Herein, we described a novel plasmonic CRISPR Cas12a assay for the visual, colorimetric detection of grapevine viral infections. Our assay generates rapid and specific colorimetric signals for nucleic acid amplicons by combining the unique target-induced incriminate single-stranded DNase activity of Cas12a with plasmon coupling of DNA functionalized gold nanoparticles. The practical applicability of our plasmonic assay was successfully demonstrated through the detection of emerging red-blotch viral infections in grapevine samples collected from commercial vineyards.
Development of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants through simulation-guided engineering and noncovalent DNA catalysis.
Herein, we report a bottom-up approach
to assemble a series of
stochastic DNA walkers capable of probing dynamic interactions occurring
at the bio–nano interface. We systematically investigated the
impact of varying interfacial factors, including intramolecular interactions,
orientation, cooperativity, steric effect, multivalence, and binding
hindrance on enzymatic behaviors at the interfaces of spherical nucleic
acids. Our mechanistic study has revealed critical roles of various
interfacial factors that significantly alter molecular binding and
enzymatic behaviors from bulk solutions. The improved understanding
of the bio–nano interface may facilitate better design and
operation of nanoparticle-based biosensors and/or functional devices.
We successfully demonstrate how improved understanding of the bio–nano
interface help rationalize the design of amplifiable biosensors for
nucleic acids and antibodies.
Herein, we develop an isothermal proximity CRISPR Cas12a assay that harnesses the target-induced collateral cleavage activity of Cas12a for the quantitative profiling of gene expression and detection of proteins with high sensitivity and specificity.
Colloidal
nanoparticle biosensors capable of on-particle biocatalysis
are powerful tools for amplified detection of biomolecules. The development
and practical uses of such concentric amplifiers can be complicated
because of the on-particle biorecognition that involves varying interfacial
factors at the biomolecule–nanoparticle interfaces. Herein,
we reason that a nanoparticle biosensor equipped with an in-solution
biorecognition element may be better fabricated, predicted, controlled,
and performed. The in-solution biorecognition shall also be streamlined
with the on-particle biocatalysis so that the overall analytical and
kinetic performance is not compromised. As a testbed, we introduce
a concentric DNA amplifier driven by an enzyme-powered three-dimensional
DNA nanomachine, where a DNA walker can be instantly assembled onto
a spherical nucleic acid (SNA) track through a polyadenosine anchor.
As such, the free DNA walker can participate in reactions in a homogeneous
solution before assembling to the SNA track. The instant and stable
assembly enabled by both adsorption and complementary base pairing
also ensures rapid on-particle biocatalysis. We demonstrate that the
in-solution biorecognition effectively eliminates the binding hindrance
encountered by the on-particle biorecognition and thus significantly
reduced energy barriers for the detection of nucleic acids and proteins.
Because of the in-solution biorecognition, our system can also be
plugged readily into complex DNA strand displacement networks for
rapid signal amplification.
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