Peptide nucleic acid modified magnetic beads for intercalator based electrochemical detection of DNA hybridization
Source abstract
Abstract
The specific binding of peptide nucleic acid (PNA) to its complementary DNA target is combined with magnetic separation to enable discrimination against single nucleotide polymorphisms (SNP). PNA probes with biotin label at 5'-end were attached to strepavidin coated superparamagnetic iron oxide beads. PNA modified beads were then challenged with non-complementary, SNP containing and perfect-match DNA targets. PNA probe showed no affinity towards non-complementary DNA. The non-specific binding of SNP containing DNA target was suppressed by the washing step of the beads by using sodium dodecylsulfate in blank buffer solution. Then, an electro-active intercalator, 7-dimethyl-amino-1,2-benzophenoxazinium salt (Meldola’s blue, MDB) was introduced to the beads. MDB intercalated between the double-helix of the hybrid molecules on the beads. After removing the excessive MDB, the beads were collected from the solution by immersing a biotin modified carbon paste electrode into the solution. Specific hybridization between PNA probe and DNA target was determined by monitoring the voltammetric peak of MDB. Numerous factors affecting the MDB signal, such as target DNA concentration, intercalator concentration and accumulation time were investigated. MDB signal indicated a detection limit of 2 pM in connection with 20 min hybridization time.
Source: openalex_inverted_index · Quality: baseline
Research context
OpenAlex topics: Advanced biosensing and bioanalysis techniques · DNA and Nucleic Acid Chemistry · Biosensors and Analytical Detection
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan
References (33)
Show source-provided references
1. M. Ramsey, DNA chips: state-of-the-art, Nat. Biotechnol. 16 (1998) 40–44.10.1038/nbt0198-40 ↗
2. T.G. Drummond, M.G. Hill, J. Barton, Electrochemical DNA biosensors, Nat. Biotechnol. 21 (2003) 1192–1199.10.1038/nbt873 ↗
3. J.J. Gooding, Electrochemical DNA hybridization biosensors, Electroanalysis 14 (2002) 1149–1156.10.1002/1521-4109(200209)14:17<1149::AID-ELAN1149>3.0.CO;2-8 ↗
4. E. Palecek, F. Jelen, Electrochemistry of nucleic acids and development of DNA sensors, Crit. Rev. Anal. Chem. 3 (2002) 261–270.10.1080/10408340290765560 ↗
5. J. Wang, Electrochemical nucleic acid biosensors, Anal. Chim. Acta 469 (2002) 63–71.10.1016/S0003-2670(01)01399-X ↗
6. K. Kerman, M. Kobayashi, E. Tamiya, Recent trends in the electrochemical DNA biosensor technology, Meas. Sci. Technol. 15 (2003) R1–R11.10.1088/0957-0233/15/2/R01 ↗
7. M. Egholm, O. Buchhardt, P.E. Nielsen, R.H. Berg, Peptide nucleic acids (PNA): oligonucleotide analogs with an achiral peptide backbone, J. Am. Chem. Soc. 114 (1992) 1895–1897.
8. J. Wang, DNA biosensors based on peptide nucleic acid (PNA) recognition layers, Biosens. Bioelectron. 13 (1998) 757–762.10.1016/S0956-5663(98)00039-6 ↗
9. P.E. Nielsen, M. Egholm, R.H. Berg, O. Buchhardt, Peptide nucleic acids (PNA): potential antisense and anti-gene agents, Anti-cancer Drug Des. 8 (1993) 53–63.
10. D.F. Doyle, D.A. Braasch, C.G. Simmons, B.A. Janowski, D.R. Corey, Inhibition of gene expression inside cells by peptide nucleic acids: effect of mRNA target sequence, mismatched bases, and PNA length, Biochemistry 40 (2001) 53–64.
11. M.R. Lewis, F. Jia, F. Gallazzi, Y. Wang, J. Zhang, N. Shenoy, S.Z. Lever, M. Hannink, Radiometal-labeled peptide–PNA conjugates for targeting bcl-2 expression: preparation, characterization, and in vitro mRNA binding, Bioconjugate. Chem. 13 (2002) 1176–1180.
