Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

First characterization of a biphasic, switch-like DNA amplification

We report the first DNA amplification chemistry with switch-like characteristics: the chemistry is biphasic, with an expected initial phase followed by an unprecedented high gain burst of product oligonucleotide in a second phase. The first and second phases are separated by a temporary plateau, with the second phase producing 10 to 100 times more product than the first. The reaction is initiated when an oligonucleotide binds and opens a palindromic looped DNA template with two binding domains. Upon loop opening, the oligonucleotide trigger is rapidly amplified through cyclic extension and nicking of the bound trigger. Loop opening and DNA association drive the amplification reaction, such that reaction acceleration in the second phase is correlated with DNA association thermodynamics. Without a palindromic sequence, the chemistry resembles the exponential amplification reaction (EXPAR). EXPAR terminates at the initial plateau, revealing a previously unknown phenomenon that causes early reaction cessation in this popular oligonucleotide amplification reaction. Here we present two distinct types of this biphasic reaction chemistry and propose dominant reaction pathways for each type based on thermodynamic arguments. These reactions create an endogenous switch-like output that reacts to approximately 1 pM oligonucleotide trigger. The chemistry is isothermal and can be adapted to respond to a broad range of input target molecules such as proteins, genomic bacterial DNA, viral DNA, and microRNA. This rapid DNA amplification reaction could potentially impact a variety of disciplines such as synthetic biology, biosensors, DNA computing, and clinical diagnostics.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

Impedimetric genosensor for ultratrace detection of hepatitis B virus DNA in patient samples assisted by zeolites and MWCNT nano-composites

Nanocrystals of zeolites (Nanocrys Zeo) and Multi-walled carbon nanotubes (MWCNT) based diagnostic genosensor was employed for detection of polymerase chain (PCR) amplified HBVDNA in blood of hepatitis B patients. The ssDNA-nanocomposite modified electrode was characterized by cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The hybridization between ss DNA probe and target ss DNA was detected by reduction in current, generated by interaction of methylene blue (MB) with free guanine (3'G) of ssDNA. Nanocrys zeo were deposited on the Fluorine doped tin oxide glass electrode (FTO) by drop-casting method for better immobilization of ss DNA while MWCNTs are incorporated into the zeolite-assembly to enhance the electro-conductivity of the present genosensor. The ssDNA-nanocomposite modified FTO electrode exhibited optimum current within 5s, at pH 5.6, and incubation temperature of 45°C. The value of charge transfer resistance (Rct) was linear with the number of copies of target DNA between 150 and 10(6) copies/ml. The limit of detection (LOD) of the sensor was 50 copies/ml. Within and between batches coefficients of variation (CV) were 2.5% and 3.2% respectively. Results obtained with our genosensor were also correlated with those by RT-PCR and r(2) value found with good accuracy of 97%. The electrode was reused by dipping it into 0.1M NaOH for 3min and lost 50% of its initial activity in 4 weeks. Furthermore the technique employed for detection of HBV is EIS, which is convenient and required less analysis time.

Highly sensitive visual detection of mutant DNA based on polymeric nanoparticles-participating amplification

Taking advantage of the nanoparticles' large surface area and structural repeating characteristics, polymeric nanoparticles-participating polymerization-based amplification system was designed to enhance the sensitivity of detection.

Scaling up an electrochemical signal with a catalytic hairpin assembly coupling nanocatalyst label for DNA detection

A new strategy for the electrochemical detection of DNA based on catalytic hairpin assembly combined with nanocatalyst label-based redox cycling reaction signal amplification. A superior detection limit of 0.3 aM toward DNA was achieved.

A cascade signal amplification strategy for ultrasensitive colorimetric detection of BRCA1 gene

Schematic illustration of a colorimetric biosensor for breast cancer1 gene detection based on DNAzyme assistant DNA recycling and rolling circle amplification.

Electron transfer and fluorescence “turn-off” based CdTe quantum dots for vancomycin detection at nanogram level in aqueous serum media

Mode of interaction of GSH-CdTe QDs with vancomycin and the mechanism of the fluorescence “turn-off” process.