Real-time monitoring of DNA hybridization and melting processes using a fiber optic sensor

Nanotechnology

Volumn 23, Issue 6, 2012, Pages

  Delport, Filip ^a   Pollet, Jeroen ^a   Janssen, Kris ^a   Verbruggen, Bert ^a   Knez, Karel ^a   Spasic, Dragana ^a   Lammertyn, Jeroen ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

DNA HYBRIDIZATION; DNA MELTING; DNA PROBE; DNA STRANDS; HIGH RESOLUTION; HYBRIDIZATION CONDITIONS; MELTING PROCESS; NANOBEADS; REAL TIME MONITORING; SENSOR PLATFORM; SENSOR SURFACES; SIGNAL AMPLIFICATIONS; SILICA NANOPARTICLES;

DNA; MELTING; METAL MELTING; NANOPARTICLES; PLASMONS; POLYMERASE CHAIN REACTION; SENSORS; SIGNAL PROCESSING; SILICA;

SURFACE PLASMON RESONANCE;

DNA; NANOPARTICLE; SILICON DIOXIDE;

ARTICLE; CHEMISTRY; DNA DENATURATION; DNA PROBE; EQUIPMENT DESIGN; INSTRUMENTATION; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; SURFACE PLASMON RESONANCE;

BASE SEQUENCE; DNA; DNA PROBES; EQUIPMENT DESIGN; NANOPARTICLES; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; SILICON DIOXIDE; SURFACE PLASMON RESONANCE;

EID: 84855921871     PISSN: 09574484     EISSN: 13616528     Source Type: Journal    
DOI: 10.1088/0957-4484/23/6/065503     Document Type: Article

References (39)

