DNA Based Biosensors Yingli Fu Biological Resources Engineering University of Maryland, College Park December 10, 2003

Outline Introduction Principles of DNA biosensors Types of DNA biosensors Improvement of DNA biosensors DNA biosensor miniaturization References

Introduction Biosensor: DNA biosensor: Motivated by the application to clinical diagnosis and genome mutation detection

DNA Structure DNA structures---double helix (complementary)  4 bases: Adenine (A), Guanine (G), Thymine (T), and Cytosine (C)  sugar (deoxyribose)  phosphate group

DNA Stability Hydrogen bonding between base pairs Stacking interaction between bases along axis of double-helix Size and base content and sequence

Principles of DNA biosensors Nucleic acid hybridization ---rennealing b/w the ssDNAs from different sources  Perfect match ---stable dsDNA, strong hybridization  One or more base mismatches ----weak hybridization

Forms of DNA Biosensors Electrodes Chips Crystals

Immobilization of DNA Probe onto Transducer Surface Thiolated DNA for self assembly onto gold transducers Covalent linkage to the gold surface via functional alkanethiol-based monolayers Use of biotylated DNA for complex formation with a surface-confined avidin or strepavidin Covalent (carbodiimide) coupling to functional groups on carbon electrodes simple adsorption onto carbon surfaces

Types of DNA Based Biosensors Optical, Electrochemical and Piezoelectric

Molecular Beacon Based Optical Fiber DNA Biosensors ‘Ligate and light’. Schematics diagram of real-time monitoring of the nucleic acid ligation process by a MB.

Piezoelectric DNA Biosensors quartz crystal microbalance (QCM) transducers Immobilized DNA probe Target DNA Form duplex---mass increase Decrease in crystal’s resonance frequency

Piezoelectric DNA Biosensors (cont’s) Frequency–time response of a PNA/QCM to additions of the target (T) and mismatch (M) oligonucleotides. The hybridization event results in decreased frequency, reflecting the increased mass of the crystal.

Electrochemical DNA Biosensor DNA-immobilized electrodes, based on detection of hybridization  redox intercalators to recognize dsDNA  DNA-mediated electron transfer using mediators  Use of ferrocene-labeled oligonucleotide probes that hybrize to immobilized DNA Enzyme labels were used to amplify the signal and improve the sensitivity  Peroxidase  Glucose dehydrogenase (GDH)

Electrochemical DNA Biosensor--- An Example Amperometric DNA sensor using the pyrroquinoline quinone glucose dehydrogenase- avidin conjugate Kazunori Ikebukuro, Yumiko Kohiki, Koji Sode * Biosensors and Bioelectronics 17 (2002)

Material and Methods pyrroquinoline quinone-dependent glucose dehydrogenase ((PQQ)GDH) for DNA hybridization labeling Detection via biotin-avidin binding Target and probe DNA sequence:  Target DNA: 5’-bio-TCGGCATCAATACTCATC-3’.  Probe DNA: 5’-bio-GATGAGTATTGATGCCGA-3’  Control DNA: 5’-bio-CTGATGAACATACTATCT-3’

Material and Methods (cont’s)

Results

Conclusions The (PQQ)GDH/avidin conjugate based DNA biosensor is highly sensitive and selective to the target Salmonla invA virulence gene The sensor response increased with the addition of glucose and in the presence of 6.3 mM glucose the response increased with increasing DNA in the range 5.0x10^8-1.0x10^5 This DNA biosensor would be applicable for single nuleotide polymorphism detection

Improvement Fluorescent Bioconjugated Nanoparticles DNA dendrimers

Fluorescent Bioconjugated Nanoparticles---signal amplification

Results

DNA dendrimers---increase sensitivity Schematic drawing showing the hybridization detection at the dendrimer/QCM biosensor. The 38-mer probe is attached to the core dendrimer by complementary oligonucleotide (a( - )) binding on one (a( + )) of the outer arms. The probe sequence for target hybridization is 5-GGG GAT CGA AGA CGA TCA GAT ACC GTC GTA GTC TTA AC-3.

DNA biosensor miniaturization

Concept of DNA microarray Figure 2

DNA microarray

DNA Microarray (cont’s) The fluorescence intensities for each spot is indicative of the relative aboundance of the corresponding DNA probe in the Nucleic acid target samples

The light directed probe array synthesis process used for the preparation of Affymetrix’s Gene Chip Affymetrix’s Gene Chip

DNA biosensor not limited to DNA detection, but more…

References Kazunori Ikebukuro, Yumiko Kohiki, Koji Sode Amperometric DNA sensor using the pyrroquinoline quinone glucose dehydrogenase-avidin conjugate. Biosens. Bioelectron. 17,1075—1080 Wang, J SURVEY AND SUMMARY From DNA biosensors to gene chips. Nucleic Acids Res. 28(16), Wang, J., M. Jiang. T. W. Nilsen, R. C. Getts Dendritic nucleic acid probes for DNA Biosensors. J. AM. CHEM. SOC. 120, Zhao, X., R. Tapec-Dytioco, and W. Tan Ultrasensitive DNA Detection Using highly fluorescent bioconjugated nanoparticles. J. AM. CHEM. SOC. 125, Zhai, J., H. Cui, and R.Yang DNA based biosensors. Biotechnol. Adv. 15(1),43-58