Structural studies of oligonucleotides containing G-quadruplex motifs using AFM

Abstract

G-quadruplex DNAs are cyclic arrays of four guanine bases binding by Hoogsteen hydrogen bonds, found in the telomeric regions of chromosomes and in transcriptional regulatory regions of several important oncogenes. Here, we used high resolution atomic force microscopy (AFM) to observe a specific guanine (G) tetrad mediated complex formation of oligonucleotides containing a G-quadruplex motifs (G-ODN) combined with a palindromic sequence under physiological extracellular conditions. These oligonucleotides have been investigated in correlation to their immunostimulatory effects. We observed structural dependence on ion concentration and G-ODN concentration, where high concentration self-assembled DNA networks were formed. Ó 2003 Elsevier Inc. All rights reserved. Keywords: AFM; Palindromic sequence oligonucleotides; G-wire; Self-assembled DNA network; Nanowire DNA is a duplex molecule where two self-complementary strands are held together by Watson–Crick base pairing. Besides, DNA G (guanine)-rich sequences can form arrays of four hydrogen bonds in which each base acts as both donor and acceptor of two hydrogen bonds with other guanines, and the pairing between bases is of the Hoogsteen type [1]. These so-called Gquadruple