The Helicity of a DNA 2 Fluoro DNA Hybrid Duplex Structure

Abstract

Md Gias Uddin, Salman M Ahmad, Robert Tseng, Benjamin E Ley, Yoel P Ohayon, Ruojie Sha and Nadrian C Seeman

Structural DNA nanotechnology is a system whereby branched DNA molecules are fashioned into objects, or 1D, 2D and 3D lattices, as well as nanomechanical devices. Normally, one is dealing with the usual B-form DNA molecule, but variations on this theme can lead to alterations in both the structures and the properties of the constructs. 2’-Fluoro DNA (FDNA), wherein one of the hydrogen atoms of the 2’ carbon is replaced by a fluorine atom, is a minimal steric perturbation on the structure of the DNA backbone. The helical structure of this duplex is of great interest for applications in structural DNA nanotechnology, because the DNA-FDNA hybrid assumes an A-form double helix, without the instabilities associated with RNA. Here we have used an atomic force microscopic method to estimate the helicity of DNA-FDNA hybrids, and we find that the structure contains 11.8 nucleotide pairs per helical turn with an error of ± 0.6 nucleotide pairs, similar to other A-form molecules.

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