Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

From: Biophysical Journal | Date: February 1, 2007| Author: Smith, Jeremy C; Topham, Christopher M | Copyright information

ABSTRACT

Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformera in heteroduplexes with nucleic acids that adopt Mike basepair stacking. Quantum chemical calculations...

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