Triple Helix Formation in a Topologically Controlled DNA Nanosystem

Smart Target-Initiated Catalytic DNA Junction Circuit Amplification Strategy for the Ultrasensitive Electrochemiluminescence Detection of MicroRNA

One of the highly attractive research directions in the electrochemiluminescence (ECL) field is how to regulate and improve ECL efficiency. Quantum dots (QDs) are highly promising ECL materials due to their adjustable luminescence size and strong luminous efficiency. MoS2 NSs@QDs, an ECL emitter, is synthesized via hydrothermal methods, and its ECL mechanism is investigated using cyclic voltammetry and ECL-potential curves. Then, a stable and vertical attachment of a triplex DNA (tsDNA) probe to the MoS2 nanosheets (NSs) is applied to the electrode. Next, an innovative ECL sensor is courageously empoldered for precise and ultrasensitive detection of target miRNA-199a through the agency of ECL-resonance energy transfer (RET) strategy and a dextrous target-initiated catalytic three-arm DNA junction assembly (CTDJA) based on a toehold strand displacement reaction (TSDR) signal amplification approach. Impressively, the ingenious system not only precisely regulates the distance between energy donor-acceptor pairs leave energy less loss and more ECL-RET efficiency, but also simplifies the operational procedure and verifies the feasibility of this self-assembly process without human intervention. This study can expand MoS2 NSs@QDs utilization in ECL biosensing applications, and the proposed nucleic acid amplification strategy can become a miracle cure for ultrasensitive detecting diverse biomarkers, which helps researchers to better study the tumor mechanism, thereby unambiguously increasing cancer cure rates and reducing the risk of recurrence.

Electrochemical biosensor strategy combining DNA entropy-driven technology to activate CRISPR-Cas13a activity and triple-stranded nucleic acids to detect SARS-CoV-2 RdRp gene

By merging DNA entropy-driven technology with triple-stranded nucleic acids in an electrochemical biosensor to detect the SARS-CoV-2 RdRp gene, we tackled the challenges of false negatives and the high cost of SARS-CoV-2 detection. The approach generates a CRISPR-Cas 13a-activated RNA activator, which then stimulates CRISPR-Cas 13a activity using an entropy-driven mechanism. The activated CRISPR-Cas 13a can cleave Hoogsteen DNA due to the insertion of two uracil (-U-U-) in Hoogsteen DNA. The DNA tetrahedra changed on the electrode surface and can therefore not construct a three-stranded structure after cleaving Hoogsteen DNA. Significantly, this DNA tetrahedron/Hoogsteen DNA-based biosensor can regenerate at pH = 10.0, which keeps Hoogsteen DNA away from the electrode surface, allowing the biosensor to function at pH = 7.0. We could use this technique to detect the SARS-CoV-2 RdRp gene with a detection limit of 89.86 aM. Furthermore, the detection method is very stable and repeatable. This technique offers the prospect of detecting SARS-CoV-2 at a reasonable cost. This work has potential applications in the dynamic assessment of the diagnostic and therapeutic efficacy of SARS-CoV-2 infection and in the screening of environmental samples.

Photochemical modifications for DNA/RNA oligonucleotides

Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.

Establishment of a universal and sensitive plasmonic biosensor platform based on the hybridization chain reaction (HCR) amplification induced by a triple-helix molecular switch

Herein, we established a universal and sensitive plasmonic sensing strategy for biomolecule assays by coupling the hybridization chain reaction (HCR) strategy and a triple-helix molecular switch. Upon the recognition of the target, a single-stranded DNA as a universal trigger (UT) was released from the triple-helix molecular switch (THMS). Thus, the HCR process can be triggered between two hairpins M1 and M2, resulting in the aggregation of gold nanoparticles (AuNPs) via the hybridization between the tail sequence on M1 (or M2) and a DNA-AuNP probe with a dramatic change in the absorbance at 521 nm. More specifically, the strategy, which was conducted by the introduction of target-specific recognition of THMS and universalized by virtue of altering the aptamer or DNA sequence without changing the triple-helix structure, enables simple design for multiple target detection. By taking advantage of THMS, this strategy could enable stable and sensitive detection of a variety of targets including nucleic acids, small molecules and proteins, which may possess great potential for practical applications.

Triggering nucleic acid nanostructure assembly by conditional kissing interactions

Nucleic acids are biomolecules of amazing versatility. Beyond their function for information storage they can be used for building nano-objects. We took advantage of loop–loop or kissing interactions between hairpin building blocks displaying complementary loops for driving the assembly of nucleic acid nano-architectures. It is of interest to make the interaction between elementary units dependent on an external trigger, thus allowing the control of the scaffold formation. To this end we exploited the binding properties of structure-switching aptamers (aptaswitch). Aptaswitches are stem–loop structured oligonucleotides that engage a kissing complex with an RNA hairpin in response to ligand-induced aptaswitch folding. We demonstrated the potential of this approach by conditionally assembling oligonucleotide nanorods in response to the addition of adenosine.

AFM-based single-molecule observation of the conformational changes of DNA structures

Direct visualization of the biomolecules of interest is a straightforward way to elucidate the physical properties of individual molecules and their reaction processes. Atomic force microscopy (AFM) enables direct imaging of biomolecules in suitable solution conditions. As AFM visualizes the molecules at a nanometer-scale spatial resolution, a versatile observation platform is required for precise imaging of the molecules in action. The DNA origami technology allows precise placement of target molecules in a designed nanostructure, enabling their detection at the single-molecule level. We used DNA origami technology for visualizing the detailed movement of target molecules in reactions using high-speed AFM (HS-AFM), which enables the analysis of dynamic movement of biomolecules with a subsecond time resolution. By combining the DNA origami system and HS-AFM, DNA conformational changes, including G-quadruplex formation and disruption and B-Z transition, were visualized. In addition, enzyme-based reactions such as DNA recombination were also visualized at the single-molecule level using this combined observation system. Moreover, the enzyme-based reaction could be directly regulated in the DNA origami frame by imposing structural stress on the substrate DNAs to elucidate the reaction mechanism. These target-orientated observation systems should contribute to a detailed analysis of biomolecular motions in real time at molecular resolution.

Triplex-forming oligonucleotides: a third strand for DNA nanotechnology

DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.

Triplex DNA Nanostructures: From Basic Properties to Applications

Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.

pH-Stimulated Reconfiguration and Structural Isomerization of Origami Dimer and Trimer Systems

Reversible pH-responsive dimer or trimer origami structures are assembled by bridging origami frames with pH-responsive units. The cyclic pH-stimulated separation and reassembly of dimer origami structures is demonstrated using i-motif or Hoogsteen-type (C-G·C⁺ or T-A·T) interactions. The duplex-bridged dimer T₁-T₂ is separated by the pH-induced formation of an i-motif structure (pH = 4.5), and the dimer is reassembled at pH = 7.0. The duplex-bridged dimer, T₃-T₄, is separated at pH = 4.5 through the formation of C-G·C⁺ triplex structures and is reassembled to the dimer at pH = 7.0. Similarly, the T-A·T triplex-bridged dimer, T₅-T₆, is separated at pH = 9.5 and is reassembled at neutral pH. Finally, a trimer, T₃-T₇-T₆, that includes C-G·C⁺ and T-A·T pH-responsive bridges reveals pH-programmed cleavage to selectively yield the dimers T₃-T₇ or T₇-T₆, which reassemble to the trimer at pH = 7.0. A linear three-frame origami structure bridged by duplexes including caged i-motif units undergoes pH-stimulated isomerization to a bent structure (pH = 4.5) through the formation of i-motif complex and bridging T-A·T triplex units.