We have developed hybridization-sensitive fluorescent oligonucleotide probes that, in the presence of quencher strands, undergo efficient fluorescence quenching through the formation of partial DNA/DNA duplexes. In the presence of target RNA, rapid displacement of the quencher strands results in highly enhanced fluorescence.
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http://dx.doi.org/10.1039/c7ra13349a | DOI Listing |
Bioconjug Chem
January 2025
Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1,Canada.
The ability to label synthetic oligonucleotides with fluorescent probes has greatly expanded their nanotechnological applications. To continue this expansion, it is essential to develop approachable, modular, and tunable fluorescent platforms. In this study, we present the synthesis and incorporation of an amino-formyl-thieno[3,2-]thiophene (AFTh) handle at the 5'-position of DNA oligonucleotides.
View Article and Find Full Text PDFTalanta
January 2025
School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China.
Sensitive and accurate detection and imaging of different microRNAs (miRNAs) in cancer cells hold great promise for early disease diagnosis. Herein, a DNA tetrahedral scaffold (DTS)-corbelled autonomous-motion (AM) molecular machine based fluorescent sensing platform was designed for simultaneous detection of two types of miRNAs (miRNA-21 and miRNA-155) in HeLa cells. Locking-strand-silenced DNAzymes (P:L duplex) were firstly grafted at the loop of target-analogue-embedded double-stem hairpin substrates (TDHS) of DTS, making the sensor in a "signal off" state due to the closely distance between modified fluorophores (FAM and Cy5) with the corresponding quenchers (BHQ1 and BHQ2).
View Article and Find Full Text PDFMicromachines (Basel)
November 2024
Department of Intelligent and Control Systems, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8502, Fukuoka, Japan.
DNA chemical reaction networks can perform complex information processing through careful design of reaction kinetics, which involves the reaction network structure, rate constants, and initial concentrations. The toehold-mediated strand displacement reaction (TMSDR) is a key mechanism in creating DNA circuits, offering a rational design approach by integrating individually designed TMSDRs. Tools such as VisualDSD and NUPACK facilitate the efficient design of these systems by allowing precise tuning of reaction parameters.
View Article and Find Full Text PDFACS Appl Mater Interfaces
January 2025
School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
Sensitive and accurate determination of acetamiprid is highly desirable for guaranteeing food safety. In this Letter, an energy-transfer-based dual-mode biosensor was developed using zinc-based metal-organic frameworks (Zn-MOFs) acting as both photoelectrochemical (PEC) and electrochemiluminescent (ECL) donors and Pt@CuO cubic nanocrystals (CNs) as the energy acceptor for detecting acetamiprid. By integration of aptamer recognition with two-step DNA circuit amplification (entropy-driven DNA cycle and DNA walker), the detection of acetamiprid was converted into the assay of abundant intermediate DNA strands.
View Article and Find Full Text PDFAnal Chem
December 2024
MOE Key Laboratory of Luminescence Analysis and Molecular Sensing, College of Chemistry and Chemical Engineering, Institute of Developmental Biology and Regenerative Medicine, Southwest University, Chongqing 400715, P. R. China.
Rapid and sensitive detection of DNA adenine methyltransferase (Dam) activity is crucial for both research and clinical applications. Herein, we utilize two types of spherical nucleic acids (SNAs) to specific response assemble into 3D space-confined DNA nanoaggregates that enable the rapid and sensitive detection of Dam activity. The SNAs feature 3D order DNA scaffolds that serve as cores for anchoring signal hairpin probes (S-HPs) and target hairpin probes (T-HPs).
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