ArticleThe journal of physical chemistry. A2019
Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.
Article in The journal of physical chemistry. A, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Structural integrity and side-chain interaction at the loop region of the bridge helix modulate Cas9 substrate discrimination.Nucleic acids research · 2025Article
- A DNA unwinding equilibrium serves as a checkpoint for CRISPR-Cas12a target discrimination.Nucleic acids research · 2023Article
- Design of the elusive proteinaceous oxygen donor copper site suggests a promising future for copper for MRI contrast agents.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- EPR Spectroscopy Provides New Insights into Complex Biological Reaction Mechanisms.The journal of physical chemistry. B · 2022Review
- Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM.The CRISPR journal · 2022Article
- 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Measurement of distances between spectroscopic labels (e.g., spin labels, fluorophores) attached to specific sites of biomolecules is an important method for studying biomolecular complexes. ALLNOX (Addition of Labels and Linkers) has been developed as a program to model interlabel distances based on an input macromolecule structure. Here, we report validation of ALLNOX using measured distances between nitroxide spin labels attached to specific sites of a protein-DNA complex. The results demonstrate that ALLNOX predicts average interspin distances that matched with values measured with pairs of labels attached at the protein and/or DNA. This establishes a solid foundation for using spin labeling in conjunction with ALLNOX to investigate complexes without high-resolution structures. With its high degree of flexibility for the label or the target biomolecule, ALLNOX provides a useful tool for investigating the structure-function relationship in a large variety of biological molecules.
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Registered trials
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