Issue 9, 2010

The structure of a γ-modified peptide nucleic acid duplex

Abstract

This paper presents the results of an NMR spectroscopy and distance-restrained molecular dynamics (MD) study of a γ-methylated, palindromic, 8-base pair peptide nucleic acid (γ-PNA) duplex. The goal of this study was to examine the impact of the γ-backbone modification on the structure of the PNA duplex. The 2D NMR information involving the backbone methyl group, especially the NOEs between the methyl protons and those of the amide and methylene groups of the backbone, led to distance restraints useful in the elucidation of the structure of the backbone of γ-PNA. Integration of the NOE peaks resulted in 138 inter-proton distance restraints, which were used in ten independent simulated annealing followed by 2 ns restrained MD runs. These simulations led to the conclusion that the γ-PNA duplex adopts a general P-form helical structure similar to that observed for non-modified PNA but with a smaller base pair rise, which is an A-like helical feature, and a slight helical bending towards the major groove (PDB ID 2KVJ). These properties of the γ-PNA duplex may be induced by the γ-methyl group. A similar effect of the methyl group was revealed by a previous NMR study of single stranded γ-PNA [A. Dragulescu-Andrasi, S. Rapireddy, B. M. Frezza, C. Gayathri, R. R. Gil and D. H. Ly, J. Am. Chem. Soc., 2006, 128, 10258–10267]. It appears that the steric constraint exerted by the γ-methyl on the backbone orientation is relatively independent of the base pairing and stacking and thus is likely to manifest when other substituents are introduced at the γ-position of the PNA.

Graphical abstract: The structure of a γ-modified peptide nucleic acid duplex

Supplementary files

Article information

Article type
Paper
Submitted
02 Feb 2010
Accepted
16 Mar 2010
First published
13 Apr 2010

Mol. BioSyst., 2010,6, 1619-1629

The structure of a γ-modified peptide nucleic acid duplex

W. He, M. J. Crawford, S. Rapireddy, M. Madrid, R. R. Gil, D. H. Ly and C. Achim, Mol. BioSyst., 2010, 6, 1619 DOI: 10.1039/C002254C

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