DNA nano-carrier for repeatable capture and release of biomolecules

Terahertz Wave Accelerates DNA Unwinding: A Molecular Dynamics Simulation Study

Unwinding the double helix of the DNA molecule is the basis of gene duplication and gene editing, and the acceleration of this unwinding process is crucial to the rapid detection of genetic information. Based on the unwinding of six-base-pair DNA duplexes, we demonstrate that a terahertz stimulus at a characteristic frequency (44.0 THz) can serve as an efficient, nonthermal, and long-range method to accelerate the unwinding process of DNA duplexes. The average speed of the unwinding process increased by 20 times at least, and its temperature was significantly reduced. The mechanism was revealed to be the resonance between the terahertz stimulus and the vibration of purine connected by the weak hydrogen bond and the consequent break in hydrogen bond connections between these base pairs. Our findings potentially provide a promising application of terahertz technology for the rapid detection of nucleic acids, biomedicine, and therapy.

Novel Stable DNA Nanoscale Material and Its Application on Specific Enrichment of DNA

DNA nanostructures are a new type of technology for constructing nanomaterials that has been developed in recent years. By relying on the complementary pairing of DNA molecules to form a double-stranded property, DNA molecules can construct a variety of nanoscale structures of 2D and 3D shapes. However, most of the previously reported DNA nanostructures rely solely on hydrogen bonds to maintain structural stability, resulting in DNA structures that can be maintained only at low temperature and in the presence of Mg²⁺, which greatly limits the application of DNA nanostructures. This study designed a DNA nanonetwork structure (nanonet) and changed its topological structure to DNA nanomesh by using DNA topoisomerase to make it thermally stable, while escaping the dependence on Mg²⁺, and the stability of the structure can be maintained in a nonsolution state. Moreover, the nanomesh also has a large amount of ssDNA (about 50%), providing active sites capable of exerting biological functions. Using the above characteristics, we prepared the nanomesh into a device capable of adsorbing specific DNA molecules, and used the device to enrich DNA. We also tried to mount antibodies using DNA probes. Preliminary results show that the DNA nanomesh also has the ability to enrich specific proteins.

Recent Advances of Plasmonic Gold Nanoparticles in Optical Sensing and Therapy

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Gold nanoparticles with special surface plasmon resonance have been widely used in sensing and therapy because of their easy preparation, unique optical properties, excellent biocompatibility, etc. The applications of gold nanoparticles in chemo/biosensing, imaging, and therapy reported in 2016-2019, are summarized in this review. Regarding the gold nanoparticle-based sensing or imaging, sensing mechanisms and strategies are provided to illustrate the concepts for designing sensitive and selective detection platforms. Gold nanoparticlemediated therapy is introduced by surface plasmon resonance-based therapy and delivery-based therapy. Beyond the sole therapeutic system, platforms through synergistic therapy are also discussed. In the end, discussion of the challenges and future trends of gold nanoparticle-based sensing and therapy systems is described.

DNA Nanotweezers and Graphene Transistor Enable Label-Free Genotyping

Electronic DNA-biosensor with a single nucleotide resolution capability is highly desirable for personalized medicine. However, existing DNA-biosensors, especially single nucleotide polymorphism (SNP) detection systems, have poor sensitivity and specificity and lack real-time wireless data transmission. DNA-tweezers with graphene field effect transistor (FET) are used for SNP detection and data are transmitted wirelessly for analysis. Picomolar sensitivity of quantitative SNP detection is achieved by observing changes in Dirac point shift and resistance change. The use of DNA-tweezers probe with high-quality graphene FET significantly improves analytical characteristics of SNP detection by enhancing the sensitivity more than 1000-fold in comparison to previous work. The electrical signal resulting from resistance changes triggered by DNA strand-displacement and related changes in the DNA geometry is recorded and transmitted remotely to personal electronics. Practical implementation of this enabling technology will provide cheaper, faster, and portable point-of-care molecular health status monitoring and diagnostic devices.

Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex

Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing Hg^II-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C–Hg^II–T containing duplex, three T–Hg^II–T containing duplexes and one native duplex containing T–T pair without Hg^II. Our structures suggest that both C–T and T–T pairs are flexible in interacting with the Hg^II ion with various binding modes including N3–Hg^II–N3, N4–Hg^II–N3, O2–Hg^II–N3 and N3–Hg^II–O4. Our studies also reveal that the overall conformations of the C–Hg^II–T and T–Hg^II–T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as Sr^II. These results provide detailed insights into the interactions between Hg^II and nucleobases and the structural basis for the rational design of C–Hg^II–T or T–Hg^II–T containing DNA nanodevices in the future.

Highly specific SNP detection using 2D graphene electronics and DNA strand displacement

Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.