOI: 10.1093/nar/gkq047.10.1093/nar/gkq047Search in Google Scholar PubMed PubMed Central
Wu, Y. R., Yang, C. Y. J., Moroz, L. L., & Tan, W. H. (2008). Nucleic acid beacons for long-term real-time intracellular monitoring. Analytical Chemistry, 80, 3025-3028. DOI: 10.1021/ac702637w.10.1021/ac702637wSearch in Google Scholar PubMed PubMed Central
Xiao, Y., Rowe, A. A., & Plaxco, K. W. (2007). Electrochemical detection of parts-per-billion Lead via an electrode-bound DNAzyme assembly. Journal of the American Chemical Society, 129, 262-263. DOI: 10.1021/ja067278x.10.1021/ja067278xSearch in Google Scholar PubMed
Xu, H., & Hepel, M. (2011). “Molecular beacon”-based fluorescent assay for selective detection of glutathione and cysteine. Analytical Chemistry, 83, 813-819. DOI: 10.1021/ac102850y.10.1021/ac102850ySearch in Google Scholar PubMed
Xue, J. P., Shan, L. L., Chen, H. Y., Li, Y., Zhu, H. Y., Deng, D. W., Qian, Z. Y., Achilefu, S., & Gu, Y. Q. (2013). Visual detection of STAT5B gene expression in living cell using the hairpin DNA modified gold nanoparticle beacon. Biosensors and Bioelectronics, 41, 71-77. DOI: 10.1016/j.bios.2012.06.062.10.1016/j.bios.2012.06.062Search in Google Scholar PubMed
Ye, Y., & Stivers, J. T. (2010). Fluorescence-based highthroughput assay for human DNA (cytosine-5)-methyltransferase 1. Analytical Biochemistry, 401, 168-172. DOI: 10.1016/j.ab.2010.02.032.10.1016/j.ab.2010.02.032Search in Google Scholar PubMed PubMed Central
Yi, J. W., Park, J. S., Singh, N. J., Lee, J., II., Kim, K. S., & Kim, B. H. (2011). Quencher-free molecular beacon: Enhancement of the signal-to-background ratio with graphene oxide. Bioorganic & Medicinal Chemistry Letters, 21, 704-706. DOI: 10.1016/j.bmcl.2010.12.004.10.1016/j.bmcl.2010.12.004Search in Google Scholar PubMed
Yin, H. S., Zhou, Y. L., Zhang, H. X., Meng, X. M., & Ai, S. Y. (2012). Electrochemical determination of microRNA-21 based on graphene, LNA integrated molecular beacon, AuNPs and biotin multifunctional bio bar codes and enzymatic assay system. Biosensors and Bioelectronics, 33, 247-253. DOI: 10.1016/j.bios.2012.01.014. 10.1016/j.bios.2012.01.014Search in Google Scholar PubMed
Zeng, X. D., Zhang, X. L., Yang, W., Jia, H. Y., & Li, Y. M. (2012). Fluorescence detection of adenosine triphosphate through an aptamer-molecular beacon multiple probe. Analytical Biochemistry, 424, 8-11. DOI: 10.1016/j.ab.2012.01. 021.Search in Google Scholar
Zhang, M., Yin, B. C., Tan, W. H., & Ye, B. C. (2011). A versatile graphene-based fluorescence “on/off” switch for multiplex detection of various targets. Biosensors and Bioelectronics, 26, 3260-3265. DOI: 10.1016/j.bios.2010.12.037.10.1016/j.bios.2010.12.037Search in Google Scholar PubMed
Zhang, J. Q., Wang, Y. S., Xue, J. H., He, Y., Yang, H. X., Liang, J., Shi, L. F., & Xiao, X. L. (2012). A gold nanoparticles-modified aptamer beacon for urinary adenosine detection based on structure-switching/fluorescence- “turning on” mechanism. Journal of Pharmaceutical and Biomedical Analysis, 70, 362-368. DOI: 10.1016/j.jpba.2012. 05.032.Search in Google Scholar
Zhang, D. W., Zhao, M. M., He, H. Q., & Guo, S. X. (2013a). Real-time monitoring of disintegration activity of catalytic core domain of HIV-1 integrase using molecular beacon. Analytical Biochemistry, 440, 120-122. DOI: 10.1016/j.ab.2013.05.032.10.1016/j.ab.2013.05.032Search in Google Scholar PubMed
Zhang, J., Sun, Y., Xu, B., Zhang, H., Gao, Y., Zhang, H. Q., & Song, D. Q. (2013b). A novel surface plasmon resonance biosensor based on graphene oxide decorated with gold nanorod-antibody conjugates for determination of transferrin. Biosensors and Bioelectronics, 45, 230-236. DOI: 10.1016/j.bios.2013.02.008.upa, A., & Hepel, M. (2012). Mercury/homocysteine ligation-induced ON/OFFswitching of a T-T mismatch-based oligonucleotide molecular beacon. Analytical Chemistry, 84, 4970-4978. DOI: 10.1021/ac300632u.10.1021/ac300632uSearch in Google Scholar PubMed
Zhang, K., Wang, K., Xie, M. H., Zhu, X., Xu, L., Yang, R. L., Huang, B., & Zhu, X. L. (2014). DNA-templated silver nanoclusters based label-free fluorescent molecular beacon for the detection of adenosine deaminase. Biosensors and Bioelectronics, 52, 124-128. DOI: 10.1016/j.bios.2013.08.049.10.1016/j.bios.2013.08.049Search in Google Scholar PubMed
Zheng, Y. J., Huang, Z. J., Chen, J., Wang, K., Liu, A. L., Lin, X. H., & Zheng, W. (2013). Enzyme-based E-RNA sensor array with a hairpin probe: Specific detection of gene mutation. Sensors and Actuators B: Chemical, 181, 227-233. DOI: 10.1016/j.snb.2013.01.051.10.1016/j.snb.2013.01.051Search in Google Scholar
Zhou, Z. X., Du, Y., Zhang, L. B., & Dong, S. J. (2012a). A label-free, G-quadruplex DNAzyme-based fluorescent probe for signal-amplified DNA detection and turn-on assay of endonuclease. Biosensors and Bioelectronics, 34, 100-105. DOI: 10.1016/j.bios.2012.01.024.10.1016/j.bios.2012.01.024Search in Google Scholar PubMed
Zhou, J., Lu, Q., Tong, Y., Wei, W., & Liu, S. Q. (2012b). Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide. Talanta, 99, 625-630. DOI: 10.1016/j.talanta.2012.06.049. DOI: 10.1016/j.cbpa.2004.08.010.10.1016/j.talanta.2012.06.049Search in Google Scholar PubMed
© 2015 Institute of Chemistry, Slovak Academy of Sciences
