Cited by 36RNA and protein synthesis mechanismsDNA and Nucleic Acid ChemistryProtein Structure and Dynamics

Role of Unsatisfied Hydrogen Bond Acceptors in RNA Energetics and Specificity

Siegfried, Nathan A., Kierzek, Ryszard, Bevilacqua, Philip C.·2010·Journal of the American Chemical Society

Abstract

RNA plays essential roles in much of biology. These functions are dictated by structures mediated by hydrogen bonding, stacking, electrostatics, and steric interactions. Roles of unsatisfied hydrogen bond functionalities in these structures are less well understood. Herein, we evaluated the energetic contributions of unsatisfied hydrogen bonding groups by placing chemically modified substituents in select internal positions in RNA helices and conducting thermodynamic studies. We find that unsatisfied carbonyl groups make exceptional contributions to structure formation (approximately 3 kcal/mol in free energy), most likely due to a combination of strain and dehydration effects. Thus, unsatisfied hydrogen bonding groups are likely key determinants in the folding energetics and specificity of many RNA and DNA molecules and may be especially important in tertiary structure interactions.

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Crossref · 10.1021/ja9107726

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  • The G:2-thio-C base-pair is only 0.6 kcal/mol less stable than a standard G:C base-pair at an internal position in an RNA duplex, and replacement of G with inosine to generate an I:2-thio-C base-pair has almost no effect.

    “Interestingly, the G:2-thio-C base-pair is only 0.6 kcal/mol less stable than a standard G:C base-pair at an internal position in a RNA duplex, and replacement of G with inosine (I) to generate an I:2-thio-C base-pair has almost no effect [38], suggesting that RNA templates that include either G or I residues should also be examined.”

    From The eightfold path to non-enzymatic RNA replication (2012) · cites this paper as [38]

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Authors
Siegfried, N. A., Kierzek, R., & Bevilacqua, P. C.
Affiliations
Pennsylvania State University (US)
Corresponding author
  • Siegfried, Nathan A.
  • Bevilacqua, Philip C.
Venue
Journal of the American Chemical Society
Published
2010-03-26
Volume
132
Issue
15
Pages
5342-5344
ISSN
  • 0002-7863 (ISSN-L)
  • 1520-5126
OpenAlex
W2065160396
Cited by
36
References
43
Citations by year
2025: 3 · 2024: 1 · 2021: 2 · 2020: 2 · 2019: 2 · 2018: 4 · 2016: 3 · 2015: 3 · 2014: 4 · 2013: 5 · 2012: 1
FWCI
1.56
Type
journal article
Language
en
Open access
closed
Locations
  • Journal of the American Chemical Society (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
chemically modified nucleotides, carbonyl compounds, thermodynamic contribution, dehydration effects, RNA tertiary structure, RNA-DNA interactions
MeSH terms
Hydrogen Bonding, RNA, Thermodynamics, Base Pairing

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