Recent advances in RNA research have posed new directives in biology and chemistry to uncover the complex roles of ribonucleic acids in cellular processes. Innovative techniques to visualize native RNAs, particularly, short, low-abundance RNAs in live cells, can dramatically impact current research on the roles of RNAs in biology. Herein, we report a novel method for real-time, microRNA imaging inside live cells based on programmable oligonucleotide probes, which self-assemble through the Cascade Hybridization Reaction (CHR).

We report on an autonomous DNA-based machine that amplifies the detection of M13 phage single-stranded (ss) DNA. The machine is unique in that it makes use of both the genetic and catalytic properties of DNA. Upon recognition of the input viral DNA, the machine is activated and synthesizes a peroxidase-mimicking DNAzyme, which, in turn, generates colorimetric or chemiluminescence readout signals. Multiple rounds of isothermal strand replication, which lead to strand displacement and activation of the DNAzyme moiety, constitute two consecutive levels of signal amplification for this novel detection paradigm that rivals PCR for sensitivity.Amplification is a fundamental element in bioanalysis. Enzymes, [1] DNAzymes, [2] and lately, nanoparticles [3] or nanocontainers [4] are widely employed for the sensitive detection of biorecognition events. Within these efforts, the amplified and sensitive detection of DNA is particularly challenging and directed to the analysis of pathogens, the detection of genetic disorders, and for forensic applications.[5] PCR provides a general protocol for the amplified detection of DNA. Although the PCR method is time consuming and not free of limitations, it provides the most versatile method to detect minute amounts of DNA. The design of alternative approaches for the sensitive detection of DNA is in continuous demand. Substantial research efforts have been directed lately to the development of DNA-based machines.[6] A DNA-based machine that cleaves RNA by a DNAzyme, [7] DNA-based tweezers, [8,9] autonomous DNA walkers on prearchitectured tracks, [10][11][12][13] and signal-triggered switchable structural transformations between duplex DNA and Gquadruplex configurations [14] were reported. The use of the DNA machines as computing systems [15][16][17] or as sensor systems [18,19] was discussed. Herein we report on an isothermic autonomous DNA machine for the generation of DNAzyme labels. We demonstrate activation of the DNA machine by the analyzed DNA, which allows it to self-detect. The resulting synthesized DNAzyme acts as a peroxidase-mimicking enzyme and as an amplifying label for the analysis of the target DNA. The machine employs colorimetric or chemiluminescent readout signals for the detection of the target DNA. The paradigm developed in the present study represents an approach that might complement or substitute the PCR method. In contrast with the PCR and real-time-PCR (RT-PCR) methods that require thermal replication cycles, costly optical labels, and dedicated instrumentation, the procedure developed by us proceeds isothermally, reaches a sensitivity limit of 10 À14 m, is cost-effective, and can be visually imaged. The uniqueness of the new paradigm is the amplification of the analyzed DNA by two consecutive steps: the autonomous synthesis and displacement of a nucleic acid that is generated by a biomolecular machine on a DNA template, and the self assembly of the displaced strand into a biocatalytic DNAzyme label that enables the colorimetric or chemiluminescent imaging o...

Circular DNA is used as a template for the amplified detection of M13 phage ssDNA by a rolling circle amplification (RCA) process that synthesizes DNAzyme chains, thus enabling the colorimetric or chemiluminescent detection of the analyte.

Nucleic acid amplification techniques have been among the most powerful tools for biological and biomedical research, and the vast majority of the bioassays rely on thermocycling that uses time-consuming and expensive Peltier-block heating. Here, we introduce a plasmonic photothermal method for quantitative real-time PCR, using gold bipyramids and light to achieve ultrafast thermocycling. Moreover, we successfully extend our photothermal system to other biological assays, such as isothermal nucleic acid amplification and restriction enzyme digestion.

Gold‐nanoparticle‐functionalized enzymes act as “biocatalytic inks” for the generation of metallic nanowires via dip‐pen nanolithography. Deposition of nanoparticle‐modified oxidases or a phosphatase followed by development with their respective substrates and metal salts results in nanowires (see figure). This concept may be extended to the generation of other nanostructures via enzyme‐catalyzed particle growth.