Small molecule approaches towards targeted nucleic acid degradation
Lead Research Organisation:
University of Cambridge
Department Name: Chemistry
Abstract
Theme: Industrial Biotechnology and Bioenergy
Advances in nucleic acid manipulation and editing technologies have revolutionised the way biological research is conducted - it is becoming increasingly hard to imagine carrying out molecular biology work without, for example, RNA interference or CRISPR-based systems. However, currently employed approaches are genetic and lack the flexibility of small molecule systems. Several small molecules that target and degrade nucleic acids are known but they lack the modularity of the genetic systems.
My PhD project concerns design of small molecule systems for RNA and DNA degradation that would benefit from flexibility offered by small molecules while retaining the modularity genetic systems. I have synthesised small molecule systems to target RNA substrates with particular RNA modifications as well as small molecules that bind and degrade particular nucleic acid secondary structures and demonstrated with proof-of-concept experiments that they indeed are capable of targeted nucleic acid degradation. The next (and the key) step will be evaluation of these molecules in several cellular systems, to distinguish different types of cells by distribution of their RNA modifications and to specifically target cells with particular pathologies.
My work allows unprecedented level of control of cellular nucleic acid contents and extends the capabilities as well the scope of targeted nucleic acid degradation approaches.
Advances in nucleic acid manipulation and editing technologies have revolutionised the way biological research is conducted - it is becoming increasingly hard to imagine carrying out molecular biology work without, for example, RNA interference or CRISPR-based systems. However, currently employed approaches are genetic and lack the flexibility of small molecule systems. Several small molecules that target and degrade nucleic acids are known but they lack the modularity of the genetic systems.
My PhD project concerns design of small molecule systems for RNA and DNA degradation that would benefit from flexibility offered by small molecules while retaining the modularity genetic systems. I have synthesised small molecule systems to target RNA substrates with particular RNA modifications as well as small molecules that bind and degrade particular nucleic acid secondary structures and demonstrated with proof-of-concept experiments that they indeed are capable of targeted nucleic acid degradation. The next (and the key) step will be evaluation of these molecules in several cellular systems, to distinguish different types of cells by distribution of their RNA modifications and to specifically target cells with particular pathologies.
My work allows unprecedented level of control of cellular nucleic acid contents and extends the capabilities as well the scope of targeted nucleic acid degradation approaches.
Publications
Mikutis S
(2020)
meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategy for the Study of RNA Methylation.
in ACS central science
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011194/1 | 01/10/2015 | 31/03/2024 | |||
| 1943340 | Studentship | BB/M011194/1 | 01/10/2017 | 30/09/2021 | Sigitas Mikutis |
| Description | RNA is a biomolecule with diverse roles in a cell, many of them relevant to disease. One of the ways functions of RNA are controlled are through chemical modifications. The methods to probe these modifications are lacking and the available ones are all follow similar methodologies. I have developed an independent method, with a novel mechanism, to probe these modifications.Using our method, we have found many previously unknown RNA species decorated with RNA modifications, paving the way to finding new targets in disease. |
| Exploitation Route | The developed method is already being adapted by some of the leading research groups in the world to probe RNA modifications, which will expand the basic knowledge on them as well as will help identifying novel disease biomarkers. |
| Sectors | Pharmaceuticals and Medical Biotechnology |
| Title | CLICK-Seq |
| Description | CLICK-Seq is a tool to map RNA modifications that combines metabolic hijacking and click chemistry strategies to yield a quantifiable output - degradation of RNA species containing a particular modification. This method is less biased and lower-input than other state-of-the-art methods, thus has the potential to expand the knowledge of these modifications. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | The method has greatly expanded the known space of methylated lncRNAs as well as intronic and intergenic RNA species. The method is being adapted (via collaborations) to be used by the world-leading research groups in the RNA modifications field. |
| URL | https://pubs.acs.org/doi/10.1021/acscentsci.0c01094 |
| Description | Collaboration with Kouzarides group |
| Organisation | University of Cambridge |
| Department | Gurdon Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We are providing our expertise in RNA modification enzyme substrate characterisation to validate some of the findings from the Kouzarides group. |
| Collaborator Contribution | Kouzarides group is world-leading in RNA modification research and are extensively delving into new types of RNA methylation and relevant methylases. |
| Impact | A research paper is in preparation |
| Start Year | 2020 |
| Description | Collaboration with Shi group |
| Organisation | Boston Children's Hospital |
| Country | United States |
| Sector | Hospitals |
| PI Contribution | We have developed a system to probe RNA modifications and determine substrates of RNA modifying enzymes. |
| Collaborator Contribution | Shi group has validated our method using mass spectrometry-based methods. |
| Impact | This collaboration has resulted in a high-impact publication. |
| Start Year | 2020 |
| Description | Collaboration with Tzelepis group |
| Organisation | University of Cambridge |
| Department | Milner Therapeutics Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have designed chemical systems to probe RNA modifications and carried out basic validation |
| Collaborator Contribution | Tzelepis group has carried out an in-depth characterisation of the aforementioned systems. |
| Impact | This collaboration has resulted in a high-impact publication. This was a multidisciplinary effort, joining together chemistry, chemical biology, cellular biology and molecular biology. |
| Start Year | 2020 |
| Description | Collaboration with Vassiliou group |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We have supplied our collaborators with chemical systems relevant to our research. |
| Collaborator Contribution | Our collaborators have provided us with biological models on which we evaluated the chemical systems we developed. |
| Impact | This is ongoing collaboration which should results in a high-impact publication in the coming months. |
| Start Year | 2019 |
| Title | METHOD FOR TARGETED NUCLEIC ACID CLEAVAGE |
| Description | The present invention provides methods for the non-enzymatic cleavage of target nucleic acids, for example for use in epigenomic and epitranscriptomic mapping and therapy. The method comprises contacting a target nucleic acid molecule with a bifunctional probe comprising a cleavage group and a covalent binding group such that the bifunctional probe covalently binds to the target nucleic acid molecule and cleaves the 5 target nucleic acid molecule bound thereto. Also provided is a method of selectively cleaving a target nucleic acid in a cell, a method for determining the modification of nucleic acid molecules by a nucleic acid modification enzyme in a cell, and a bifunctional probe for use in the methods. |
| IP Reference | WO2022034177 |
| Protection | Patent application published |
| Year Protection Granted | 2022 |
| Licensed | No |
| Impact | Discussions ongoing with a venture capital firm to establish a Cambridge-based spin-out |