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Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?
Atul Rangadurai1, Huiqing Zhou1, Dawn K Merriman2
1Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
Insights
Hoogsteen base pairs are less stable in A-RNA than B-DNA due to structural differences. Altering A-RNA geometry reduces this energetic cost, revealing key insights into nucleic acid structure and function.
Area of Science:
- Molecular Biology
- Biophysics
- Structural Biology
Background:
- Hoogsteen (HG) base pairs are less energetically favored in A-RNA compared to B-DNA, a phenomenon not fully understood.
- This energetic difference is significant, exceeding 1 kcal/mol for specific HG base pairs.
Purpose of the Study:
- To investigate the factors contributing to the destabilization of HG base pairs in A-RNA.
- To compare the energetic costs of HG base pair formation in A-RNA versus B-DNA.
Main Methods:
- Nuclear Magnetic Resonance (NMR) spectroscopy
- Optical melting experiments
- Molecular dynamics (MD) simulations
- Modified nucleotides
Main Results:
- Removing the 2'-hydroxyl group did not stabilize HG base pairs in A-RNA.
- Modifying A-RNA structure to mimic B-DNA geometry reduced the energetic cost of HG base pair formation.
- A-form geometry incurs a 1.5-4 kcal/mol penalty for syn purines and an additional 3-4 kcal/mol penalty for purine-pyrimidine HG base pairs compared to B-DNA.
Conclusions:
- A-form geometry inherently disfavors syn purines due to steric constraints and requires significant sugar-backbone rearrangements.
- The energetic penalty for HG base pair formation in A-RNA is significantly higher than in B-DNA, influenced by base accessibility and hydrogen bonding requirements.
- These findings highlight fundamental structural and energetic differences between A-RNA and B-DNA, impacting their biological roles and responses to modifications.
Abstract:
A(syn)-U/T and G(syn)-C+ Hoogsteen (HG) base pairs (bps) are energetically more disfavored relative to Watson-Crick (WC) bps in A-RNA as compared to B-DNA by >1 kcal/mol for reasons that are not fully understood. Here, we used NMR spectroscopy, optical melting experiments, molecular dynamics simulations and modified nucleotides to identify factors that contribute to this destabilization of HG bps in A-RNA. Removing the 2'-hydroxyl at single purine nucleotides in A-RNA duplexes did not stabilize HG bps relative to WC. In contrast, loosening the A-form geometry using a bulge in A-RNA reduced the energy cost of forming HG bps at the flanking sites to B-DNA levels. A structural and thermodynamic analysis of purine-purine HG mismatches reveals that compared to B-DNA, the A-form geometry disfavors syn purines by 1.5-4 kcal/mol due to sugar-backbone rearrangements needed to sterically accommodate the syn base. Based on MD simulations, an additional penalty of 3-4 kcal/mol applies for purine-pyrimidine HG bps due to the higher energetic cost associated with moving the bases to form hydrogen bonds in A-RNA versus B-DNA. These results provide insights into a fundamental difference between A-RNA and B-DNA duplexes with important implications for how they respond to damage and post-transcriptional modifications.
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