Dual catalytic DNA circuit-induced gold nanoparticle aggregation: An enzyme-free and colorimetric strategy for amplified detection of nucleic acids. 2020

Hadi Ravan, and Mojdeh Amandadi, and Mehdi Hassanshahian, and Shahram Pourseyedi
Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran. Electronic address: ravan@uk.ac.ir.

An enzyme-free dual catalytic DNA circuit for amplified detection of nucleic acids has been developed. The system functions based on a cyclic self-assembly of two auxiliary hairpins (H1 and H2) and three biotinylated hairpin oligonucleotides (H3, H4 and H5), in the format of two molecular circuits. In the upstream circuit, a target initiator (I) besides H1 and H2 hairpins constructs H1-H2 duplexes that trigger the operation of a subsequent circuit. In the downstream circuit, the H1-H2 duplex initiates cascaded self-assembly reactions, produces triplex H3-H4-H5, as sensing system, and releases the H1-H2 duplex as the catalyst for the self-assembly of additional hairpins. The H3-H4-H5 triplex acts as the scaffolds for assembling and orienting the streptavidin-functionalized gold nanoparticles (SA-AuNPs) into a lattice-like arrangement that generates a DNA-SA-AuNP cross-linked network, resulting in a dramatic pale red-to-blue color change. By ingeniously engaging two catalytic circuits with feedback amplification capabilities, the system can detect the target nucleic acid with an LOD value of 5 femtomolar and unambiguously discriminate spurious targets (i.e. targets containing substitution, insertion, and deletion nucleotides) without instrumentation. Simple and convenient operation of the assay makes the DNA circuit appropriate for point-of-care monitoring in resource-constrained settings.

UI MeSH Term Description Entries
D003124 Colorimetry Any technique by which an unknown color is evaluated in terms of standard colors. The technique may be visual, photoelectric, or indirect by means of spectrophotometry. It is used in chemistry and physics. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D006046 Gold A yellow metallic element with the atomic symbol Au, atomic number 79, and atomic weight 197. It is used in jewelry, goldplating of other metals, as currency, and in dental restoration. Many of its clinical applications, such as ANTIRHEUMATIC AGENTS, are in the form of its salts.
D015374 Biosensing Techniques Any of a variety of procedures which use biomolecular probes to measure the presence or concentration of biological molecules, biological structures, microorganisms, etc., by translating a biochemical interaction at the probe surface into a quantifiable physical signal. Bioprobes,Biosensors,Electrodes, Enzyme,Biosensing Technics,Bioprobe,Biosensing Technic,Biosensing Technique,Biosensor,Electrode, Enzyme,Enzyme Electrode,Enzyme Electrodes,Technic, Biosensing,Technics, Biosensing,Technique, Biosensing,Techniques, Biosensing
D053768 Metal Nanoparticles Nanoparticles produced from metals whose uses include biosensors, optics, and catalysts. In biomedical applications the particles frequently involve the noble metals, especially gold and silver. Metal Nanocrystals,Metallic Nanocrystals,Metallic Nanoparticles,Metal Nanocrystal,Metal Nanoparticle,Metallic Nanocrystal,Metallic Nanoparticle,Nanocrystal, Metal,Nanocrystal, Metallic,Nanocrystals, Metal,Nanocrystals, Metallic,Nanoparticle, Metal,Nanoparticle, Metallic,Nanoparticles, Metal,Nanoparticles, Metallic
D055029 Inverted Repeat Sequences Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions. Hairpin Loop Sequence,Inverted Repeat Sequence,Inverted Tandem Repeats,Palindromic Repeat Sequences,Sequence Palindromes,Stem-Loop Sequence,Hairpin Loop Sequences,Inverted Tandem Repeat,Palindrome, Sequence,Palindromes, Sequence,Palindromic Repeat Sequence,Repeat Sequence, Inverted,Repeat Sequence, Palindromic,Repeat Sequences, Inverted,Repeat Sequences, Palindromic,Repeat, Inverted Tandem,Repeats, Inverted Tandem,Sequence Palindrome,Sequence, Hairpin Loop,Sequence, Inverted Repeat,Sequence, Palindromic Repeat,Sequence, Stem-Loop,Sequences, Hairpin Loop,Sequences, Inverted Repeat,Sequences, Palindromic Repeat,Sequences, Stem-Loop,Stem Loop Sequence,Stem-Loop Sequences,Tandem Repeat, Inverted,Tandem Repeats, Inverted
D021881 DNA, Catalytic Molecules of DNA that possess enzymatic activity. Catalytic DNA,Deoxyribozymes,DNAzyme,DNAzymes,Deoxyribozyme

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