Search

Occurrence and application of oligonucleotide probes have promoted great progress in the biochemical analysis field due to their unique biological and chemical properties. In this work, a long-stem shaped multifunctional molecular beacon (LS-MMB) that is responsive to a cancer-related gene, p53, is well-prepared. By designing the probe with long-paired bases at its two ends and short-paired bases between the middle region and the 3' end, the LS-MMB is intelligently endowed with the ability to recognize the target analyte, serve as the polymerization primer/template, and signal the hybridization event synchronously, which is distinctly advantageous over the traditional molecular beacons (MBs). Moreover, it is excitingly found that the LS-MMB can be employed to exert intramolecular and intermolecular interactions for strand displacement amplification (SDA) without the involvement of any assistant probes; this therapy results in a really easy and rapid sensing system that provides an extremely low background noise and high target output signal. In this case, an excellent sensitivity and specificity to detect target gene down to picomolar level and resolution to even one nucleotide variation are achieved, respectively. In addition, the application potential for real genomic DNA analysis is realized. We envision that the probe of LS-MMB can act as a universal platform for biosensing and biomedical research.

As one of the most exciting building blocks, DNA has gained increasing attention in the construction of promising nanostructures for various biological and medical purposes. In this contribution, we have developed an easily constructed DNA nanoassembly-based biosensing system that consists of one signal hairpin probe (SHP) and one label-free hairpin probe (LHP) for target p53 gene analysis. The probes of SHP and LHP were designed to be incapable of interacting with each other in the absence of the p53 gene. When the target gene is introduced, the 3' end of SHP (or LHP) hybridizes with the middle region of LHP (or SHP), leading to polymerase-sustained DNA nanoassembly. Because one target species can exhaust many building scaffolds to execute the programmable nanoassembly in one-pot approach, the fluorescence intensity of SHP is greatly enhanced in the presence of target gene in a simple and robust manner. The practical applicability was successfully demonstrated by screening target gene extracted from cancer cells. We believe this intriguing sensing strategy and desirable assay ability would provide new opportunities to develop versatile biochemical analysis methods., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Facile assembly of intelligent DNA nanoobjects with the ability to exert in situ visualization of intracellular microRNAs (miRNAs) has long been concerned in the fields of DNA nanotechnology and basic medical study. Here, we present a driving primer (DP)-triggered polymerization-mediated metastable assembly (PMA) strategy to prepare a well-ordered metastable DNA nanoarchitecture composed of only two hairpin probes (HAPs), which has never been explored by assembly methods. Its structural features and functions are characterized by atomic force microscope (AFM) and gel electrophoresis. Even if with a metastable molecular structure, this nanoarchitecture is relatively stable at physiological temperature. The assembly strategy can be expanded to execute microRNA-21 (miRNA-21) in situ imaging inside cancer cells by labelling one of the HAPs with fluorophore and quencher. Compared with the conventional fluorescence probe-based in situ hybridization (FISH) technique, confocal images revealed that the proposed DNA nanoassembly can not only achieve greatly enhanced imaging effect within cancer cells, but also reflect the miRNA-21 expression level sensitively. We believe that the easily constructed DNA nanoarchitecture and in situ profiling strategy are significant progresses in DNA assembly and molecule imaging in cells., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

In this work, we have proposed a chain anadiplosis-structured DNA nanowire by using two well-defined assembly strands (AS1 and AS2). The presence of a target analyte would drive the single-stranded AS1 dissociate from the pre-formatted nanowire, converting into a fully double-stranded form responsible for extensive accumulation of G-rich cleavage fragment1 (GCF1) because of an autonomously performed polymerization/nicking/displacement process. In turn, the produced GCF1 is able to hybridize with the un-peeled AS2, allowing the replication over AS2 to occur and generate large amounts of G-rich cleavage fragment2 (GCF2) with the ability to hybridize with the un-peeled AS1, thereafter initiating new enzymatic reactions for further collection of GCF1. Because the reactions occur repeatedly, the assembled nanowires gradually dissociated and completely collapsed in the end, achieving the goal of substantial signal amplification for the colorimetric readout of the target analytes. The sensing feasibility is firstly verified by one trigger primer (TP), and then exemplified with the detection of the target, the kras oncogene, with high sensitivity and specificity. As a proof-of-concept strategy, the intelligent signal readout pathway and desired assay ability provide unique insights into the materials research and biological studies.

