A Differential Fluorescent Receptor for Nucleic Acid Analysis

Bengtson, Hillary N.; Kolpashchikov, Dmitry M.

doi:10.1002/cbic.201300657

Cited by 11 publications

(4 citation statements)

References 61 publications

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“…The LOD of SDA was in subnanomolar range similar to other aptameric sensors that do not used signal amplification strategies . For SDA, the LOD could be limited by an aptamer-dye dissociation constant.…”

Section: Resultsmentioning

confidence: 99%

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Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons

et al. 2019

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Hybridization probes have been used for the detection of single nucleotide variations (SNV) in DNA and RNA sequences in the mix-and-read formats. Among the most conventional are Taqman probes, which require expensive quantitative polymerase chain reaction (qPCR) instruments with melting capabilities. More affordable isothermal amplification format requires hybridization probes that can selectively detect SNVs isothermally. Here we designed a split DNA aptamer (SDA) hybridization probe based on a recently reported DNA sequence that binds a dapoxyl dye and increases its fluorescence (Kato, T.; Shimada, I.; Kimura, R.; Hyuga, M., Light-up fluorophore-DNA aptamer pair for label-free turn-on aptamer sensors. Chem. Commun. 2016, 52, 4041−4044). SDA uses two DNA strands that have low affinity to the dapoxyl dye unless hybridized to abutting positions at a specific analyte and form a dye-binding site, which is accompanied by up to a 120-fold increase in fluorescence. SDA differentiates SNV in the inhA gene of Mycobacterium tuberculosis at ambient temperatures and detects a conserved region of the Zika virus after isothermal nucleic acid sequence based amplification (NASBA) reaction. The approach reported here can be used for detection of isothermal amplification products in the mix-and-read format as an alternative to qPCR.

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Section: Resultsmentioning

confidence: 99%

“…The LOD of SDA was in subnanomolar range similar to other aptameric sensors that do not used signal amplification strategies. 38 For SDA, the LOD could be limited by an aptamer-dye dissociation constant. Typical dissociation constants for an aptameric complex is from picomolar to mid nanomolar range.…”

Section: Analytical Chemistrymentioning

confidence: 99%

Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons

et al. 2019

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“…Multicomponent probes can also be designed to tolerate SNVs , or to detect a selected SNV, while being tolerant to other SNVs in the analyzed sequences . The latter is important to maintain binding affinity to highly mutagenic viral sequences.…”

Section: Addressing the Selectivity Issuementioning

confidence: 99%

Evolution of Hybridization Probes to DNA Machines and Robots

Kolpashchikov

2019

Acc. Chem. Res.

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Hybridization probes are RNA or DNA oligonucleotides or their analogs that bind to specific nucleotide sequences in targeted nucleic acids (analytes) via Watson−Crick base pairs to form probe−analyte hybrids. Formation of a stable hybrid would indicate the presence of a DNA or RNA fragment complementary to the known probe sequence. Some of the well-known technologies that rely on nucleic acid hybridization are TaqMan and molecular beacon (MB) probes, fluorescent in situ hybridization (FISH), polymerase chain reaction (PCR), antisense, siRNA, and CRISPR/cas9, among others. Although invaluable tools for DNA and RNA recognition, hybridization probes suffer from several common disadvantages including low selectivity under physiological conditions, low affinity to folded single-stranded RNA and double-stranded DNA, and high cost of dye-labeled and chemically modified probes. Hybridization probes are evolving into multifunctional molecular devices (dubbed here "multicomponent probes", "DNA machines", and "DNA robots") to satisfy complex and often contradictory requirements of modern biomedical applications. In the definition used here, "multicomponent probes" are DNA probes that use more than one oligonucleotide complementary to an analyzed sequence. A "DNA machine" is an association of a discrete number of DNA strands that undergoes structural rearrangements in response to the presence of a specific analyte. Unlike multicomponent probes, DNA machines unify several functional components in a single association even in the absence of a target. DNA robots are DNA machines equipped with computational (analytic) capabilities. This Account is devoted to an overview of the ongoing evolution of hybridization probes to DNA machines and robots. The Account starts with a brief excursion to historically significant and currently used instantaneous probes. The majority of the text is devoted to the design of (i) multicomponent probes and (ii) DNA machines for nucleic acid recognition and analysis. The fundamental advantage of both designs is their ability to simultaneously address multiple problems of RNA/DNA analysis. This is achieved by modular design, in which several specialized functional components are used simultaneously for recognition of RNA or DNA analytes. The Account is concluded with the analysis of perspectives for further evolution of DNA machines into DNA robots.

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“… 1 ). Among these attempts are the developments of molecular beacons 2 3 4 5 6 7 8 , conformationally constrained binary probes 9 10 11 , probes modified with artificial nucleotides such as peptide nucleic acids (PNAs) 8 12 13 14 and locked nucleic acids (LNAs) 14 15 16 17 etc. Thermodynamic approaches such as an elevated hybridization temperature (close to the duplex melting point) 18 19 or high concentrations of chaotropic agents in hybridization buffers 19 20 21 are often used to weaken non-complementary strand interactions in order to increase specificity.…”

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Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

Khodakov

Khodakova

Huang

et al. 2015

Sci Rep

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Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.

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A Differential Fluorescent Receptor for Nucleic Acid Analysis

Cited by 11 publications

References 61 publications

Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons

Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons

Evolution of Hybridization Probes to DNA Machines and Robots

Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

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