CBE Seminar (Hybrid): NMR Structure and Dynamics of Quadruplex DNA and Their Ligands Interactions

Abstract: Our laboratory has been using NMR spectroscopy in combination with complementary methods to uncover 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 understanding of functional roles in relation with the genetics of human diseases. A large number of short tandem repeats consist of repeating units of two to six base-pair motifs of DNA. A fraction of DNA repeats lies within genes and their regulatory regions.

DNA with its canonical Watson-Crick paired duplex plays a major role in 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 most well-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 were found to be caused by hexanucleotide GGGGCC repeats expansions. I-motif formation relies on intercalation of hemi-protonated C+…C base pairs that stabilize quadruplex structure. Our lab recently described a new family of tetrahelical structures that differ significantly from G-quadruplexes despite containing the G-quadruplex folding motif (e.g. d[(GGGNn)3GGG]). These sequences with Nn=AGCGA adopt topologies characterized by the tetrahelical core of AGCGA repeats, connected with edge-type loops of different lengths, stabilized by G-G base pairs in N1-carbonyl symmetric geometry. Notably, different DNA structures open diverse possibilities for targeting through their local and dynamic features.

GGGAGCG repeats occur in the regulatory regions of genes responsible for neurological disorders, cancer and abnormalities in bone and cartilage development. We showed that bis-quinolinium ligand 360A with reported high affinity for G-quadruplex structures and selective telomerase inhibition, exhibits strong binding to VK2. Upon binding, 360A does not induce a conformational switch 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 offers insights into the stabilization of an AGCGA-quadruplex by a heterocyclic ligand and provides guidelines for rational design of novel VK2 binding molecules with selectivity for different DNA secondary structures.

Bio: Janez Plavec is the head of the Slovenian NMR Centre at the National Institute of Chemistry and professor of structural biology at the University of Ljubljana. He obtained his diploma in 1987 at the UL department of chemistry and chemical techonolgy and received his M.Sc. degree in 1990 at the same department. His Ph.D degree was conferred by Uppsala University, Uppsala, Sweden, in 1995. He was a Fulbright fellow at Georgia Institute of Technology in 2002. He has been employed at NIC since 1987. He has chaired the Slovenian NMR center since 1996.

His research interests include studies of structure and dynamics of bio-macro-molecular systems with NMR, structural studies of nucleotides and the building blocks of nucleic acids, protein structure, interactions of small molecures and metal ions with DNA and RNA. He has co-authored over 260 original scientific papers, over 150 invited lectures at international conferences and has supervised 18 doctoral students. 

Host: Alon Gorodetsky