Kinetics of Strand Displacement Reaction with Acyclic Artificial Nucleic Acids.

Toehold-mediated strand displacement (TMSD) reaction, one of the DNA nanotechnologies, has great potential as s biological programmable platform in the cellular environment. Various artificial nucleic acids have been developed to improve stability and affinity for biological applications. However, the lack of understanding of the kinetics of TMSD reaction among artificial nucleic acids has limited their applications.

Color-Changing Fluorescent Barcode Based on Strand Displacement Reaction Enables Simple Multiplexed Labeling.

Fluorescence imaging techniques have contributed to our understanding of various biological phenomenon; however, fluorescence spectral overlap significantly restricts multiplexing capability. Several strategies have been reported to overcome this limitation by utilizing the superior programmability of DNA technologies and nanostructures, but in practice, it remains challenging to achieve broad adoption of these multiplexed detection methods due to the complexities of these DNA designs. Here we report a color-changing fluorescent barcode (CCFB) approach that enables multiple labeling with simple and small nucleic acid structure design based on sequential toehold-mediated strand displacement reaction.

Preparation of Artificial Hexaplex Composed of Non-Natural Nucleic Acid.

This article describes synthetic procedures for acyclic D-threoninol nucleic acid tethering of bifacial nucleobases. Because these nucleobases have complementary hydrogen bonding sites on both sides, their oligomers can form a hexaplex. These hexaplexes are suitable for use as metal or pH sensors and as supramolecular motifs.

Microheater-integrated zinc oxide nanowire microfluidic device for hybridization-based detection of target single-stranded DNA.

Detection of cell-free DNA (cfDNA) has an impact on DNA analysis in liquid biopsies. However, current strategies to detect cfDNA have limitations that should be overcome, such as having low sensitivity and requiring much time and a specialized instrument. Thus, non-invasive and rapid detection tools are needed for disease prevention and early-stage treatment.

Bifurcated synthesis of methylene-lactone- and methylene-lactam-fused spirolactams via electrophilic amide allylation of γ-phenylthio-functionalized γ-lactams.

New synthetic methods for spirolactams bearing an α-methylene-γ-butyrolactone or its analogous methylene-lactam have been developed. The allylation of γ-phenylthio-functionalized γ-lactams with 2-(acetoxy)methyl acrylamides was accomplished by using 2.5 equivalents of NaH to give the corresponding adducts in excellent yields.

Selective binding of nucleosides to gapped DNA duplex revealed by orientation and distance dependence of FRET.

Herein we used orientation and distance dependence of Förster resonance energy transfer (FRET) to analyze the binding of nucleosides to a gapped DNA duplex. Binding isotherms and information on the structures of the complexes were obtained by monitoring FRET between pyrene and perylene, which were introduced into the DNA through d-threoninol. FRET efficiency significantly changed upon formation of a duplex with a 1-nucleotide gap and a nucleoside.