Search

Simultaneous self-assembly of two distinct DNA origami nanostructures folded with the same scaffold strand was achieved in a single pot. Relative yields were tuned by adjusting concentrations of the competing strands, correlating well with folding kinetics of individual structures. These results can faciliate efficient fabrication of multi-structure systems and materials. [ABSTRACT FROM AUTHOR]

We constructed a rotary DNA origami device and tested its stepping operation on a mica substrate by sequential strand displacement with four different sets of signal DNA strands. This work paves the way for building a variety of dynamic rotary DNA nanodevices which respond to multiple signals. [ABSTRACT FROM AUTHOR]

We present a polymer-enhanced capillary transient isotachophoresis (PectI) selection methodology for acquisition of high-affinity (kinetically inert) DNA aptamers capable of recognizing distinct microbial cell surfaces, which requires only a single electrophoretic separation between particles (free cells and cells bound with aptamers) and molecules (unbound or dissociated DNA) in free solution. [ABSTRACT FROM AUTHOR]

The mechanism of DNA assembly is revealed by analyzing the energy barriers during nucleation and growth. The assembly is controlled by two competing parameters: the conformation adjustment rate of DNA strands and the spreading rate of new strands on the nuclei surface, both of which are temperature dependent and can be tuned by sequence design. [ABSTRACT FROM AUTHOR]

A strategy for the electrochemical detection of DNA based on catalytic hairpin assembly combined with nanocatalyst label-based redox cycling reaction signal amplification. A superior detection limit of 0.3 aM toward DNA can be achieved. [ABSTRACT FROM AUTHOR]

An ultrasensitive cytosensor based on DNA-rolling-circle-amplification-directed enzyme-catalyzed polymerization is demonstrated. As a proof of concept, the cytosensor shows excellent sensitivity for MCF-7 cell detection with a lower detection limit of 12 cells per mL. [ABSTRACT FROM AUTHOR]

Linear and cross-linked dynamic constitutional frameworks generated from reversibly interacting linear PEG/core constituents and cationic sites shed light on the dominant coiling versus linear DNA binding behaviours, closer to the histone DNA binding wrapping mechanism. [ABSTRACT FROM AUTHOR]

The activity of uracil-DNA glycosylase (UDG), an enzyme in the base excision repair, is detected at a high sensitivity by a DNA substrate containing only one uracil through a label-free fluorescent approach, which is also successfully applied for the measurement of UDG inhibitors. [ABSTRACT FROM AUTHOR]

Here we introduce an enzyme-free and colorimetric detection strategy for small molecule adenosine. The approach is based on the adenosine–aptamer binding triggered liberation of an initiator strand that consecutively catalyzes DNA hairpins hybridized from singles to couples. These couples induce gold nanoparticles assembled via crosslinking, which could be visualized by a color change. [ABSTRACT FROM AUTHOR]

Here, we highlight the strategies for the synthesis and tuning of a variety of metal nanostructures and nanoassemblies with oligonucleotides and their applications. We have discussed the importance of and need for various metal nanostructures and the role and suitability of DNA in building these nanostructures and nanoassemblies. A large part of this article is devoted to the discussion of DNA-mediated synthetic methods for metal nanostructures. The synthetic strategies are categorized into two groups – strategy 1 that uses DNA as the ligand for metal nanoparticles and subsequent assembly or modification and strategy 2 that uses DNA template-directed assemblies of metal nanoparticles. [ABSTRACT FROM AUTHOR]

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical attributes and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that target single base mismatches in duplex DNA through metallo-insertion. [ABSTRACT FROM AUTHOR]

A logical switching MB is established, with an “ON/OFF” switching function. In this study, thiolated DNA can participate as a switching controller to regulate the fluorescent increments of other DNA input signals. Assisted by gold nanoparticles and DNA branch migration, one and two-switch systems have been achieved. [ABSTRACT FROM AUTHOR]

A DNA nano-zipper built from double crossover structures is demonstrated in this work. The open and close states of the zipper are reversibly controlled by the temperature switch. [ABSTRACT FROM AUTHOR]

DNA single strands can be applied as templates for the self-assembly of Py≡dU chromophores in H2O with optical properties that are very similar to Py≡dU stacks that are covalently attached to DNA. The chirality, however, of the non-covalent stacks is opposite to that of the covalent stacks. [ABSTRACT FROM AUTHOR]

We have demonstrated an efficient phosphorescence energy transfer (PET) system for ultrasensitive detection of DNA. [ABSTRACT FROM AUTHOR]

A simple, isothermal and autocatalytic system for the amplified detection of DNA was ingeniously designed based on target-triggered Y-shaped junction probe assembly, followed with a nicking endonuclease-mediated cascade recycling process. A superior detection limit of 0.1 pM towards the target DNA with an excellent selectivity could be achieved. [ABSTRACT FROM AUTHOR]

This study is the first to investigate the interactions of hemin with a G-triplex DNA of T1 using different DNA binding assays. The low intrinsic peroxidatic activity of hemin could be significantly enhanced using T1. Furthermore, much decreased oxidation enhancement by T2 or T3 with one key guanine mutation was observed, and the observed peroxidatic activity of T1 should be directly due to the G-triplex complexed with hemin. [ABSTRACT FROM AUTHOR]

