Energetics and cooperativity of tertiary hydrogen bonds in RNA structure

Scott K. Silverman, Thomas R. Cech

Research output: Contribution to journalArticle

Abstract

Tertiary interactions that allow RNA to fold into intricate three- dimensional structures are being identified, but little is known about the thermodynamics of individual interactions. Here we quantify the tertiary structure contributions of individual hydrogen bonds in a 'ribose zipper' motif of the recently crystallized Tetrahymena group I intron P4-P6 domain. The 2'-hydroxyls of P4-P6 nucleotides C109/A184 and A183/G110 participate in forming the 'teeth' of the zipper. These four nucleotides were substituted in all combinations with their 2'-deoxy and (separately) 2'-methoxy analogues, and thermodynamic effects on the tertiary folding ΔG°' were assayed by the Mg2+ dependence of electrophoretic mobility in nondenaturing gels. The 2'- deoxy series showed a consistent trend with an average contribution to the tertiary folding ΔG°' of -0.4 to -0.5 kcal/mol per hydrogen bond, contributions were approximately additive, reflecting no cooperativity among the hydrogen bonds. Each 'tooth' of the ribose zipper (comprising two hydrogen bonds) thus contributes about - 1.0 kcal/mol to the tertiary folding ΔG°'. Single 2'-methoxy substitutions destabilized folding by ~ 1 kcal/mol, but the trend reversed with multiple 2'-methoxy substitutions; the folding ΔG°' for the quadruple 2'-methoxy derivative was approximately unchanged relative to wild-type. On the basis of these data and on temperature-gradient gel results, we conclude that entropically favorable hydrophobic interactions balance enthalpically unfavorable hydrogen bond deletions and steric clashes for multiple 2'-methoxy substitutions. Because many of the 2'-deoxy derivatives no longer have the characteristic hydrogen- bond patterns of the ribose zipper motif but simply have individual long- range ribose-base or ribose-ribose hydrogen bonds, we speculate that the energetic value of -0.4 to -0.5 kcal/mol per tertiary hydrogen bond may be more generally applicable to RNA folding.

Original languageEnglish (US)
Pages (from-to)8691-8702
Number of pages12
JournalBiochemistry
Volume38
Issue number27
DOIs
StatePublished - Jul 6 1999

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Ribose
Hydrogen
Hydrogen bonds
RNA
Fasteners
Substitution reactions
Thermodynamics
Tooth
Nucleotides
Gels
RNA Folding
Derivatives
Tetrahymena
Electrophoretic mobility
Hydrophobic and Hydrophilic Interactions
Hydroxyl Radical
Thermal gradients
Introns
Temperature

ASJC Scopus subject areas

  • Biochemistry

Cite this

Energetics and cooperativity of tertiary hydrogen bonds in RNA structure. / Silverman, Scott K.; Cech, Thomas R.

In: Biochemistry, Vol. 38, No. 27, 06.07.1999, p. 8691-8702.

Research output: Contribution to journalArticle

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