ArticleNucleic acids research2012
Sequence dependence of isothermal DNA amplification via EXPAR.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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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.
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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.
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Who cites it
33 citing papers in PubMed, 119 citations in OpenAlex.
- Robust Sequence Design Space for the Isothermal Exponential Amplification of Short Oligonucleotides.Small (Weinheim an der Bergstrasse, Germany) · 2024Article
- One-Tube Nested PCR Coupled with CRISPR-Cas12a for Ultrasensitive Nucleic Acid Testing.ACS omega · 2024Article
- Three-way junction structure-mediated reverse transcription-free exponential amplification reaction for pathogen RNA detection.Analytical and bioanalytical chemistry · 2024Article
- Replication elongates short DNA, reduces sequence bias and develops trimer structure.Nucleic acids research · 2024Article
- Integrating Genomic Data with the Development of CRISPR-Based Point-of-Care-Testing for Bacterial Infections.Current clinical microbiology reports · 2024Review
- Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections.International journal of molecular sciences · 2023Review
- Trigging stepwise-strand displacement amplification lights up numerous G-quadruplex for colorimetric signaling of serum microRNAs.iScience · 2023Article
- Suitability evaluation of toehold switch and EXPAR for cell-free MicroRNA biosensor development.Biotechnology notes (Amsterdam, Netherlands) · 2023Article
- Programmable molecular circuit discriminates multidrug-resistant bacteria.Materials today. Bio · 2022Article
- The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk.International journal of molecular sciences · 2022Review
- Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Three-Way Junction-Induced Isothermal Amplification with High Signal-to-Background Ratio for Detection of Pathogenic Bacteria.Sensors (Basel, Switzerland) · 2021Article
- Engineering Infrequent DNA Nicking Endonuclease by Fusion of aFrontiers in microbiology · 2021Article
- Point of Care Diagnostics in the Age of COVID-19.Diagnostics (Basel, Switzerland) · 2020Review
- Review
- Article
- Physical and chemical template-blocking strategies in the exponential amplification reaction of circulating microRNAs.Analytical and bioanalytical chemistry · 2020Article
- Isothermal digital detection of microRNAs using background-free molecular circuit.Science advances · 2020Article
- A label-free aptamer-based biosensor for microRNA detection by the RNA-regulated fluorescence of malachite green.RSC advances · 2019Article
- A mathematical model for a biphasic DNA amplification reaction.Journal of the Royal Society, Interface · 2019Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Isothermal nucleic acid amplification is becoming increasingly important for molecular diagnostics. Therefore, new computational tools are needed to facilitate assay design. In the isothermal EXPonential Amplification Reaction (EXPAR), template sequences with similar thermodynamic characteristics perform very differently. To understand what causes this variability, we characterized the performance of 384 template sequences, and used this data to develop two computational methods to predict EXPAR template performance based on sequence: a position weight matrix approach with support vector machine classifier, and RELIEF attribute evaluation with Naïve Bayes classification. The methods identified well and poorly performing EXPAR templates with 67-70% sensitivity and 77-80% specificity. We combined these methods into a computational tool that can accelerate new assay design by ruling out likely poor performers. Furthermore, our data suggest that variability in template performance is linked to specific sequence motifs. Cytidine, a pyrimidine base, is over-represented in certain positions of well-performing templates. Guanosine and adenosine, both purine bases, are over-represented in similar regions of poorly performing templates, frequently as GA or AG dimers. Since polymerases have a higher affinity for purine oligonucleotides, polymerase binding to GA-rich regions of a single-stranded DNA template may promote non-specific amplification in EXPAR and other nucleic acid amplification reactions.
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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.