Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes

Nucleic Acids Research

Volumn 36, Issue 15, 2008, Pages

  Brewood, Greg P ^a   Rangineni, Yaswanth ^b   Fish, Daniel J ^a   Bhandiwad, Ashwini S ^a   Evans, David R ^c   Solanki, Raj ^b,d   Benight, Albert S ^a,d  

^a Portland Bioscience Inc   (United States)

^b Portland State University   (United States)

^c SHARP LABORATORIES OF AMERICA   (United States)

^d PORTLAND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA HAIRPIN; SINGLE STRANDED DNA; GOLD;

ARTICLE; CONTROLLED STUDY; COVALENT BOND; DIFFERENTIAL SCANNING CALORIMETRY; DNA DENATURATION; ELECTRIC CAPACITANCE; ELECTRICAL PARAMETERS; GOLD INTERDIGITATED MICROELECTRODE; IMPEDANCE; INTERMETHOD COMPARISON; MELTING POINT; MICROELECTRODE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SURFACE PROPERTY; TEMPERATURE DEPENDENCE; TEMPERATURE MEASUREMENT; THERMODYNAMICS; ULTRAVIOLET SPECTROSCOPY; CHEMISTRY; GENETIC PROCEDURES; OLIGONUCLEOTIDE PROBE; SOLUTION AND SOLUBILITY; TEMPERATURE; ULTRAVIOLET SPECTROPHOTOMETRY;

BIOSENSING TECHNIQUES; CALORIMETRY, DIFFERENTIAL SCANNING; DNA, SINGLE-STRANDED; GOLD; MICROELECTRODES; NUCLEIC ACID DENATURATION; OLIGONUCLEOTIDE PROBES; SOLUTIONS; SPECTROPHOTOMETRY, ULTRAVIOLET; TEMPERATURE; THERMODYNAMICS;

EID: 50849142843     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn436     Document Type: Article

References (28)

1. Finot,E., Bourillot,E., Meunier-Prest,R., Lacroute,Y., Legay,G., Cherkaoui-Malki,M., Latruffe,N., Siri,O., Braunstein,P. and Dereux,A. (2003) Performance of interdigitated nanoelectrodes for electrochemical DNA biosensor. Ultramicroscopy, 97, 441-449.
2. Meunier-Prest,R., Raveau,S., Finot,E., Legay,G., Cherkaoui-Malki, M. and Latruffe,N. (2003) Direct measurement of the melting temperature of supported DNA by electrochemical method. Nucleic Acids Res., 31 e150.
3. SantaLucia,J. Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
4. SantaLucia,J. Jr and Hicks,D. (2004) The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct., 33, 415-440.
5. Breslauer,K.J. (1994) Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. Methods Mol. Biol., 26, 347-372.
6. Breslauer,K.J., Frank,R., Blocker,H. and Marky,L.A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA, 83, 3746-3750.
7. Hall,T.S., Pancoska,P., Riccelli,P.V., Mandell,K. and Benight,A.S. (2001) Sequence context and thermodynamic stability of a single basepair mismatch in short deoxyoligonucleotide duplexes. J. Am. Chem. Soc. 123, 11811-11812.
8. Hillen,W., Goodman,T.C., Benight,A.S., Wartell,R.M. and Wells,R.D. (1981) High resolution experimental and theoretical thermal denaturation studies on small overlapping restriction fragments containing the Escherichia coli lactose genetic control region. J. Biol. Chem. 256, 2762-2766.
9. Marky,L.A. and Breslauer,K.J. (1982) Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules. Biopolymers 21, 2185-2194.
10. Marky,L.A. and Breslauer,K.J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers, 26, 1601-1620.
11. Owczarzy,R., Vallone,P.M., Gallo,F.J., Paner,T.M., Lane,M.J. and Benight,A.S. (1997) Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers, 44, 217-239.
12. Wartell,R.M. and Benight,A.S. (1985) Thermal denaturation of DNA molecules: A comparison of theory with experiment. Phys. Rep., 126, 67-107.
13. Dimitrov,R. and Zuker,M. (2004) Prediction of hybridization and melting for double-stranded nucleic acids. Biophys. J., 87, 215-226.
14. Herne,T.M. and Tarlov,M.J. (1997) Characterization of DNA Probes Immobilized on Gold Surfaces. J. Am. Chem. Soc., 119, 8916-8920.
15. Yang,M., McGovern,M.E. and Thompson,M. (1997) Genosensor technology and the detection of interfacial nucleic acid chemistry. Analytica Chimica Acta, 346, 259-275.
16. de-los-Santos-Álvarez,P.M., Jesus Lobo-Castanon,M., Miranda-Ordieres, A.J. and Tunon-Blanco,P. (2004) Current strategies for electrochemical detection of DNA with solid electrodes. Anal. Bioanal. Chem., 378, 104-118.
17. Fan,C., Plaxco,K.W. and Heeger,A.J. (2003) Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA. Proc. Natl Acad. Sci. USA, 100, 9135-9137.
18. Pividori,M.I., Merkoçi,A. and Alegret,S. (2000) Electrochemical genosensor design: Immobilisation of oliognucleotides onto transducer surfaces and detection methods. Biosens. Bioelectron., 15, 291-303.
19. Wang,J. (2002) Electrochemical nucleic acid biosensors. Anal. Chim. Acta., 469, 63-71.
20. Sturtevant,J.M. (1987) Biochemical applications of differential scanning calorimetry. Ann. Rev. Phys. Chem., 38, 463-488.
21. Vallone,P.M., Paner,T.M., Hilario,J., Lane,M.J., Faldasz,B.D. and Benight,A.S. (1999) Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability. Biopolymers, 50, 425-442.
22. Macdonald,J.R. (1992) Impedance Spectrscopy. Ann. Biomed. Eng., 20, 289-305.
23. Owczarzy,R. (1999) Predictions of short DNA duplex thermodynamics and evaluation of next nearest neighbor interactions. Ph.D. Thesis. University of Illinois at Chicago, Chicago.
24. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
25. Markham,N.R. and Zuker,M. (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res., 33, W577-W581.
26. Vallone,P.M. and Butler,J.M. (2004) AutoDimer: A screening tool for primer-dimer and hairpin structures. BioTechniques, 37, 226-231.
27. Halperin,A., Buhot,A. and Zhulina,E.B. (2006) On the hybridization isotherms of DNA microarrays: The Langmuir model and its extensions. J. Phys.: CondensMatter, 18, S463-S490.
28. Tyagi,S. and Kramer,F.R. (1996) Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.