Glimpsing the Future of Nanotechnology in Nucleic Acid Detection and Analysis

Allen W Nicholson^*

Departments of Biology and Chemistry, Temple University, Philadelphia, PA, USA

*Corresponding Author:

Allen W Nicholson
Director, Departments of Biology and Chemistry
Temple University, Philadelphia, PA, USA
Tel: 215-204-8854
Fax: 215-204-6646
E-mail: anichol@temple.edu

Received date: March 05, 2013; Accepted date: March 06, 2013; Published date: March 08, 2013

Citation: Nicholson AW (2013) Glimpsing the Future of Nanotechnology in Nucleic Acid Detection and Analysis. J Anal Bioanal Tech 4:e113. doi: 10.4172/2155-9872.1000e113

Copyright: © 2013 Nicholson AW. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Ongoing advances in molecular biotechnology continue to generate envelope-pushing applications in biology and medicine. Current molecular biotechnology, based on key discoveries made over forty years ago in bacterial genetics and nucleic acid biochemistry, has never looked back. An essential methodology has been the ability to detect and quantify gene activity, which progressed from measuring the expression of single (or several) genes, to the genome-wide analysis of gene expression using microarrays. Here, the fundamental driving reaction is the reversible association of an RNA or DNA with a complementary sequence to form a stable duplex structure. This reaction could be followed by radiometric or optical readout. Subsequent advancement in materials research and computer science provided the means to monitor and analyze global patterns of expression of thousands of genes simultaneously.

The continuing need to improve the sensitivity of nucleic acid detection, without sacrificing accuracy, reflects the importance of specific DNA or RNA (e.g. viral RNA or miRNA) sequences as disease indicators at the single cell level. Amplification technologies such as PCR provide highly sensitive detection by exponentially increasing the amount of the target nucleic acid, achieved through the action of a polymerase in either temperature-cycling or isothermal modes. The output signal can be provided by fluorescence of a dye bound to the amplified product, and quantitation of the target nucleic acid can be achieved by qPCR protocols, with appropriate standards and controls. Despite the importance of amplification technologies, effective disease diagnosis is now demanding even more sensitive methods to handle vanishingly small sample sizes. In single-cell genomic analyses, detecting trace levels of biomarkers associated with a viral infection or a transformed cell is pushing the limits of current methods, and there is keen interest in establishing robust, amplification-free technologies. Thus, while single-cell PCR is routinely accomplished, there are ongoing issues of amplification errors, false positives, and the inability to recover the original sample in the reaction for further analysis. Nanotechnological approaches are beginning to meet these challenges. In nanopore-based technologies, changes in ion current can be detected as a function of nucleic acid chain migration through the pores, and the various types of nucleic acids (e.g., single-stranded vs. double- stranded RNA, DNA) can be distinguished and their levels measured. Fluorescence or other optical signal can be monitored following nucleic acid chain binding to appropriately modified, water-soluble nanoparticles. Self-assembled surface monolayers or nanopatches of DNA or RNA can provide direct detection of nucleic acid biomarkers without the need for an amplification step or the use of attached reporter groups. Specifically, nucleic acid chains carrying alkylthiol linkers can spontaneously form monolayers or nanopatches on gold surfaces, which can capture complementary RNAs or DNAs. The binding reaction leads to a change in topographical parameter, such as height, that can be detected by atomic force microscopy (AFM). Moreover, since AFM analysis of self-assembled monolayers or nanopatches can be carried out in aqueous buffers, the captured nucleic acid could be recovered after detection and subjected to additional analyses. This opens up the possibility of multistep, nano-based analyses of nucleic acid biomarkers. A cautionary note is due, as the exquisite sensitivities of these approaches will need to be addressed: at the sub-attomole level, false positives and intrinsically higher backgrounds can be persistent problems. Moreover, biomarkers that may ordinarily be present in low amounts, and only become indicative of a disease state when their levels are increased, also could lead to an incorrect diagnosis. On the other hand, a digital (i.e. yes/no) output is essentially unambiguous, and could be achievable in the detection of a virus-specific RNA in cellular samples.

What could be the outcome of successfully developing nano-based detection technologies? Point-of-care devices are envisioned that could provide rapid, robust and accurate detection of key disease biomarkers using very small samples obtained at the bedside or in the field. The devices also would have the ability to perform multiple analyses on the same sample. For example, a viral RNA capture and detection reaction using a nucleic acid nanopatch can be followed by sequence analysis of the viral RNA to determine the viral genotype. Enhanced detection sensitivity would allow earlier detection of trace metastatic cells, for example, providing earlier therapeutic intervention and a more favorable treatment outcome. While there still is much to do, the promise remains very bright for bringing nanotechnology-based diagnostic devices to research laboratories and patient bedsides.