Abstract:Detection of viruses is critical for controlling disease spread. Recent emerging viral threats, including Zika virus, Ebola virus, and SARS-CoV-2 responsible for coronavirus disease 2019 (COVID-19) highlight the cost and difficulty in responding rapidly. To address these challenges, we develop a platform for low-cost and rapid detection of viral RNA with DNA nanoswitches that mechanically reconfigure in response to specific viruses. Using Zika virus as a model system, we show nonenzymatic detection of viral RN… Show more
“…Advantages of DNA nanostructures for biosensing include the highly precise design based on base pairing, the large surface-to-volume ratios and the low-cost synthesis of functionalized DNA strands. So far, DNA nanostructures have been used to detect nucleic acids (including microRNAs 19 , viral RNAs 65 and pathogenic DNA 66 ), antigens 67 , antibodies 68 and small molecules 40 , as well as in sensing in vivo pH changes 43 . Fig.…”
Section: Dna Nanotechnology Applicationsmentioning
confidence: 99%
“…The example shown is a DNA nanoswitch made from a long M13 scaffold strand and short complementary backbone oligonucleotides. When the single-stranded detectors of the nanoswitch bind to viral RNA, the nanoswitch reconfigures to a looped ‘on’ state that can be visualized on a gel 65 . b | DNA nanostructures are used as carriers to deliver drugs to specific sites in the body or to cellular compartments.…”
Section: Dna Nanotechnology Applicationsmentioning
DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.
“…Advantages of DNA nanostructures for biosensing include the highly precise design based on base pairing, the large surface-to-volume ratios and the low-cost synthesis of functionalized DNA strands. So far, DNA nanostructures have been used to detect nucleic acids (including microRNAs 19 , viral RNAs 65 and pathogenic DNA 66 ), antigens 67 , antibodies 68 and small molecules 40 , as well as in sensing in vivo pH changes 43 . Fig.…”
Section: Dna Nanotechnology Applicationsmentioning
confidence: 99%
“…The example shown is a DNA nanoswitch made from a long M13 scaffold strand and short complementary backbone oligonucleotides. When the single-stranded detectors of the nanoswitch bind to viral RNA, the nanoswitch reconfigures to a looped ‘on’ state that can be visualized on a gel 65 . b | DNA nanostructures are used as carriers to deliver drugs to specific sites in the body or to cellular compartments.…”
Section: Dna Nanotechnology Applicationsmentioning
DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.
“…There are some companies developing quicker and lower-cost tests based on novel sensors. 9 Alternative antigen- or antibody-detection approaches remain unproven, again maybe creating a statistical bias that could directly affect public health policies. 10 Whilst initial reports claim a sensitivity of 100%, more recent studies exhibit levels as low as 30%; 11 others report 72 or 81% in different settings.…”
There
is an urgent need for ultrarapid testing regimens to detect
the severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] infections
in real-time within seconds to stop its spread. Current testing approaches
for this RNA virus focus primarily on diagnosis by RT-qPCR, which
is time-consuming, costly, often inaccurate, and impractical for general
population rollout due to the need for laboratory processing. The
latency until the test result arrives with the patient has led to
further virus spread. Furthermore, latest antigen rapid tests still
require 15–30 min processing time and are challenging to handle.
Despite increased polymerase chain reaction (PCR)-test and antigen-test
efforts, the pandemic continues to evolve worldwide. Herein, we developed
a superfast, reagent-free, and nondestructive approach of attenuated
total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy
with subsequent chemometric analysis toward the prescreening of virus-infected
samples. Contrived saliva samples spiked with inactivated γ-irradiated
COVID-19 virus particles at levels down to 1582 copies/mL generated
infrared (IR) spectra with a good signal-to-noise ratio. Predominant
virus spectral peaks are tentatively associated with nucleic acid
bands, including RNA. At low copy numbers, the presence of a virus
particle was found to be capable of modifying the IR spectral signature
of saliva, again with discriminating wavenumbers primarily associated
with RNA. Discrimination was also achievable following ATR-FTIR spectral
analysis of swabs immersed in saliva variously spiked with virus.
Next, we nested our test system in a clinical setting wherein participants
were recruited to provide demographic details, symptoms, parallel
RT-qPCR testing, and the acquisition of pharyngeal swabs for ATR-FTIR
spectral analysis. Initial categorization of swab samples into negative
versus positive COVID-19 infection was based on symptoms and PCR results
(
n
= 111 negatives and 70 positives). Following training
and validation (using
n
= 61 negatives and 20 positives)
of a genetic algorithm-linear discriminant analysis (GA-LDA) algorithm,
a blind sensitivity of 95% and specificity of 89% was achieved. This
prompt approach generates results within 2 min and is applicable in
areas with increased people traffic that require sudden test results
such as airports, events, or gate controls.
“…3 In biosensing, dynamic DNA nanoswitches have been programmed to detect viral RNA such as SARS-CoV-2, Zika and Dengue. 4 DNA nanostructures can also assist in the assembly of nanoparticles to create metamaterials such as sparsely packed colloidal crystals. 5 The invention of DNA origami boosted the design and development of DNA nanostructures in the past decade.…”
DNA origami is typically used to fold a long single-stranded DNA scaffold into nanostructures with complex geometries using many short DNA staple strands. Integration of RNA into nucleic acid nanostructures...
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