Charge Transport within a Three-Dimensional DNA Nanostructure Framework

Three-dimensional (3D) DNA nanostructures have shown great promise for various applications including molecular sensing and therapeutics. Here we report kinetic studies of DNA-mediated charge transport (CT) within a 3D DNA nanostructure framework. A tetrahedral DNA nanostructure was used to investigate the through-duplex and through-space CT of small redox molecules (methylene blue (MB) and ferrocene (Fc)) that were bound to specific positions above the surface of the gold electrode. CT rate measurements provide unambiguous evidence that the intercalative MB probe undergoes efficient mediated CT over longer distances along the duplex, whereas the nonintercalative Fc probe tunnels electrons through the space. This study sheds new light on DNA-based molecular electronics and on designing high-performance biosensor devices

Directed Amination of Aryl Methyl Ethers Mediated by Ti(NMe₂)₄ at Room Temperature

An efficient C–O amination of aryl methyl ethers has been achieved. This transformation proceeds via imine-directed Ti­(IV)-mediated cross-coupling reactions between aryl methyl ethers and Ti­(NR₂)₄ at room temperature, straightforwardly leading to a series of arylamines. This protocol features a wide substrate scope, exclusive regioselectivity, and mild reaction conditions

Coordination-Mediated Programmable Assembly of Unmodified Oligonucleotides on Plasmonic Silver Nanoparticles

DNA-decorated metal nanoparticles have found numerous applications, most of which rely on thiolated DNA (SH-DNA)-modified gold nanoparticles (AuNPs). Whereas silver nanoparticles (AgNPs) are known to have stronger plasmonic properties than AuNPs, modification of AgNPs with SH-DNA is technically challenging, partially due to the instability of Ag–S bonding. Here we demonstrate a facile approach to self-assemble unmodified DNA on AgNPs by exploiting intrinsic silver–cytosine (Ag–C) coordination. The strong Ag–C coordination allows for the ready formation of DNA-AgNP conjugates, which show favorable stability under conditions of high ionic strength and high temperature. These nanoconjugates possess much higher efficient molecular recognition capability and faster hybridization kinetics than thiolated DNA-modified AgNPs. More importantly, we could programmably tune the DNA density on AgNPs with the regulation of silver–cytosine coordination numbers, which in turn modulated their hybridizability. We further demonstrated that these DNA-AgNP conjugates could serve as excellent building blocks for assembling silver and hybrid silver–gold nanostructures with superior plasmonic properties

Directed Amination of Aryl Methyl Ethers Mediated by Ti(NMe₂)₄ at Room Temperature

An efficient C–O amination of aryl methyl ethers has been achieved. This transformation proceeds via imine-directed Ti­(IV)-mediated cross-coupling reactions between aryl methyl ethers and Ti­(NR₂)₄ at room temperature, straightforwardly leading to a series of arylamines. This protocol features a wide substrate scope, exclusive regioselectivity, and mild reaction conditions

Directed Amination of Aryl Methyl Ethers Mediated by Ti(NMe₂)₄ at Room Temperature

An efficient C–O amination of aryl methyl ethers has been achieved. This transformation proceeds via imine-directed Ti­(IV)-mediated cross-coupling reactions between aryl methyl ethers and Ti­(NR₂)₄ at room temperature, straightforwardly leading to a series of arylamines. This protocol features a wide substrate scope, exclusive regioselectivity, and mild reaction conditions

Convection-Driven Pull-Down Assays in Nanoliter Droplets Using Scaffolded Aptamers

One of the great challenges in cellular studies is to develop a rapid and biocompatible analytical tool for single-cell analysis. We report a rapid, DNA nanostructure-supported aptamer pull-down (DNaPull) assay under convective flux in a glass capillary for analyzing the contents of droplets with nano- or picoliter volumes. We have demonstrated that the scaffolded aptamer can greatly improve the efficiency of target molecules’ pull down. The convective flux allows complete reaction in <5 min, which is an 18-fold improvement compared to purely diffusive flux (traditional model of the stationary case). This established DNaPull assay can serve as a rapid and sensitive analytical platform for analyzing a variety of bioactive molecules, including small molecules [ATP, limit of detecton (LOD) of 1 μM], a drug (cocaine, LOD of 1 μM), and a biomarker (thrombin, LOD of 0.1 nM). Significantly, the designed microfluidic device compartmentalizes live cells into nanoliter-sized droplets to present single-cell samples. As a proof of concept, we demonstrated that cellular molecules (ATP) from a discrete number of HNE1 cells (zero to five cells) lysed inside nanoliter-sized droplets can be analyzed using our DNaPull assay, in which the intracellular ATP level was estimated to be ∼3.4 mM. Given the rapid assay feature and single-cell sample analysis ability, we believe that our analytical platform of convection-driven DNaPull in a glass capillary can provide a new paradigm in biosensor design and will be valuable for single-cell analysis