1. Ellington A D and Szostak J W 2002 Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures Nature 355 8502
2. Jhaveri S, Rajendran M and Ellington A D 2000 In vitro selection of signaling aptamers Nature Biotechnol. 18 12937
3. Dillenback L M, Goodrich G P and Keating C D 2006 Temperature-programmed assembly of DNA : Au nanoparticle bioconjugates Nano Lett. 6 1623 (Pubitemid 43166096)
4. Jakobsen U, Simonsen A C and Vogel S 2008 DNA-controlled assembly of soft nanoparticles J. Am. Chem. Soc. 130 104627
5. Liu S H, Zhang Z H, Wang Y B, Wang F K and Han M Y 2005 Surface-functionalized silica-coated gold nanoparticles and their bioapplications Talanta 67 45661
6. Hurst S J, Hill H D and Mirkin C A 2008 Three-dimensional hybridization with polyvalent DNA-gold nanoparticle conjugates J. Am. Chem. Soc. 130 12192200
7. Zhao W A, Chiuman W, Lam J C F, McManus S A, Chen W, Cui Y G, Pelton R, Brook M A and Li Y F 2008 DNA aptamer folding on gold nanoparticies: from colloid chemistry to biosensors J. Am. Chem. Soc. 130 36108 (Pubitemid 351456065)
8. Wang F, Tan W B, Zhang Y, Fan X P and Wang M Q 2006 Luminescent nanomaterials for biological labelling Nanotechnology 17 R113
9. Wang L, Zhao W J and Tan W H 2008 Bioconjugated silica nanoparticles: development and applications Nano Res. 1 99115
10. Zhao X J, Tapec-Dytioco R and Tan W H 2003 Ultrasensitive DNA detection using highly fluorescent bioconjugated nanoparticles J. Am. Chem. Soc. 125 114745 (Pubitemid 37210079)
11. Wang Y Y, Wang Y S and Liu B 2008 Fluorescent detection of ATP based on signaling DNA aptamer attached silica nanoparticles Nanotechnology 19 415605
12. Huang Y W, Huang T H M and Wang L S 2010 Profiling DNA methylomes from microarray to genome-scale sequencing Technol. Cancer Res. Treat. 9 13947
13. von Nickisch-Rosenegk M, Marschan X, Andresen D, Abraham A, Heise C and Bier F F 2005 On-chip PCR amplification of very long templates using immobilized primers on glassy surfaces Biosens. Bioelectron. 20 14918 (Pubitemid 40051236)
14. OBrien M J, Brueck S R J, Perez-Luna V H, Tender L M and Lopez G P 1999 SPR biosensors: simultaneously removing thermal and bulk-composition effects Biosens. Bioelectron. 14 14554 (Pubitemid 29089096)
15. Piliarik M, Parova L and Homola J 2009 High-throughput SPR sensor for food safety Biosens. Bioelectron. 24 1399404
16. Wang J L, Munir A, Li Z H and Zhou H S 2009 Aptamer-Au NPs conjugates-enhanced SPR sensing for the ultrasensitive sandwich immunoassay Biosens. Bioelectron. 25 1249
17. Fixman M and Freire J J 1977 Theory of DNA melting curves Biopolymers 16 2693704 (Pubitemid 8255435)
18. Moreira C S, Lima A M N, Neff H and Thirstrup C 2008 Temperature- dependent sensitivity of surface plasmon resonance sensors at the goldwater interface Sensors Actuators B 134 85462
19. Pollet J, Janssen K P F, Knez K and Lammertyn J 2011 Real-time monitoring of solid-phase PCR using fiber-optic SPR Small 7 10036
20. Chen Y and Lu Z H 2007 Dye sensitized luminescent europium nanoparticles and its time-resolved fluorometric assay for DNA Anal. Chim. Acta 587 1806 (Pubitemid 46356287)
21. Meng F H, Engbers G H M and Feijen J 2004 Polyethylene glycol-grafted polystyrene particles J. Biomed. Mater. Res. A 70A 4958 (Pubitemid 38849812)
22. Delport F, Deres A, Hotta J, Pollet J, Verbruggen B, Sels B, Hofkens J and Lammertyn J 2010 Improved method for counting DNA molecules on biofunctionalized nanoparticles Langmuir 26 15947
23. Pollet J, Delport F, Janssen K P F, Jans K, Maes G, Pfeiffer H, Wevers M and Lammertyn J 2009 Fiber optic SPR biosensing of DNA hybridization and DNA-protein interactions Biosens. Bioelectron. 25 8649
24. Stoeva S I, Lee J S, Smith J E, Rosen S T and Mirkin C A 2006 Multiplexed detection of protein cancer markers with biobarcoded nanoparticle probes J. Am. Chem. Soc. 128 83789
25. Hurst S J, Lytton-Jean A K R and Mirkin C A 2006 Maximizing DNA loading on a range of gold nanoparticle sizes Anal. Chem. 78 83138 (Pubitemid 44932099)
26. Wang R H, Tombelli S, Minunni M, Spiriti M M and Mascini M 2004 Immobilisation of DNA probes for the development of SPR-based sensing Biosens. Bioelectron. 20 96774 (Pubitemid 39458158)
27. Jans K, Bonroy K, De Palma R, Reekmans G, Jans H, Laureyn W, Smet M, Borghs G and Maes G 2008 Stability of mixed PEO-thiol SAMs for biosensing applications Langmuir 24 394954 (Pubitemid 351568996)
28. Templeton A C, Chen S W, Gross S M and Murray R W 1999 Water-soluble, isolable gold clusters protected by tiopronin and coenzyme A monolayers Langmuir 15 6676
29. Singh R and Lillard J W 2009 Nanoparticle-based targeted drug delivery Exp. Mol. Pathol. 86 21523
30. Jans H, Stakenborg T, Jans K, de Broek B V, Peeters S, Bonroy K, Lagae L, Borghs G and Maes G 2010 Increased stability of mercapto alkane functionalized Au nanoparticles towards DNA sensing Nanotechnology 21 285608
31. Lee C Y, Gong P, Harbers G M, Grainger D W, Castner D G and Gamble L J 2006 Surface coverage and structure of mixed DNA/alkylthiol monolayers on gold: characterization by XPS, NEXAFS, and fluorescence intensity measurements Anal. Chem. 78 331625
32. Weckx S, Carlon E, De Vuyst L and Van Hummelen P 2007 Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using Gibbs free energy in a nearest-neighbor model J. Phys. Chem. B 111 1358390 (Pubitemid 350275462)
33. Crothers D M and Zimm B H 1964 Theory of melting transition of synthetic polynucleotidesevaluation of stacking free energy J. Mol. Biol. 9 1
34. Bruno J G and Kiel J L 1999 In vitro selection of DNA aptamers to anthrax spores with electrochemiluminescence detection Biosens. Biolectron. 14 45764 (Pubitemid 29333570)
35. Neter J, Kutner M, Wasserman W and Nachtsheim C 1996 Applied Linear Statistical Models 4th edn (New York: McGraw Hill) p 1408
36. Fiche J B, Buhot A, Calemczuk R and Livache T 2007 Temperature effects on DNA chip experiments from surface plasmon resonance imaging: isotherms and melting curves Biophys. J. 92 93546 (Pubitemid 46203223)
37. Norambuena P A, Copeland J A, Krenkova P, Stambergova A and Macek M 2009 Diagnostic method validation: high resolution melting (HRM) of small amplicons genotyping for the most common variants in the MTHFR gene Clin. Biochem. 42 130816
38. Jin R C, Wu G S, Li Z, Mirkin C A and Schatz G C 2003 What controls the melting properties of DNA-linked gold nanoparticle assemblies? J. Am. Chem. Soc. 125 164354 (Pubitemid 36206246)
39. Mocanu D, Kolesnychenko A, Aarts S, Dejong A T, Pierik A, Coene W, Vossenaar E and Stapert H 2008 Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing Anal. Biochem. 380 8490