An anti-galvanic replacement reaction (AGRR) of copper(ii) ions reduced by ultra-small ssDNA-templated silver nanoclusters forming Ag–Cu alloy nanoparticles was observed. The reaction is against the classic galvanic theory and was monitored sensitively by the light-scattering technique. [ABSTRACT FROM AUTHOR]

A DNA molecule is rotated under a transversal electric field to be perpendicular to a longitudinal, multicomponent microfluidic flow. Positioning the interface allows us to control DNA unzipping with spatio-temporal resolution. This demonstrates that a microfluidic gradient can be applied at the single molecule level for a dynamic intramolecular stimulation. [ABSTRACT FROM AUTHOR]

With the use of a chemistry-based artificial restriction DNA cutter (combination of Ce(iv)–EDTA and a pair of pcPNA), both an antibiotic-resistance gene and a fluorescent reporter protein gene were incorporated into the targeted site through homologous recombination in human cells. [ABSTRACT FROM AUTHOR]

A method based on electrogenerated chemiluminescence (ECL) for detection of DNA methylation and assay of the methyltransferase activity is developed, and it is demonstrated that the label-free ECL method is capable of detecting methyltransferase with a detection limit of 3 × 10−6 U mL−1, using a supersandwich amplification technique. [ABSTRACT FROM AUTHOR]

A sensitive fluorescent sensor for sequence-specific recognition of dsDNA was established with a molecular beacon (MB) based upon the formation of parallel triplex DNA in the presence of Ag+ under neutral pH environment. [ABSTRACT FROM AUTHOR]

Single-stranded DNA was utilized as a probe tip for single-molecule DNA detection. Hybridization of the DNA tip and target DNA induces electron tunneling through the resulting DNA duplex. It is demonstrated that the DNA tip allows not only genetic detection but also discovery of single-nucleotide polymorphisms at the single-molecule level. [ABSTRACT FROM AUTHOR]

We report a reagentless and reusable “signal-on” electrochemical DNA sensor that utilizes oligo-thymine as a flexible spacer. This sensor design is sensitive, specific, and selective; it is potentially generalizable for detection of a wide range of biomedical-relevant nucleic acid sequences. [ABSTRACT FROM AUTHOR]

We herein report a power-free microfluidic chip for fluorescent DNA detection with high single-nucleotide polymorphism discrimination, using a DNA intercalator and graphene oxide. [ABSTRACT FROM AUTHOR]

We present a unique, label-free and resettable molecular keypad lock that utilizes DNA-modulated Ag nanoclusters (Ag NCs) as signal responsers. The present work demonstrates the first example that exonuclease-catalyzed DNA hydrolysis reaction could be used to achieve the RESET function of a molecular keypad without complicated procedures. [ABSTRACT FROM AUTHOR]

We report a novel approach for effectively separating DNA molecules in free solution. The method uses a bare narrow open capillary without any sieving matrices to resolve a wide size-range of DNA fragments at efficiencies of more than a million plates per meter routinely. [ABSTRACT FROM AUTHOR]

Using the RNA transcript as a template, RNA-templated DNA origami structures were constructed by annealing with designed DNA staple strands. RNA-templated DNA origami structures were folded to form seven-helix bundled rectangular structures and six-helix bundled tubular structures. The chemically modified RNA–DNA hybrid origami structures were prepared by using RNA templates containing modified uracils. [ABSTRACT FROM AUTHOR]

A unique capability of Endonuclease IV in discrimination of mismatches neighboring a natural abasic site in DNA strands has been demonstrated, which enables genotyping of SNPs with high discrimination factors and differentiation of as low as 0.1–0.01% of target DNA strands from a large background of single-base different interfering strands. [ABSTRACT FROM AUTHOR]

The high SNP discrimination ratio of 360 : 1, 100% target-specific hybridization at 25 °C, detection limit of 101 copies, and differentiation of 101 to 107 copies of the PCR product of high-risk HPV genotypes in clinical samples ensure the application of the 9G membrane in a convenient platform for DNA genotyping. [ABSTRACT FROM AUTHOR]

Benzo-fused cyclobutanols were developed as novel DNA cleaving molecules. The molecules nick a strand of supercoiled DNA under acidic conditions. By contrast, almost no activity was observed under neutral or basic conditions. [ABSTRACT FROM AUTHOR]

1,10-Phenanthroline-5,6-dione and l-tyrosine methyl ester react to form phenanthroline–oxazine (PDT) from which [Cu(PDT)2](ClO4)2 and [Ag(PDT)2]ClO4·2MeOH are obtained. Binding to calf-thymus DNA by Ag(i) and Cu(ii) PDT complexes exceed bis-1,10-phenanthroline analogues and the minor groove binding drugs, pentamidine and netropsin. Furthermore, unlike the artificial metallonuclease, [Cu(phen)2]2+, the [Cu(PDT)2]2+ complex does not cleave DNA in the presence of added reductant indicating unique interaction with DNA. [ABSTRACT FROM AUTHOR]

