In nucleic acid nanotechnology, strand
displacement is a widely
used mechanism where one strand from a hybridized duplex is exchanged
with an invading strand that binds to a toehold, a single-stranded
region on the duplex. It is used to perform logic operations on a
molecular level, initiate cascaded reactions, or even for in vivo diagnostics and treatments. While systematic experimental
studies have been carried out to probe the kinetics of strand displacement
in DNA with different toehold lengths, sequences, and mismatch positions,
there has not been a comparable investigation of RNA or RNA–DNA
hybrid systems. Here, we experimentally study how toehold length,
toehold location (5′ or 3′ end of the strand), and mismatches
influence the strand displacement kinetics. We observe reaction acceleration
with increasing toehold length and placement of the toehold at the
5′ end of the substrate. We find that mismatches closer to
the interface of toehold and duplex slow down the reaction more than
remote mismatches. A comparison of RNA and DNA displacement with hybrid
displacement (RNA invading DNA or DNA invading RNA) is partly explainable
by the thermodynamic stabilities of the respective toehold regions,
but also suggests that the rearrangement from B-form to A-form helix
in the case of RNA invading DNA might play a role in the kinetics.
Capsules with an aqueous core and a wax shell perfectly encapsulate their contents at room temperature, while the contents are released above the melting temperature of the wax.
Peroxidyme Amplified Radical Chain Reaction (PARCR), a novel enzyme-free system that achieves exponential amplification of a visible signal, is presented. Typical enzyme-free amplification systems that produce a visible readout suffer from long reaction times, low sensitivity, and narrow dynamic range. PARCR employs photocatalyzed nonlinear signal generation, enabling unprecedented one-pot, naked-eye detection of a catalytic reporter from 1 μm down to 100 pm. In this reaction, hemin-binding peroxidase-mimicking DNAzymes ("peroxidymes") mediate the NADH-driven oxidation of a colorless, nonfluorescent phenoxazine dye (Amplex Red) to a brightly colored, strongly fluorescent product (resorufin); illumination with green light initiates multiple radical-forming positive-feedback loops, rapidly producing visible levels of resorufin. Collectively, these results demonstrate the potential of PARCR as an easy-to-use readout for a range of detection schemes, including aptamer labels, hybridization assays, and nucleic acid amplification.
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