Poster abstracts

Poster number 17 submitted by Munira Fouz

Backbone branched nucleic acids: Orthogonal duplex stability and synergy as a nanotag scaffold

Munira Fouz (Department of Chemistry, Carnegie Mellon University), Alessandra Zimmermann (Department of Chemistry, Carnegie Mellon University), Subha R. Das (Department of Chemistry, Carnegie Mellon University)

Abstract:
DNA and RNA assemblies rely on crossovers to form three way junctions (3WJ) or four way junctions (4WJ) that enhance nanostructures beyond simple helical duplexes. Here we show that direct incorporation of branches within the backbone provide simple means to enhance DNA and RNA assemblies. Copper (I) promoted azide- alkyne cycloaddition (CuAAC), commonly referred to as click chemistry is a specific reaction that can covalently link an azide and an alkyne under simple conditions, creating a triazole linkage. Standard phosphoramide chemistry allows incorporation of azide and alkyne groups with nucleic acid sequences of interest, to generate a stable backbone branched structure after a click reaction. Melting curves of these branched sequences show that the linked sequences behave as separate duplexes when hybridized to their complementary sequences. However the branched sequences can act as a single unit creating an efficient scaffold for a fluorescent nanotag that gives rise to a multi chromophore system. Intercalating dyes within the branched duplexes add up to a higher extinction co-efficient of donor dyes which can excite an acceptor dye of interest, via efficient Foster resonance energy transfer for multiplex assays. Such brighter nanotags are of significance for biological imaging applications.

Keywords: Backbone branched nucleic acids, Click chemistry, Foster resonance energy transfer