A label-free, colorimetric method has been developed for ultrasensitive detection of nucleic acids that is based on photoinduced silver ion (Ag+) reduction around DNA bases. The assay system is capable of directly detecting bacterial genomic DNA without the need for PCR amplification. [ABSTRACT FROM AUTHOR]

Based on the K-doped graphene–CdS:Eu NC composites and the nicking endonuclease (NEase) assisted strand-scission cycle, we have developed an ultrasensitive and selective electrochemiluminescence (ECL) DNA biosensor using the G-quadruplex–hemin-based DNAzyme which acts as an electrocatalyst for the reduction of H2O2, the coreactant of CdS:Eu NCs ECL. [ABSTRACT FROM AUTHOR]

SP1 protein as a new type of biological nanopore is described and is utilized to distinguish single-stranded DNA at the single-molecule level. Using the SP1 nanopore to investigate single molecule detection broadens the existing research areas of pore-forming biomaterials from unsymmetrical biological nanopores to symmetrical biological nanopores. This novel nanopore could provide a good candidate for single-molecule detection and characterization of biomaterial applications. [ABSTRACT FROM AUTHOR]

A 6-mer oligonucleotide containing a fluorescent BodU moiety has been used as a novel fluorescent probe for the 3′-overhang of telomeric DNA based on competition between non-fluorescent tetramolecular and fluorescent (3+1) intermolecular G-quadruplexes. [ABSTRACT FROM AUTHOR]

It is demonstrated that the shapes and magnitudes of DNA writhe can be precisely manipulated solely through maneuvering the nucleotide sequence of DNA and without the assistance of topoisomerases. [ABSTRACT FROM AUTHOR]

Paper strips containing DNA-conjugated microgels (MG) are used to achieve sensitive DNA detection in three steps: target DNA promoted ligation of a DNA primer to the MG-bound DNA, rolling circle amplification (RCA) between the primer and a circle DNA, and hybridization of the RCA products and a fluorescent DNA probe. [ABSTRACT FROM AUTHOR]

A chelator and a pro-chelator that can be activated by H2O2and subsequently sequesters iron and attenuates the Fenton reaction have been developed; both molecules are fluorescent excitable by visible light, and H2O2-activation, as well as iron-chelation, induces remarkable changes in fluorescence. [ABSTRACT FROM AUTHOR]

A novel modular strategy towards the assembly of DNA-based catalysts containing a covalently anchored metal complex is presented. [ABSTRACT FROM AUTHOR]

A molecular beacon that incorporates components of an artificially expanded genetic information system (Aegis) in its stem is shown not to be opened by unwanted stem invasion by adventitious standard DNA; this should improve the “darkness” of the beacon in real-world applications. [ABSTRACT FROM AUTHOR]

Cyanine dyes attached to DNA via a rigid linker show useful fluorescence and FRET properties without altering the stability of duplex DNA. [ABSTRACT FROM AUTHOR]

A dinuclear ruthenium(ii) complex groove binds to DNA and this interaction results in distinctive color changes that are dependent on both DNA sequence and structure. [ABSTRACT FROM AUTHOR]

The triarylpyridines are potent G-quadruplex ligands that are highly discriminating against duplex DNA and show promising selectivity between intramolecular quadruplexes. [ABSTRACT FROM AUTHOR]

The chromophores pyrene and bordipyrromethenylbenzene directly linked to the 5-position of uridine are tolerated and recognized as thymine derivatives by DNA polymerases in primer extension experiments. [ABSTRACT FROM AUTHOR]

We demonstrate that DNA oligonucleotides covalently coupled to colloidal microgel can be manipulated by T4 DNA ligase for DNA ligation and by Phi29 DNA polymerase for rolling circle amplification (RCA). We also show that the long single-stranded RCA product can generate intensive fluorescence upon hybridization with complementary fluorescent DNA probe. We believe DNA–microgel conjugates can be explored for the development of DNA based bioassays and biosensors. [ABSTRACT FROM AUTHOR]

We report here sequence-specific liquid/liquid extraction of single-stranded DNA using reverse micelles (water-in-oil microemulsions), in which hybridization between a DNA-surfactant and a target DNA having a complementary sequence allows selective transport of the target DNA to an organic phase from a mixture of DNA oligonucleotides. [ABSTRACT FROM AUTHOR]

A DNAzyme-based label-free method for the colorimetric detection of DNA is introduced, with a supramolecular hemin–G-quartet complex as the sensing element and a 36-mer single-strand DNA as the analyte that is detected at 10 nM. [ABSTRACT FROM AUTHOR]

The kinetics of DNA duplex formation was affected by the addition of PEGs with different masses (MW = 200–8000) to an aqueous solution; for each condition, two duplexes (5′-TAGGTTATAA-3′/5′-TTATAACCTA-3′ and 5′-CAGGTCACAG-3′/5′-CTGTGACCTG-3′) with different stabilities were formed after overcoming the same association activation energy barrier, suggesting that the formation of consecutive GC base pairs in the helices rather than the helix terminus is the initiation nucleus for DNA duplex formation not only in the absence, but also in the presence of PEGs. [ABSTRACT FROM AUTHOR]