ArticleJournal of the American Chemical Society2012
Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 50 citations in OpenAlex.
- The Bacteriophage VMY 22 Has Enhanced the Stability of Its Functional Proteins via Adaptive Evolution in a Temperature-Varying Environment.Bioengineering (Basel, Switzerland) · 2026Article
- Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies.ACS chemical biology · 2022Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Organic radical materials in biomedical applications: State of the art and perspectives.Exploration (Beijing, China) · 2022Article
- Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions.Chemical science · 2020Article
- Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.The journal of physical chemistry. A · 2019Article
- Structural rearrangements in mRNA upon its binding to human 80S ribosomes revealed by EPR spectroscopy.Nucleic acids research · 2018Article
- Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA.Beilstein journal of organic chemistry · 2018Article
- Directional mechanical stability of Bacteriophage φ29 motor's 3WJ-pRNA: Extraordinary robustness along portal axis.Science advances · 2017Article
- Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA.RNA (New York, N.Y.) · 2017Article
- Complementary-addressed site-directed spin labeling of long natural RNAs.Nucleic acids research · 2016Article
- Three-way junction conformation dictates self-association of phage packaging RNAs.RNA biology · 2016Article
- Prohead RNA: a noncoding viral RNA of novel structure and function.Wiley interdisciplinary reviews. RNA · 2016Review
- A Nitroxide-Tagged Platinum(II) Complex Enables the Identification of DNA G-Quadruplex Binding Mode.Chemistry (Weinheim an der Bergstrasse, Germany) · 2016Article
- Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.Biochemistry · 2016Article
- Doubly Spin-Labeled RNA as an EPR Reporter for Studying Multicomponent Supramolecular Assemblies.Biophysical journal · 2015Article
- Pulse dipolar ESR of doubly labeled mini TAR DNA and its annealing to mini TAR RNA.Biophysical journal · 2015Article
- An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.Methods in enzymology · 2015Article
- Recognition of nucleic acid junctions using triptycene-based molecules.Angewandte Chemie (International ed. in English) · 2014Article
- Diverse self-association properties within a family of phage packaging RNAs.RNA (New York, N.Y.) · 2014Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron-Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (H(T) and H(L)) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which H(T) and H(L) stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.
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