With the biological significance and important advances of nano-scale DNA devices, scientific activities have been directed toward developing molecular machinery. In this work, we present a novel two-wheel drive-based DNA nanomachine composed of one signaling recognition probe (SRP), one label-free recognition probe (LRP), and one driving primer (DP). Target DNA hybridization can activate LRP-based wheel driving by resorting to DP-mediated polymerization/nicking/displacement cycles. This in turn results in the accumulation of nicked strand 1 (NS1) that can initiate extended SRP-based wheel driving. As a result, the hairpin structure of SRP is stretched and pre-quenched fluorescence is restored. Meanwhile, lots of nicked strand 2 (NS2) are produced, which could hybridize perfectly with SRP and lead to further fluorescence amplification. It is worth noting that, because the nanomachine operation relies strongly on inputted target trigger, the unwanted background is completely eliminated. The detection limit of 1 pM and an excellent capability to recognize the single-base mutation were achieved. Significantly, the interrogating of target trigger extracted from cancer cells is already available, reflecting the potential for practical applications. As a proof-of-concept building, the unique analytical properties would significantly benefit the DNA nanomachines and reveal great promise in biochemical and biomedical studies., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

• The DNA dendrimers display super-stability in serum after annealing. • The sgc8-DNA dendrimers show specific binding to target cells in blood. • The sgc8-DNA dendrimers-Dox specifically induce DNA damage of the target cells evidenced by the comet tail, and can trace the target cells in mice. Recent development of aptamer-nanomaterial assemblies witnesses a great success. However, the instability and off-target imperfection of the aptamer-nanomaterial assemblies still need to be improved for clinical theranostic development. Here, we show the aptamer sgc8-hybridized DNA dendrimers with engineering simplicity, robust biostability and target specificity. We introduced a trigger to a mixture of intelligently-designed oligonucleotides to initiate programmable hybridization/polymerization process that was controlled by substrates/byproducts equilibration cycles, yielding nick-sealed sgc8DNA dendrimers after ligation with sgc8-Linkers. The molecular entity and biostability, targeting specificity and theranostic efficacy of the sgc8-DNA dendrimers were characterized by physicochemistry, molecular and cellular biology and in vivo models. The DNA dendrimers showed super-stability in FBS-containing culture medium or in serum for more than 36 h and were resistant to 100 °C-annealing and physiological DNase. The sgc8-DNA dendrimers specifically distinguished target CCRF-CEM cells from the cognate ones, and bound to CCRF-CEM even in the presence of many interfering cells or in blood. The highly-branched dendrimers provided huge surface interfaces to load doxorubicin by G-C hybrids at a molar ratio over 350, and specifically delivered doxorubicin to nuclei of CCRF-CEM evidenced by DNA synthesis arrest and comet tail, thus preventing doxorubicin's non-selective cytotoxicity. The sgc8-DNA dendrimers showed specific capturing of circulating CCRF-CEM cells and in vivo theranostic effects on implanted tumors. The novel and stable sgc8-DNA dendrimers with high pay-load may be best-suited for cancer theranostics. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) have been identified as important biomarkers with great significance for diagnosis and treatment of various diseases. However, their unique properties, such as small size, high sequence homology, and low abundance, make quantitative analysis of miRNAs extremely challenging. Herein, we reported a cascade catalytic hairpin assembly (CCHA) for sensitive and selective detection of miRNA with three kinds of hairpin probes (HP1, HP2, and HP3). In the presence of target miRNA, a series of toehold-mediated intermolecular DNA strand displacement and hybridization was activated among HP1, HP2, and HP3 to assembly numbers of DNA nanoobjects. During this period, the fluorescence response was greatly intensified to indicate the presence and expression level of interested target miRNA. We have demonstrated that the proposed method exhibits a high assay sensitivity to detect low concentration target and an excellent sequence specificity to distinguish even a single-nucleotide difference in vitro. Moreover, we also demonstrated that our design enables the intracellular imaging of miRNA in live cancer and normal cells. These results showing the promising potential of our CCHA for powerful biosensing, clinic diagnosis, or prognosis. [Display omitted] • We have developed a target-triggered cascade catalytic hairpin assembly (CCHA) using three hairpin probes. • The CCHA system can be used for robustly detection of miRNA-21. • The CCHA system can be applied to image intracellular miRNA in various types of cell lines. • This unique method holds promising potential for biomedical study and clinical molecular diagnostics. [ABSTRACT FROM AUTHOR]