How do the energetics of the stereoelectronic gauche and anomeric effects modulate the conformation of nucleos(t)ides?

The determination of the energetics of the temperature-dependent two-state N $ S pseudorotational equilibrium through 3JHH analysis in 36 nucleos(t)ides and 3 abasic sugars has allowed us for the first time to quantify the strength of various nucleobase-dependent anomeric and gauche effects, and how their interplay finally steers the sugar conformation. The plots of the pDdependent thermodynamics have given an independent method for the determination of pKas of all naturally-occurring nucleobases showing that the energetics for the protonation deprotonation equilibrium is indeed transmitted through the anomeric effect to drive the two-state N $ S pseudorotational equilibrium (energy pump). This means that any change of the pKa of a specific nucleobase due to DNA/RNA folding, or H-bonding or any site-specific metal-ion complexation would promote specific local change of DNNRNA conformation by transmission of the energetics of the altered aromatic character of the heterocyclic agycone to steer the sugar-phosphate backbone conformation through the tuning of the strength of anomeric effect. The pseudorotation concept was introduced to describe the continuous interconversions of puckered forms of the cyclopentane ring (1). The furanose geometry is described by the phase angle of pseudorotation (P) and the puckering amplitude (Y,,,) (2). A statistical analysis of X-ray crystal structures of nucleosides and nucleotides has shown that North (N) [O" c P c 36'1 and South ( S ) [ 144" c P c 190'1 conformations are the most dominant forms, which has been the basis of the assumption of the two-state N 2 S pseudorotational equilibrium in solution (2,3). Fig. 1 $$r ' I > +& A J OH OH North (N) sugar (Cpvuio-Cz.-exo) South ( S ) sugar (C2-endo-C3--eno) The conformational behaviour of the pentofuranose moieties in nucleos(t)ides in solution can be understood, quantified and predicted by the relative strengths of gauche and anomeric effects (4). In 2'-deoxyribonucleosides, the 5'-OH and 3'-OH are in energetically preferred gauche orientation with 04, whereas three additional torsion angles Cg [04'-Cl'-C2'-02'], @[OT-C2'-C3'-03'] and @[02'-C2'-Cl'-N] also prefer gauche conformations in ribonucleosides. The anomeric effect in nucleos(t)ides is the tendency of one of the lone pairs on furanose oxygen to orient antiperiplanar to the glycosidic bond and results in the preference for N-type (pseudoaxial aglycone) over Stype (pseudoequatorial aglycone) conformation (Fig. 1). In crystal structures of natural N-nucleosides, the C4'-04' bond is about 0.03 A longer than the C1'-04' bond (3b). The origin of the 0-C-N anomeric effect in nucleosides and nucleotides can be described by (i) the higher electrostatic repulsions resulting from unfavourable dipole-dipole interactions which may destabilise the pseudoequatorial orientation (S-type sugar) of the aglycone at Cl', or/and (ii) a favourable overlap between a filled n electron pair orbital of the endocyclic 04' and the vacant antibonding (T* orbital of the glycosidic bond which results in the stabilisation of the pseudoaxially oriented nucleobase (N-type sugar) in terms of molecular orbital theory. The latter alternative corresponds to a hyperconjugation of one of the endocyclic oxygen (04') lone pairs to the glycosidic bond in valence bond theory (double-bondno-bond resonance form) resulting in the shortening of the endocyclic 04'-C1' bond and the increase of W-Cl'-N bond angle. The present report details the summary of our work (4) on the quantitative energetic assessment of various gauche and anomeric effects that determine the N 2 S pseudorotational equilibrium. We have used temperature-dependent endocyclic 3 J H ~ coupling constants between 278 K and 358 K to determine the relative population of the Nand S-