PROTONATION-INDUCED CONFORMATIONAL FLIPPING IN HYPERMODIFIED NUCLEIC-ACID BASE N6-(N-GLYCYLCARBONYL) ADENINE

The influence of accepting the hydrogen bond by N(3) of adenine on the conformational preferences of the N(6) substituent in modified nuclei c acid base N6-(N-glycylcarbonyl)adenine (gc6Ade) has been modeled by the protonation of N(3). The preferred orientation of the glycylcarbon yl substituent changes on the protonation of N(3). The preferred confo rmation for the N(3) protonated base is the planar, intramolecular bif urcated hydrogen-bonded structure involving the interaction of the ure ido N(11)H with the N(1) of the purine and the O(13b) of the amino aci d carboxyl. Another conformation of nearly equal stability, having the internal hydrogen bonding of O(13b) with the N(6)H, is also predicted . Such protonation or hydrogen-bonding-induced conformational flipping may enable the structural reorientation of the anticodon loop require d for the functioning of tRNA. (C) 1994 John Wiley & Sons, Inc.