Conformational flipping of the N(6) substituent in diprotonated N6-(N-glycylcarbonyl)adenines: The role of N(6)H in purine-ring-protonated ureido adenines

Abstract

Conformational transitions of the N(6) substituent, in hypermodified nucleic acid base N 6 -(N-glycylcarbonyl)adenine, gc 6 Ade, on diprotonation of the adenine ring at any two of N(1), N(3), and N(7) sites, are studied using the quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. The N(6) substituent retains the usual "distal" orientation (α = 0 • ) in (N(1), N(3)) diprotonated gc 6 Ade, but the "proximal" orientation (α = 180 • ) is preferred instead, for (N(3), N(7)) and (N(7), N(1)) diprotonated gc 6 Ade. The proximal orientation may alter the reading frame during translation. Intramolecular N(6)H. . .O(13b) hydrogen bonding is the key common feature, present in the preferred structure, for each of these variously diprotonated

Structural significance of modified nucleoside 5-taurinomethyl-2-thiouridine, τm5s2U, found at ‘wobble’ position in anticodon loop of human mitochondrial tRNALys

“…She torsion angles of N 6 -(Mthreonylcarbonyl) Adenine, t 6 Table 6) similar to the most stable conformation of anticodon loop structure of human mt tRNA Lys ( Fig. 8a; Table 5) along with this optimized conformation show hydrogen bonding interactions (Table 6) The solvent-accessible surface area (SASA) has also been calculated over the RM1 preferred most stable structure of anticodon loop structure of human mt tRNA Lys using Chimera software [61] and is shown in Fig. 9a-c. Fig.…”

“…Conformational energy calculations have been performed to understand the structural significance of various hypermodified nucleosides, for example lysidine, k 2 C [55], N(4)-acetylcytidine, ac 4 C [56], queuosine [34] present at 'wobble' (34th) position and modifications present at '3'-adjacent' (37th) position together with their protonation effect such as wybutine (yW) and hydroxywybutine (OHyW) [42,44], t 6 Ade, g 6 Ade [57,58], i 6 Ade and ms 2 i 6 Ade [59], cis-io 6 Ade, trans-io 6 Ade, cis-ms 2 io 6 Ade and trans-ms 2 io 6 Ade [60], gc 6 Ade [61], tc 6 Ade [62] as well as m 2 G and m 2 2 G which occur at the tRNA hinge region of tRNA [43].…”

Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNAPhe

“…The PM3 method is implemented in commercially available PC Spartan Pro (version 6.1.1.0, Wavefunction Inc.) software [27]. Earlier conformational preferences of various modified nucleic acid bases and protonation induced conformational changes of these have been studied [28][29][30][31][32][33][34].…”

Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37th position in anticodon loop of tRNAPhe

“…For rotation around all the exocyclic chemical bonds rigid body internal rotation has been assumed. Earlier conformational preferences of various modified nucleic acid bases and protonation induced conformational changes of these have been studied by PCILO method [43][44][45][46][47][48][49].…”