12. S. Tomac, M. Sarkar, T. Ratilainen, P. Wittung, P.E. Nielsen, B. Nordén, A. Grälund, Ionic effects on the stability and conformation of peptide nucleic acid complexes, J. Am. Chem. Soc. 118 (1996) 5544–5552.10.1021/ja960495l ↗
13. M. Egholm, O. Buchardt, L. Christensen, C. Behrens, S.M. Freier, D.A. Driver, R.H. Berg, S.K. Kim, B. Norden, P.E. Nielsen, PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules, Nature 365 (1993) 490–492.10.1038/365566a0 ↗
14. T. Ratilainen, A. Holmén, E. Tuite, P.E. Nielsen, B. Nordén, Thermodynamics of sequence-specific binding of PNA to DNA, Biochemistry 39 (2000) 7781–7791.10.1021/bi000039g ↗
15. M. Tomschik, F. Jelen, L. Havran, L. Trnková, P.E. Nielsen, E. Palecek, Reduction and oxidation of peptide nucleic acid and DNA at mercury and carbon electrodes, J. Electroanal. Chem. 476 (1999) 71–80.10.1016/S0022-0728(99)00369-1 ↗
16. J. Wang, P.E. Nielsen, M. Jiang, X. Cai, J.R. Fernandes, D.H. Grant, M. Ozsoz, A. Beglieter, M. Mowat, Mismatch-sensitive hybridization detection by peptide nucleic acids immobilized on a quartz crystal microbalance, Anal. Chem. 69 (1997) 5200–5202.10.1021/ac9706077 ↗
17. J. Wang, G. Rivas, X. Cai, M. Chicharro, C. Parrado, N. Dontha, A. Begleiter, M. Mowat, E. Palecek, P.E. Nielsen, Detection of point mutation in the p53 gene using a peptide nucleic acid biosensor, Anal. Chim. Acta 344 (1997) 111–118.10.1016/S0003-2670(97)00039-1 ↗
18. J. Wang, E. Palecek, P.E. Nielsen, G. Rivas, X. Cai, H. Shiraishi, N. Dontha, D. Luo, P.A.M. Farias, Peptide nucleic acid probes for sequence-specific DNA biosensors, J. Am. Chem. Soc. 118 (1996) 7667–7670.10.1021/ja9608050 ↗
19. D. Ozkan, P. Kara, K. Kerman, B. Meric, A. Erdem, F. Jelen, P.E. Nielsen, M. Ozsoz, DNA and PNA sensing on mercury and carbon electrodes by using methylene blue as an electrochemical label, Bioelectrochemistry 58 (2002) 119–126.10.1016/S1567-5394(02)00131-7 ↗
20. P. Kara, K. Kerman, D. Ozkan, B. Meric, A. Erdem, P.E. Nielsen, M. Ozsoz, Label free and label based electrochemical detection of hybridization by using methylene blue and peptide nucleic acid probes at chitosan modified carbon paste electrodes, Electroanalysis 14 (2002) 1685–1690.10.1002/elan.200290011 ↗
21. D. Ozkan, A. Erdem, P. Kara, K. Kerman, J.J. Gooding, P.E. Nielsen, M. Ozsoz, Electrochemical detection of hybridization using peptide nucleic acids and methylene blue on self-assembled alkanethiol monolayer modified gold electrodes, Electrochem. Commun. 4 (2002) 796–802.10.1016/S1388-2481(02)00448-4 ↗
22. K. Kerman, D. Ozkan, P. Kara, B. Meric, A. Erdem, P.E. Nielsen, M. Ozsoz, Label-free bioelectronic detection of point mutation by using peptide nucleic acid probes and methylene blue, Electroanalysis 15 (2003) 667–670.10.1002/elan.200390084 ↗
23. H. Kuhn, V.V. Demidov, J.M. Couli, M.J. Fiandaca, B.D. Gildea, M.D. Frank-Kamenetskii, Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets, J. Am. Chem. Soc. 124 (2002) 1097–1103.10.1021/ja0041324 ↗
24. M. Komiyama, S. Ye, X. Liang, Y. Yamamoto, T. Tomita, J.M. Zhou, H. Aburatani, PNA for one-base differentiating protection of DNA from nuclease and its use for SNPs detection, J. Am. Chem. Soc. 25 (2003) 3758–3762.10.1021/ja0295220 ↗
25. F. Höök, A. Ray, B. Nordén, B. Kasemo, Characterization of PNA and DNA immobilization and subsequent hybridization with DNA using acoustic-shear-wave attenuation measurements, Langmuir 17 (2001) 8305–8312.10.1021/la0107704 ↗
26. M. Uhlin, E. Hornes, O. Olsvik, Advances in Biomagnetic Separations, Eaton Publishing, Natick, 1994.
27. J. Wang, A.N. Kawde, A. Erdem, M. Salazar, Magnetic bead-based label-free electrochemical detection of DNA hybridization, Analyst 126 (2001) 2020–2024.10.1039/b106343j ↗
28. J. Wang, D. Xu, A. Erdem, R. Polsky, M.A. Salazar, Genomagnetic electrochemical assays of DNA hybridization, Talanta 56 (2002) 931–938.10.1016/S0039-9140(01)00653-1 ↗
29. E. Palecek, M. Fojta, F. Jelen, New approaches in the development of DNA sensors: hybridization and electrochemical detection of DNA and RNA at two different surfaces, Bioelectrochemistry 56 (2002) 85–90.
30. G.D. Reid, D.J. Whittaker, M.A. Day, D.A. Turton, V. Kayser, J.M. Kelly, G.S. Beddard, Femtosecond electron-transfer reactions in mono- and polynucleotides and in DNA, J. Am. Chem. Soc. 124 (2002) 5518–5527.10.1021/ja0172363 ↗
31. C. Gurtner, C.F. Edman, R.E. Formosa, M.J. Heller, Photoelectrophoretic transport and hybridization of DNA oligonucleotides on unpatterned silicon substrates, J. Am. Chem. Soc. 122 (2000) 8589–8594.10.1021/ja000487b ↗
32. D. Ozkan, A. Erdem, P. Kara, K. Kerman, B. Meric, J. Hassmann, M. Ozsoz, Allele-specific genotype detection of Factor V Leiden mutation from polymerase chain reaction amplicons based on label-free electrochemical genosensor, Anal. Chem. 74 (2002) 5931–5936.10.1021/ac0257905 ↗
33. J. Sambrook, E.F. Fritsch, T. Maniatis, Molecular Cloning: A Laboratory Manual, second ed., Cold Spring Harbor, New York, 1989.