PhD student
Institute of Bioorganic Chemistry Polish Academy of Sciences, Poland
KEY WORDS: G-quadruplexes, structural studies, NMR spectroscopy
Research topic: “Exploring the sequence-structure relationship as a starting point for the design of DNA
G-quadruplexes with a given topology — an integrative approach combining molecular simulations with experimental methods”
Principal Investigator: prof. dr hab. Zofia Gdaniec
I. Project description
Usually thought of as the canonical Watson-Crick double helix, DNA can in reality fold into many different structures, some of which have profound effects on DNA’s biological role. This project focuses on one of these non-canonical DNA forms, termed G-quadruplexes (G4), whose structure is based on the formation of the so-called G-tetrad, a planar array of four guanine bases kept together by a cyclic arrangement of hydrogen bonds. By stacking on top of each other, G-tetrads make up the core of the G-quadruplex, with four guanine tracts being connected by three intervening loops of variable sequence and conformation. Sequences capable of forming G-quadruplexes are widespread across genomes (e.g., over 700,000 seq. in the human genome) and have been found to be significantly enriched in regulatory regions, including telomeres (up to 25% of all formed G4), and gene promoters. At the same time, due to their versatility and plasticity, engineered G-quadruplex segments have also attracted attention as convenient and potentially programmable building blocks in chemistry, material sciences and nanotechnology.
Structural polymorphism of G-quadruplexes with many possible folded states (topologies) adopted depending on the sequence and environmental conditions (in particular, type and concentration of alkali metal cations) presents both opportunities and challenges to rational design. On the one hand, it allows for multiple design choices, but on the other, it requires a reliable way of predicting and controlling the structure of G-quadruplexes. Unfortunately, despite the extensive research efforts, a practical and general framework allowing for such predictions has yet to be established. Accordingly, the goal of the current project is to thoroughly understand the relation between the sequence of guanine-rich DNA strands and the structure of G-quadruplexes so as to allow for a design of DNA G-quadruplexes with a desired folded topology. Most important experimental techniques that will be applied throughout the project include: DNA synthesis on solid support, NMR spectroscopy, CD and UV spectroscopies, as well as, electrophoretic methods.