ArticleNucleic acids research2011
Optimization of turn-back primers in isothermal amplification.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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
34 citing papers in PubMed.
- Development of a Highly Multiplexed RT-LAMP Assay for Coverage of Genetic Sequence Diversity.Analytical chemistry · 2025Article
- Rapid and simple detection ofFrontiers in microbiology · 2025Article
- Article
- Advances in point-of-care genetic testing for personalized medicine applications.Biomicrofluidics · 2023Review
- Positive feedback drives a secondary nonlinear product burst during a biphasic DNA amplification reaction.The Analyst · 2022Article
- Programmable design of isothermal nucleic acid diagnostic assays through abstraction-based models.Nature communications · 2022Article
- Genotype frequency of ATP7A and ATP7B mutation-related copper-associated hepatitis in a Japanese guide dog Labrador retriever population.The Journal of veterinary medical science · 2022Article
- Asymmetric stem-loop-mediated isothermal amplification of nucleic acids for DNA diagnostic assays by simple modification of canonical PCR primers.Frontiers in bioengineering and biotechnology · 2022Article
- Rapid and Specific Detection of the Poplar Black Spot Disease Caused byPlants (Basel, Switzerland) · 2021Article
- One-Step Nucleic Acid Purification and Noise-Resistant Polymerase Chain Reaction by Electrokinetic Concentration for Ultralow-Abundance Nucleic Acid Detection.Angewandte Chemie (International ed. in English) · 2020Article
- A Rapid, Sensitive, Low-Cost Assay for Detecting Hydrogenotrophic Methanogens in Anaerobic Digesters Using Loop-Mediated Isothermal Amplification.Microorganisms · 2020Article
- Dual-Priming Isothermal Amplification (DAMP) for Highly Sensitive and Specific Molecular Detection with Ultralow Nonspecific Signals.Analytical chemistry · 2019Article
- Comparison of Loop-Mediated Isothermal Amplification and Real-Time PCR Assays for Detection of Strongyloides Larvae in Different Specimen Matrices.Journal of clinical microbiology · 2019Article
- Development and validation of a loop-mediated isothermal amplification assay for the detection of Mycoplasma bovis in mastitic milk.Folia microbiologica · 2018Article
- Establishment of a universal and rational gene detection strategy through three-way junction-based remote transduction.Chemical science · 2018Article
- Amplicon Competition Enables End-Point Quantitation of Nucleic Acids Following Isothermal Amplification.Chembiochem : a European journal of chemical biology · 2017Article
- Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection.Frontiers in microbiology · 2017Article
- Ultrasensitive, rapid and inexpensive detection of DNA using paper based lateral flow assay.Scientific reports · 2016Article
- Strong-LAMP: A LAMP Assay for Strongyloides spp. Detection in Stool and Urine Samples. Towards the Diagnosis of Human Strongyloidiasis Starting from a Rodent Model.PLoS neglected tropical diseases · 2016Article
- Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The application of isothermal amplification technologies is rapidly expanding and currently covers different areas such as infectious disease, genetic disorder and drug dosage adjustment. Meanwhile, many of such technologies have complex reaction processes and often require a fine-tuned primer set where existing primer design tools are not sufficient. We have developed a primer selection system for one important primer, the turn-back primer (TP), which is commonly used in loop-mediated amplification (LAMP) and smart amplification process (SmartAmp). We chose 78 parameters related to the primer and target sequence, and explored their relationship to amplification speed using experimental data for 1344 primer combinations. We employed the least absolute shrinkage and selection operator (LASSO) method for parameter selection and estimation of their numerical coefficients. We subsequently evaluated our prediction model using additional independent experiments and compared to the LAMP primer design tool, Primer Explorer version4 (PE4). The evaluation showed that our approach yields a superior primer design in isothermal amplification and is robust against variations in the experimental setup. Our LASSO regression analysis revealed that availability of the 3'- and 5'-end of the primer are particularly important factors for efficient isothermal amplification. Our computer script is freely available at: http://gerg.gsc.riken.jp/TP_optimization/.
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.