Related Experiment Video
Updated: May 13, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic
Judit E Sponer1, Arnošt Mládek, Jiří Sponer
1Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic. judit@ncbr.chemi.muni.cz
Abstract:
Recently, it has been reported that the montmorillonite-catalyzed oligomerization of activated nucleotides exhibits remarkable enantioselectivity. In the current paper we investigate the structures and intrinsic energies of homochiral and heterochiral cyclic dinucleotides by means of accurate quantum chemical calculations in gas-phase and in bulk water. The steric effect of the clay is represented with geometrical constraints. Our computations reveal that the heterochiral dimer geometries are systematically less stable than their homochiral counterparts due to steric clashes inside the sugar-phosphate ring geometry. Thus we suggest that the homochiral selectivity observed in the cyclic dinucleotide formation in confined spaces may arise from the energetic destabilization of the heterochiral ring geometries as compared to their homochiral analogues. In the present paper we provide the first model of the 3D structure of d,l cyclic dinucleotides, which until now has eluded experimental observation.
Related Concept Videos
Regioselective Formation of Enolates
Diels–Alder Reaction: Characteristics of Dienophiles
Characteristics of Dienophiles
Generally, the best dienophiles are alkenes containing electron-withdrawing substituents such as carbonyl, nitrile, and nitro groups. The feasibility of a Diels–Alder reaction depends on...
Introduction to Mechanisms of Enzyme Catalysis
Chirality in Nature
Diversity of Archaea III
Regioselectivity and Stereochemistry of Acid-Catalyzed Hydration