Target-Responsive, DNA Nanostructure-Based E‑DNA Sensor for microRNA Analysis

Because of the short size and low abundance of microRNAs, it is challenging to develop fast, inexpensive, and simple biosensors to detect them. In this work, we have demonstrated a new generation (the third generation) of E-DNA sensor for the sensitive and specific detection of microRNAs. Our third generation of E-DNA sensor can sensitively detect microRNA target (microRNA-141) as low as 1 fM. The excellent specificity has been demonstrated by its differential ability to the highly similar microRNA analogues. In our design, the use of DNA tetrahedron ensures the stem-loop structure in well controlled density with improved reactivity. The regulation of the thermodynamic stability of the stem-loop structure decreases the background signal and increases the specificity as well. The enzymes attached bring the electrocatalytic signal to amplify the detection. The combination of these effects improves the sensitivity of the E-DNA sensor and makes it suitable to the microRNA detection. Finally, our third generation of E-DNA sensor is generalizable to the detection of other micro RNA targets (for example, microRNA-21)

Ultrasensitive Signal-On Detection of Nucleic Acids with Surface-Enhanced Raman Scattering and Exonuclease III-Assisted Probe Amplification

The methodological development of nucleic acids detection is a rapidly growing research field. Here, we report a powerful method to detect nucleic acids by an integration of surface-enhanced Raman scattering and exonuclease III-assisted probe amplification. With a unique signal-on strategy, we have demonstrated that the target DNA of MnSOD gene in concentrations as low as 1 aM can reproducibly be detected, which offers a detection limit several orders of magnitude better than the previous reports in the literature. The new biosensor exhibits an excellent specificity in differentiating DNA sequences with a single-base mismatch. As a robust, flexible, and ultrasensitive approach, it promises important applications in clinical diagnostics and DNA identification where only a very limited amount of the biological sample is available

Probing Cellular Molecules with PolyA-Based Engineered Aptamer Nanobeacon

Adenosine triphosphate (ATP) is a central metabolite that is of critical importance in many cellular processes. The development of sensitive and selective methods for the detection of ATP level in vivo is crucial in diagnostic and theranostic applications. In this work, we have developed a polyA-based aptamer nanobeacon (PAaptNB) with improved efficiency and speed of ATP analysis. We found that the dissociation constants and competitive binding kinetics of the PAaptNB could be programmably regulated by adjusting the polyA length. When the polyA length reached to 30 bases, a 10 μM detection limit for ATP assay with PAaptNB can be achieved (∼10-fold improvement compared with the conventional thiol-based aptamer nanobeacon). The feasibility of the PAaptNB for in vivo assay was further demonstrated by imaging intracellular ATP molecules. This study provides a new strategy to construct high-efficiency and high-speed biosensors for cellular molecules analysis, which holds great potential in bioanalysis and theranostic applications

MoS₂ Nanoprobe for MicroRNA Quantification Based on Duplex-Specific Nuclease Signal Amplification

MicroRNAs (miRNAs) play significant regulatory roles in physiologic and pathologic processes and are considered as important biomarkers for disease diagnostics and therapeutics. Simple, fast, sensitive, and selective detection of miRNAs, however, is challenged by their short length, low abundance, susceptibility to degradation, and homogenous sequence. Here, we report a novel design of nanoprobes for highly sensitive and selective detection of miRNAs based on MoS₂-loaded molecular beacons (MBs) and duplex-specific nuclease (DSN)-mediated signal amplification (DSNMSA). We show that MoS₂ nanosheets not only exhibit high affinity toward MBs but also act as an efficient quencher for absorbed MBs. The strong fluorescence-quenching ability of MoS₂ in combination with cyclic DSNMSA contributes to the superior sensitivity of our method, with a limit of detection 4 orders of magnitude lower than that of traditional hybridization methods. Moreover, the nanoprobes also show high selectivity for discriminating homogenous miRNA sequences with one-base differences because of the discrimination ability of MBs and DSN. Furthermore, we demonstrate that the MoS₂-loaded MB nanoprobes can be utilized for multiplexed detection of miRNAs. Given its high sensitivity and specificity, as well as the multiplexed function; this novel method as an effective tool shows a great promise for simultaneous quantitative analysis of multiple miRNAs in biomedical research and clinical diagnosis