ArticleBioinformatics (Oxford, England)2017
Primerize-2D: automated primer design for RNA multidimensional chemical mapping.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed.
- Purification of post-transcriptionally modified tRNAs for enhanced cell-free translation systems.Nucleic acids research · 2026Article
- A Physics-Inspired Approach to Improve Oligonucleotide Design and Gene Synthesis.Computational and structural biotechnology journal · 2026Article
- Compact RNA sensors for increasingly complex functions of multiple inputs.Nature chemistry · 2025Article
- Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy.Nucleic acids research · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Anti-HIV-1 Effect of the Fluoroquinolone Enoxacin and Modulation of Pro-Viral hsa-miR-132 Processing in CEM-SS Cells.Non-coding RNA · 2025Article
- CertPrime: a new oligonucleotide design tool for gene synthesis.Computational and structural biotechnology journal · 2025Article
- Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.ACS synthetic biology · 2024Article
- Using QUASR-PCR as a field-based genotyping assay for a tick acaricide resistance marker.Scientific reports · 2024Article
- Molecular mechanism of glutaminase activation through filamentation and the role of filaments in mitophagy protection.Nature structural & molecular biology · 2023Article
- Efficient 3'-pairing renders microRNA targeting less sensitive to mRNA seed accessibility.Nucleic acids research · 2023Article
- RNA:RNA interaction in ternary complexes resolved by chemical probing.RNA (New York, N.Y.) · 2023Article
- CD4 binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wild-type animals.Science immunology · 2023Article
- Electrophoretic Mobility Shift Assay (EMSA) and Microscale Thermophoresis (MST) Methods to Measure Interactions Between tRNAs and Their Modifying Enzymes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Assessment of enzymatically synthesized DNA for gene assembly.Frontiers in bioengineering and biotechnology · 2023Article
- Near-Atomic Resolution Cryo-EM Image Reconstruction of RNA.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Retron reverse transcriptase termination and phage defense are dependent on host RNase H1.Nucleic acids research · 2022Article
- Precise genome editing across kingdoms of life using retron-derived DNA.Nature chemical biology · 2022Article
- Digital Microfluidics Chips for the Execution and Real-Time Monitoring of Multiple Ribozymatic Cleavage Reactions.ACS omega · 2021Article
- High-throughput functional variant screens via in vivo production of single-stranded DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors. We report here an online tool to accelerate synthesis of large libraries of desired mutants through design and efficient organization of primers. The underlying program and graphical interface have been experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides and libraries encompassing up to 960 variants. In addition to the freely available Primerize-2D server, the primer design code is available as a stand-alone Python package for broader applications. Availability and Implementation: http://primerize2d.stanford.edu. Contact: rhiju@stanford.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.