Abstract
G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. The superior stiffness and electronic π-π overlap between consecutive G-tetrads suggest exploitation for nanotechnologies. Here we inspect the intimate link between the structure and the electronic properties, with focus on charge transfer parameters. We show that the electronic couplings between stacked G-tetrads strongly depend on the three-dimensional atomic structure. Furthermore, we reveal a remarkable correlation with the topology: a topology characterized by the absence of syn-anti G-G sequences can better support electronic charge transfer. On the other hand, there is no obvious correlation of the electronic coupling with usual descriptors of the helix shape. We establish a procedure to maximize the correlation with a global helix shape descriptor.
Highlights
Artificial G-quadruplexes engineered to assemble with four parallel G strands and no terminal loops are viable electrical conductors up to the scale of 100 nm, at odds with double-stranded DNA molecules of comparable length [1]
G-quadruplex structures can be described in terms of three topology groups [9]
We propose that, no single shape parameter is responsible for the value of the electronic coupling, the inter-guanine parameters in the combination outlined above explain the electronic couplings in the experimental structures of groups I and II, characterized by different topologies, to a fair degree of confidence
Summary
Artificial G-quadruplexes engineered to assemble with four parallel G strands and no terminal loops are viable electrical conductors up to the scale of 100 nm, at odds with double-stranded DNA molecules of comparable length [1]. Special G-rich nucleic acid sequences that occur in the telomeric region of chromosomes, as well as in regulatory and transcription regions, may fold into a quadruple motif [4]. These “monomolecular” (from a single parent strand) genetic G-quadruplexes are only 2–4 G-tetrad long and can fold with parallel or antiparallel strands. G-quadruplex folding has been observed in vivo in human cells, for both DNA and RNA [5,6]
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