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Supramolecular recognition of specific nucleic acid junction structures involved in viral insertion and DNA repair

Principal Supervisor:  Prof Mike Hannon Link opens in a new windowLink opens in a new window(Chemistry)

Co-supervisor: Dr Nik Hodges (Biosciences) and Dr Zania Stamataki (MDS)

PhD project title: Supramolecular recognition of specific nucleic acid junction structures involved in viral insertion and DNA repair

University of Registration: University of Birmingham

Project outline:

DNA and RNA structure targeting is a new frontier for molecular design. For example, there are a range of functional RNA structures found in structurally-conserved untranslated regions (UTRs) of many viruses and these are intriguing targets. These UTRs are not only highly structured but often share common structural elements that are functionally essential and so conserved as the virus evolves (drifts) genetically. Structure-affecting mutations in the UTR have been used to create live attenuated or inactivated vaccine strains showing their importance. In RNA viruses, such as HIVs, coronaviruses, dengue and zika, functional involvement of the UTR has been shown in either initiation of replication (for example by recruiting proteins or by direct interaction with the ribosome) or regulation of the replication cycle. Similarly in DNA there are a range of non-duplex structures such as junctions and these are involved when retroviruses (like HIV-1) insert their genetic code into the human genome. This project will explore how to design new agents that bind these functional structures. By binding and interfering with them, and then studying the effects, we will learn more about the role of these structures in different viral infection cycles.


We have previously shown that nanoscale metallo-supramolecular cylinders are unique nano-drug that can bind within DNA and RNA cavities (see Figure) (1, 2). These cylinders also bind bulge structures in RNA, prevent TAT protein from recognizing the binding site in the TAR sequence of HIV and arresting HIV replication in mammalian cells (3,4). They also bind to such structures in the SARS-CoV-2 viral genome and prevent its replication in cells (5).

In this project we will develop this approach to explore new designs to recognise different types of DNA and RNA structures. We will combine molecular dynamics simulations with experimental assessment of binding to the nucleic acids to identify binding preferemce, the molecular detail of structures and the most suitable agents to bind them. Chemical synthesis and design will be used to prepare the new binding agents, which will be fully characterised using a range of analytical techniques. Computational predictions will be confirmed by “wet-lab” approaches. DNA and RNA binding studies in vitro will aemploy a range of spectroscopies and complement in cellulo virology studies to assess how the DNA or RNA-binding affects different viruses inside cells.

The approach and understanding developed will represent a new roadmap for design of drugs to target RNA structural motifs across biology and nucleic acid nanoscience, that can allow us to probe the role of such structures in viral infection.


1 Rotaxanating metallo-supramolecular nano-cylinder helicates to switch DNA junction binding. C.A.J. Hooper, L. Cardo, J.S. Craig, L. Melidis, A. Garai, R.T. Egan, V. Sadovnikova, F. Burkert, L. Male, N.J. Hodges, D.F. Browning, R. Rosas, F. Liu, F.V. Rocha, M.A. Lima, S.Liu, D. Bardelang, M.J. Hannon, J. Am. Chem. Soc., 2020, 142, 20651–20660. doi: 10.1021/jacs.0c07750.

2 Binding of a Designed Anti-Cancer Drug to the Central Cavity of an RNA Three-Way Junction. S. Phongtongpasuk, S. Paulus, J. Schnabl, R. K. O. Sigel, B. Spingler, M. J. Hannon, E. Freisinger, Angew. Chem. Intl Ed, 2013, 52, 11513--11516. DOI: 10.1002/anie.201305079

3 Targeting structural features of viral genomes with a nano-sized supramolecular drug. L. Melidis, I.B. Styles, M.J. Hannon, Chem. Sci., 2021, 12, 7174-84. doi: 10.1039/D1SC00933H

4 Metallo supramolecular cylinders inhibit HIV-1 TAR-TAT complex formation and viral replication in cellulo. L. Cardo, I. Nawroth, P.J. Cail, J.A. McKeating, M. J. Hannon, Scientific Reports, 2018, 8, Article number 13342. DOI: 10.1038/s41598-018-31513-3.

5 Supramolecular cylinders target bulge structures in the 5’ UTR of the RNA genome of SARS-CoV-2 and inhibit viral replication. L. Melidis, H.J. Hill, N.J. Coltman, S.P. Davies, K. Winczura, T. Chauhan, J.S. Craig, A. Garai, C.A.J. Hooper, R.T. Egan, J.A. McKeating, N.J. Hodges, Z. Stamataki, P. Grzechnik, M.J. Hannon, Angew. Chem. Int. Ed., 2021, 60, 18144-51. doi: 10.1002/anie.202104179 BioRXive doi: 10.1101/2021.03.30.437757


BBSRC Strategic Research Priority: Understanding the rules of life Structural Biology


Techniques that will be undertaken during the project:

Molecular Dynamics simulations on DNA/RNA junctions and bulges and drugs that recognise them

Molecular probe design and chemical synthesis

Compound characterisation

DNA/RNA Binding studies using spectroscopies and gels

Growing and handling mammalian cells and treating them with the binding agents

Fluorescent microscopies and super resolution imaging of cells


Contact:  Prof Mike Hannon Link opens in a new windowLink opens in a new window