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"End-to-end" stacking of small dsRNA
Nicole Erlenbach1, Christian Grünewald2, Bisera Krstic1
1Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany.
RNA (New York, N.Y.)
|November 9, 2018
Summary
Pulsed electron-electron double resonance (PELDOR) reveals that small double-stranded RNAs stack end-to-end, forming rod-like structures driven by base-pair interactions. This stacking behavior is influenced by salt and RNA concentrations.
Area of Science:
- Biophysics
- Molecular Biology
- Structural Biology
Background:
- Pulsed electron-electron double resonance (PELDOR) is a technique for measuring intramolecular distances.
- PELDOR can also probe intermolecular interactions, such as oligomerization.
- Understanding self-assembly in nucleic acids is crucial for molecular biology.
Purpose of the Study:
- To investigate the end-to-end stacking of small double-stranded (ds) RNAs using PELDOR.
- To quantitatively determine the factors influencing dsRNA stacking, including ion concentration and RNA concentration.
- To elucidate the structural model and geometry of dsRNA stacking.
Main Methods:
- Utilized singly spin-labeled dsRNA molecules with TPA to focus on intermolecular stacking.
- Employed PELDOR spectroscopy to measure distances and distance distributions between labeled sites.
- Varied monovalent NaCl salt and dsRNA concentrations to assess stacking probability.
Main Results:
- Small dsRNAs exhibit a tendency for end-to-end stacking, forming rod-like structures due to pi-pi interactions between base pairs.
- Stacking probability was quantitatively determined as a function of NaCl and dsRNA concentrations.
- The dissociation constant (Kd) for stacking was deduced and shown to be dependent on the ratio of salt to dsRNA concentration.
- Nucleotide overhangs were shown to restrict stacking and influence the formation of dimers or suppress stacking entirely.
Conclusions:
- End-to-end stacking is a significant self-assembly mechanism for small dsRNAs.
- The stacking process is quantitatively predictable and influenced by ionic strength and molecular concentration.
- Structural modifications like nucleotide overhangs can precisely control dsRNA self-assembly, offering insights into nucleic acid structural dynamics.