A Novel Paramagnetic Relaxation Enhancement Tag for Nucleic Acids: A Tool to Study Structure and Dynamics of RNA
نویسندگان
چکیده
In this work, we present a novel 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO) radical phosphoramidite building block, which can be attached to the 5'-terminus of nucleic acids. To investigate the paramagnetic relaxation enhancement (PRE) emanating from this radical center, we incorporated the TEMPO label into various types of RNAs. We measured proton PREs for selectively (13)C-isotope labeled nucleotides to derive long-range distance restraints in a short 15 nucleotide stem-loop model system, underscoring the potential of the 5'-TEMPO tag to determine long-range distance restraints for solution structure determination. We subsequently applied the distance-dependent relaxation enhancement induced by the nitroxide radical to discern two folding states in a bistable RNA. Finally, we investigated the fast conformational sampling of the HIV-1 TAR RNA, a paradigm for structural flexibility in nucleic acids. With PRE NMR in combination with molecular dynamics simulations, the structural plasticity of this RNA was analyzed in the absence and presence of the ligand L-argininamide.
منابع مشابه
NMR of proteins and nucleic acids
This report highlights key papers, published this year, that describe advances in the development and application of NMR techniques to the study of proteins and nucleic acids. Many of the sections presented below reflect evolving trends in recent methodology developments, such as in automated NMR, membrane protein NMR and paramagnetic relaxation enhancement methods. Automated NMR methods are no...
متن کاملEnsemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule.
Paramagnetic relaxation enhancement (PRE) measurements on (1)H nuclei have the potential to play an important role in NMR structure determination of macromolecules by providing unique long-range (10-35 A) distance information. Recent methodological advances for covalently attaching paramagnetic groups at specific sites on both proteins and nucleic acids have permitted the application of the PRE...
متن کاملRNA nanotechnology breakthrough for targeted release of RNA-based drugs using cell-based aptamers
Nucleic acids play different roles besides storing information and proteins coding. For example, single-stranded nucleic acids can fold into complicated structures with capability of molecular detection, catalyzing bioreactions and therapy. The development of RNA-based therapies has been rapidly progressed in the recent years. RNA aptamers are biomolecules with a size of 10 to 50 nm that can be...
متن کاملCellular Morphology and Immunologic Properties of Escherichia coli Treated With Antimicrobial Antisense Peptide Nucleic Acid
Background & Objectives: Antisense peptide nucleic acids (PNA) that target growth essential genes show potent bactericidal properties without cell lysis. We considered the possibility that whether PNA treatment influence the bacteria total nucleic acids content and apply approach to develop a new delivery system to Dendritic cells (DCs). DCs are the most potent antigen presenting cells in th...
متن کاملA New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.
Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to...
متن کامل