Guanine Rich Oligonucleotides (GRO) are strands of DNA sequences that have a high propensity to form quadruple helical G-quartet structures known as G-DNA. Four guanine bases associate in a planar structure via using Hoogsten H-bonding which can then can stack upon each other to form a G-quadruplex DNA. The stacking of G-quartets and stability of the G-DNA is greatly enhanced by coordinating cations (K+, Na+, Sr2+, and NH4+) as well as have impact on the formation of antiparallel or parallel strands. Certain GROs can self-assemble in presence of cations to create supramolecular structures named G-wires. In the work presented here, G-wires were produced using the GRO, 5’-dGGGGTTGGGG-3’, with and without various functional modifications. Self-assembly of GRO16 G-wires in the presence of N-methyl mesoporphyrin (NMM) was also investigated and resulted in attenuation of G-wire length distribution. Using polyacrylamide Gel Electrophoresis (PAGE) with differential staining by NMM and the non-specific DNA dye SYBR Green we observe parallel G-DNA and anti-parallel structure intermediates that vary with the type of modifications to GRO16 that varied with the cations used for self-assembly. Furthermore, a comparison of attenuated and non-attenuated self-assemblies of G-wire suggest certain intermediates are favored by the presence of NMM. The result of this work helps us to understand the topologies as well as the self-assembly process of G-wires for use as a potential molecular scaffold in bio/nanomaterial applications.

Use of M-methyl mesoporphyrin as a parallel G-DNA structure probe for G-wire assembly intermediates

2019 Spring National Meeting

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