ReviewNucleic acids research2018
Engineering altered protein-DNA recognition specificity.
Review in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed.
- Recent Advancements for Enhanced Biocatalyst and Biotransformation.Molecular biotechnology · 2026Review
- Modular determinants of cleavage preference in GIY-YIG nucleases revealed by block-based DNA shuffling and directed evolution.Nucleic acids research · 2026Article
- PRIMED: predicting DNA binding residues by leveraging pre-trained protein language models.Frontiers in artificial intelligence · 2026Article
- RNA sequence design and protein-DNA specificity prediction with NA-MPNN.bioRxiv : the preprint server for biology · 2025Article
- Engineering Protein-Polyelectrolyte Interactions for Cellular Applications.Annual review of chemical and biomolecular engineering · 2025Review
- Mutations to transcription factor MAX allosterically increase DNA selectivity by altering folding and binding pathways.Nature communications · 2025Article
- Recent advances in designing synthetic plant regulatory modules.Frontiers in plant science · 2025Review
- Dynamics in Cre-loxP site-specific recombination.Current opinion in structural biology · 2024Review
- Updated understanding of the protein-DNA recognition code used by C2H2 zinc finger proteins.Current opinion in structural biology · 2024Review
- Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review.Briefings in bioinformatics · 2023Review
- An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges.Functional & integrative genomics · 2023Review
- High-throughput CRISPR technology: a novel horizon for solid organ transplantation.Frontiers in immunology · 2023Review
- Article
- Intracellular RNase activity dampens zinc finger nuclease-mediated gene editing in hematopoietic stem and progenitor cells.Molecular therapy. Methods & clinical development · 2022Article
- Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM.Nucleic acids research · 2022Article
- An Update of Nucleic Acids Aptamers Theranostic Integration with CRISPR/Cas Technology.Molecules (Basel, Switzerland) · 2022Review
- Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182.ACS omega · 2022Article
- Choosing the Right Tool for Genetic Engineering: Clinical Lessons from Chimeric Antigen Receptor-T Cells.Human gene therapy · 2021Review
- Sequence modification on demand: search and replace tools for precise gene editing in plants.Transgenic research · 2021Review
- HK022 bacteriophage Integrase mediated RMCE as a potential tool for human gene therapy.Nucleic acids research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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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.