DSSR-PyMOL cartoon-block schematics: PDB entry 1r3g

PDB-id

1r3g; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.16 Å)

Summary

1.16a x-ray structure of the synthetic DNA fragment with the incorporated 2'-o-[(2-guanidinium)ethyl]-5-methyluridine residues

Reference

Prakash TP, Lesnik E, Mohan V, Tereshko V, Egli M, Manoharan M (2004): "2'-O-[2-(Guanidinium)ethyl]-Modified Oligonucleotides: Stabilizing Effect on Duplex and Triplex Structures." Org.Lett., 6, 1971-1974. doi: 10.1021/ol0493249.

Abstract

[structure: see text] Oligonucleotides with a novel 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modification have been synthesized using a novel protecting group strategy for the guanidinium group. This modification enhances the binding affinity of oligonucleotides to RNA as well as duplex DNA (DeltaT(m) 3.2 degrees C per modification). The 2'-O-GE modified oligonucleotides exhibited exceptional resistance to nuclease degradation. The crystal structure of a palindromic duplex formed by a DNA oligonucleotide with a single 2'-O-GE modification was solved at 1.16 A resolution.