ArticleChemistry (Weinheim an der Bergstrasse, Germany)2011
Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids.
Article in Chemistry (Weinheim an der Bergstrasse, Germany), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- DNA Nanomachine (DNM) Biplex Assay for DifferentiatingInternational journal of molecular sciences · 2023Article
- Single-tube isothermal label-free fluorescent sensor for pathogen detection based on genetic signatures.Frontiers in chemistry · 2022Article
- Interrogation of highly structured RNA with multicomponent deoxyribozyme probes at ambient temperatures.RNA (New York, N.Y.) · 2020Article
- Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis.Biosensors & bioelectronics · 2020Article
- Toward a Rational Approach to Design Split G-Quadruplex Probes.ACS chemical biology · 2019Article
- Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons.Analytical chemistry · 2019Article
- A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids.Chemical communications (Cambridge, England) · 2017Article
- A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences.Electroanalysis · 2017Article
- DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection.Chemical communications (Cambridge, England) · 2016Article
- Nonequilibrium Hybridization Enables Discrimination of a Point Mutation within 5-40 °C.Journal of the American Chemical Society · 2016Article
- Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors.RNA (New York, N.Y.) · 2015Article
- Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA.Scientific reports · 2015Article
- Molecular beacons: a novel optical diagnostic tool.Archivum immunologiae et therapiae experimentalis · 2013Review
- Detection of bacterial 16S rRNA using a molecular beacon-based X sensor.Biosensors & bioelectronics · 2013Article
- Operating Cooperatively (OC) sensor for highly specific recognition of nucleic acids.PloS one · 2013Article
- Review
- DNA nanotechnology for nucleic acid analysis: DX motif-based sensor.Chembiochem : a European journal of chemical biology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.