Label-free Microarray Imaging for Direct Detection of DNA Hybridization and Single-nucleotide Mismatches

Overview

Journal Biosens Bioelectron

Specialties Biochemistry
Biotechnology

Date 2010 Jan 26

PMID 20097056

Citations 14

Authors

Emre Ozkumur

Sunmin Ahn

Ayca Yalcin

Carlos A Lopez

Elif Cevik

Rostem J Irani

Charles DeLisi

Marcella Chiari

M Selim Unlu

Affiliations

Soon will be listed here.

Abstract

A novel method is proposed for direct detection of DNA hybridization on microarrays. Optical interferometry is used for label-free sensing of biomolecular accumulation on glass surfaces, enabling dynamic detection of interactions. Capabilities of the presented method are demonstrated by high-throughput sensing of solid-phase hybridization of oligonucleotides. Hybridization of surface immobilized probes with 20 base pair-long target oligonucleotides was detected by comparing the label-free microarray images taken before and after hybridization. Through dynamic data acquisition during denaturation by washing the sample with low ionic concentration buffer, melting of duplexes with a single-nucleotide mismatch was distinguished from perfectly matching duplexes with high confidence interval (>97%). The presented technique is simple, robust, and accurate, and eliminates the need of using labels or secondary reagents to monitor the oligonucleotide hybridization.

Citing Articles

Solid-Phase Optical Sensing Techniques for Sensitive Virus Detection.

Seymour E, Ekiz Kanik F, Diken Gur S, Bakhshpour-Yucel M, Araz A, Lortlar Unlu N Sensors (Basel). 2023; 23(11).

PMID: 37299745 PMC: 10255700. DOI: 10.3390/s23115018.

Highly-Sensitive, Label-Free Detection of Microorganisms and Viruses via Interferometric Reflectance Imaging Sensor.

Bakhshpour-Yucel M, Diken Gur S, Seymour E, Aslan M, Lortlar Unlu N, Unlu M Micromachines (Basel). 2023; 14(2).

PMID: 36837980 PMC: 9960798. DOI: 10.3390/mi14020281.

Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization.

Vanjur L, Carzaniga T, Casiraghi L, Zanchetta G, Damin F, Sola L Polymers (Basel). 2021; 13(22).

PMID: 34833198 PMC: 8625010. DOI: 10.3390/polym13223897.

Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects.

Gauglitz G Anal Bioanal Chem. 2020; 412(14):3317-3349.

PMID: 32313998 PMC: 7214504. DOI: 10.1007/s00216-020-02581-0.

Label-free tomography of living cellular nanoarchitecture using hyperspectral self-interference microscopy.

Fu R, Su Y, Wang R, Lin X, Jiang K, Jin X Biomed Opt Express. 2019; 10(6):2757-2767.

PMID: 31259049 PMC: 6583342. DOI: 10.1364/BOE.10.002757.

References

Mitchell P . A perspective on protein microarrays. Nat Biotechnol. 2002; 20(3):225-9. DOI: 10.1038/nbt0302-225. View

Shen R, Fan J, Campbell D, Chang W, Chen J, Doucet D . High-throughput SNP genotyping on universal bead arrays. Mutat Res. 2005; 573(1-2):70-82. DOI: 10.1016/j.mrfmmm.2004.07.022. View

Tyagi S, Kramer F . Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol. 1996; 14(3):303-8. DOI: 10.1038/nbt0396-303. View

Cooper M . Optical biosensors in drug discovery. Nat Rev Drug Discov. 2002; 1(7):515-28. DOI: 10.1038/nrd838. View

Fei Z, Ono T, Smith L . MALDI-TOF mass spectrometric typing of single nucleotide polymorphisms with mass-tagged ddNTPs. Nucleic Acids Res. 1998; 26(11):2827-8. PMC: 147612. DOI: 10.1093/nar/26.11.2827. View

Ramdas L, Coombes K, Baggerly K, Abruzzo L, Highsmith W, Krogmann T . Sources of nonlinearity in cDNA microarray expression measurements. Genome Biol. 2001; 2(11):RESEARCH0047. PMC: 60308. DOI: 10.1186/gb-2001-2-11-research0047. View

Kelley S, Boon E, Barton J, Jackson N, Hill M . Single-base mismatch detection based on charge transduction through DNA. Nucleic Acids Res. 1999; 27(24):4830-7. PMC: 148785. DOI: 10.1093/nar/27.24.4830. View

Eisen M, Spellman P, Brown P, Botstein D . Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998; 95(25):14863-8. PMC: 24541. DOI: 10.1073/pnas.95.25.14863. View

Stears R, Martinsky T, Schena M . Trends in microarray analysis. Nat Med. 2003; 9(1):140-5. DOI: 10.1038/nm0103-140. View

10.

Ozkumur E, Yalcin A, Cretich M, Lopez C, Bergstein D, Goldberg B . Quantification of DNA and protein adsorption by optical phase shift. Biosens Bioelectron. 2009; 25(1):167-72. PMC: 2750076. DOI: 10.1016/j.bios.2009.06.033. View

11.

Wang J . From DNA biosensors to gene chips. Nucleic Acids Res. 2000; 28(16):3011-6. PMC: 108456. DOI: 10.1093/nar/28.16.3011. View

12.

Koehne J, Chen H, Cassell A, Ye Q, Han J, Meyyappan M . Miniaturized multiplex label-free electronic chip for rapid nucleic acid analysis based on carbon nanotube nanoelectrode arrays. Clin Chem. 2004; 50(10):1886-93. DOI: 10.1373/clinchem.2004.036285. View

13.

Du H, Strohsahl C, Camera J, Miller B, Krauss T . Sensitivity and specificity of metal surface-immobilized "molecular beacon" biosensors. J Am Chem Soc. 2005; 127(21):7932-40. DOI: 10.1021/ja042482a. View

14.

Yalcin A, Damin F, Ozkumur E, Di Carlo G, Goldberg B, Chiari M . Direct observation of conformation of a polymeric coating with implications in microarray applications. Anal Chem. 2008; 81(2):625-30. PMC: 2644728. DOI: 10.1021/ac801954x. View

15.

J van t Veer L, Dai H, van de Vijver M, He Y, Hart A, Mao M . Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002; 415(6871):530-6. DOI: 10.1038/415530a. View

16.

Taton T, Mirkin C, LETSINGER R . Scanometric DNA array detection with nanoparticle probes. Science. 2000; 289(5485):1757-60. DOI: 10.1126/science.289.5485.1757. View

17.

Elhadj S, Singh G, Saraf R . Optical properties of an immobilized DNA monolayer from 255 to 700 nm. Langmuir. 2005; 20(13):5539-43. DOI: 10.1021/la049653+. View

18.

Ding C, Cantor C . A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS. Proc Natl Acad Sci U S A. 2003; 100(6):3059-64. PMC: 152246. DOI: 10.1073/pnas.0630494100. View

19.

Syvanen A . Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet. 2001; 2(12):930-42. DOI: 10.1038/35103535. View

20.

Wang H, Li J, Liu H, Liu Q, Mei Q, Wang Y . Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film. Nucleic Acids Res. 2002; 30(12):e61. PMC: 117303. DOI: 10.1093/nar/gnf061. View