Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy

Abstract

Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.

Keywords: DNA; atomic force microscopy; biomolecules; biophysics; oligonucleotides.