Functional DNA directed assembly of nanomaterials for biosensing

Abstract

This review summarizes recent progress in the development of biosensors by integrating functional DNA molecules with different types of nanomaterials, including metallic nanoparticles, semiconductor nanoparticles, magnetic nanoparticles, and carbon nanotubes. On one hand, advances in nanoscale science and technology have generated nanomaterials with unique optical, electrical, magnetic and catalytic properties. On the other hand, recent progress in biology has resulted in functional DNAs, a new class of DNAs that can either bind to a target molecule (known as aptamers) or perform catalytic reactions (known as DNAzymes) with the ability to recognize a broad range of targets from metal ions to organic molecules, proteins and cells specifically. By taking advantage of the strengths in both fields, the physical and chemical properties of nanomaterials have been modulated by the target recognition and catalytic activity of functional DNAs in the presence of a target analyte, resulting in a large number of colorimetric, fluorescent, electrochemical, surface-enhanced Raman scattering and magnetic resonance imaging sensors for the detection of a broad range of analytes with high sensitivity and selectivity.

Fig. 1

Colorimetric Pb²⁺ sensors based on DNAzyme functionalized AuNP. (a) Secondary structure of the Pb²⁺-specific DNAzyme. (b) The substrate is cleaved into two pieces in the presence of Pb²⁺. (c) Pb²⁺ directed assembly of DNAzyme-linked AuNPs aligned in a head-to-tail configuration; (d) UV-vis spectra of disassembled (red) and aggregated (blue) DNAzyme-AuNPs; (e) Pb²⁺ colorimetric sensing with tunable dynamic range, monitored by the extinction ratio at 522 and 700 nm; (f) color of the AuNPs in the presence of the different divalent metal ions shown in a TLC (thin layer chromatography) plate. Reprinted with permission of ref. , copyright 2003 American Chemical Society. (g) Pb²⁺ directed assembly of DNAzyme-linked AuNPs aligned in a tail-to-tail configuration; (h) effect of nanoparticle alignment and size on the rate of color change. The small red ball represents 13 nm AuNP and the big red ball represents 42 nm AuNP. Reprinted with permission of ref. , copyright 2004 American Chemical Society.

Fig. 2

Schematics of colorimetric sensors based on aptamer directed AuNP assembly or disassembly. (a) Assembly of aptamer-functionalized AuNPs by target protein (PDGF) that can bind two aptamer molecules. (b) Disassembly of AuNPs linked by an adenosine aptamer. (c) Release of aptamer induced by addition of target molecule (adenosine) destabilized AuNPs, resulting in a red to blue color change. (d) Folding of aptamer upon binding to target molecule (adenosine) stabilized AuNPs from salt induced aggregation.

Fig. 3

Label free colorimetric sensors based on functional DNA and AuNPs. (a) Schematic of aptamer based label free sensor. Folding of aptamer upon target binding would inhibit the adsorption of aptamer on the AuNPs. The AuNPs remained dispersed in the absence of target molecule but aggregated in the presence of target molecule. (b) Schematic of DNAzyme based label free sensor. Pb²⁺ induced the cleavage of DNAzyme complex and released a short ssDNA. The AuNPs aggregated in the absence of lead but remained dispersed in the presence of lead. Reproduced with permission of ref. , copyright 2008 Wiley-VCH.

Fig. 4

(a) Amplified detection of thrombin by Au³⁺ reducing enlargement of thrombin aptamer-modified AuNPs. Reprinted with permission of ref. , copyright 2004 American Chemical Society. (b) Amplified detection of thrombin by aptamer modified Pt NPs acting as catalytic labels for the generation of chemiluminescence. Reproduced with permission of ref. , copyright 2006 Wiley-VCH.

Fig. 5

(a) Left: schematic of SERS based aptamer sensor for thrombin using Raman reporter labeled AuNPs functionalized with aptamers. The absorption of silver nanoparticles would enhance the SERS signal by forming hot spots. Right: SERS spectra of Raman reporters in the presence of 120 nM thrombin and in the absence of thrombin. Reproduced with permission of ref. , copyright of The Royal Society of Chemistry. (b) Schematic of SERS based aptamer sensor for adenosine using structure switching of aptamer. Upon addition of adenosine, folding of the aptamer would release the ssDNA labeled with Raman reporter. Hybridization of the ssDNA on the silver coated AuNP aggregate substrate generated a SERS signal. Reproduced with permission of ref. , copyright of Elsevier.

Fig. 6

(a) Schematic of a QD FRET based aptamer sensor for thrombin. Binding of the target displaced the DNA strand labeled with a quencher and enhanced the fluorescence of the QDs. (b) Schematic of fluorescent thrombin sensor based on the selective quenching of thrombin on PbS QDs capped with aptamers.

Fig. 7

(a) Schematic of QD encoded aptamer linked nanostructures for the one-pot simultaneous detection of adenosine and cocaine. AuNP 1, AuNP 2 and QDs Q1 were assembled by adenosine aptamer DNA, while AuNP 1, AuNP 3 and QDs Q2 were assembled by cocaine aptamer. The QDs’ fluorescence was quenched by nearby AuNPs. The addition of adenosine and cocaine disassembled the aggregates and increased the fluorescence. Reprinted with permission of ref. , copyright 2007 American Chemical Society. (b) Steady-state fluorescence emission spectra of mixed nanoparticles aggregated in response to target molecules or control molecules. (c) Operation of the aptamer-QD based dual biosensor for thrombin and lysozyme. Target analytes displaced the QD tagged proteins, and the displacement was monitored by electrochemical-stripping detection. Reprinted with permission of ref. , copyright 2006 American Chemical Society.

Fig. 8

(a) Schematic of MRI “turn-off” detection of thrombin with aptamer functionalized superparamagnetic iron oxide nanoparticles. Aggregation of superparamagnetic nanoparticles induced by thrombin reduced the T2 relaxation time. The right panel shows the contrast change in a T2-weighted MR image at different thrombin concentrations. (b) Schematic of MRI “turn-on” detection of adenosine. Addition of adenosine disassembled the nanoparticle aggregates and increased the T2 relaxation time. The right panel shows the contrast change in a T2-weighted MR image at different adenosine concentrations.

Fig. 9

(a) Schematic of the binding of thrombin on a SWNT-FET based aptamer sensor. (b) Real-time conductance measurements from the SWNT-FET based aptamer sensor upon addition of thrombin (bottom curve) or elastase (top curve). (c) The sensitivity of the sensor as a function of thrombin concentration. Reprinted with permission of ref. , copyright 2005 American Chemical Society.