About the lecture
Tetrahelical nucleic acids: 3D structure and dynamics in relation to function and disease
Our laboratory has been using NMR spectroscopy in combination with complementary methods to reveal structural details of four-stranded DNA architectures in relation to sequence details, presence of inorganic salts and cosolutes, pH, interaction with ligands, and folding pathways. Structural insights into DNA, including its repetitive elements, contribute to the understanding of its functional role in the context of human disease genetics. A large number of short tandem repeats consist of repeating units of two to six base pair motifs of DNA. Some of the DNA repeats are located within genes and their regulatory regions.
DNA with its canonical Watson-Crick paired duplex plays an important role in the inheritance of genetic material and gene expression. Alternative secondary structures, including quadruplexes and i-motifs, have been associated with many different biological functions of DNA. The best-studied noncanonical DNA structures are G-quadruplexes. They are formed by G-rich sequences and consist of four-stranded columnar structures. Among the various types of tandem repeat diseases, two major neurodegenerative diseases, frontotemporal dementia and amyotrophic lateral sclerosis, have been found to be caused by hexanucleotide GGGCC repeat expansions. The formation of i-motifs relies on the intercalation of hemiprotonated C+...C base pairs that stabilize the quadruplex structure. Our laboratory has recently described a new family of tetrahelical structures that are distinctly different from G-quadruplexes, although they contain the G-quadruplex folding motif (e.g., d[(GGGNn)3GGG]). These sequences with Nn=AGCGA adopt topologies characterized by a tetrahelical core of AGCGA repeats connected by edge-like loops of different lengths stabilized by G-G base pairs in N1-carbonyl symmetric geometry. The different DNA structures open up a variety of targeting possibilities due to their local and dynamic properties.
GGGAGCG repeats occur in the regulatory regions of genes responsible for neurological disorders, cancer, and abnormalities in bone and cartilage development. We have shown that the bis-quinolinium ligand 360A, reported to have high affinity for G-quadruplex structures and to selectively inhibit telomerase, exhibits strong binding to VK2. Upon binding, 360A does not induce a conformational change from VK2 to an expected G-quadruplex, but intercalates between GAGA and GCGC quartets in the central cavity of VK2. This is the first high-resolution structure of a G-quadruplex ligand intercalating into a G-rich tetrahelical fold. This unique mode of ligand binding into tetrahelical DNA architecture provides insight into the stabilization of an AGCGA-quadruplex by a heterocyclic ligand and provides guidelines for the rational design of novel VK2 binding molecules with selectivity for various DNA secondary structures.
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