Unraveling nanosecond motions in nucleic acids with high-resolution relaxometry: how dynamic is nicked DNA?

Información del proyecto

HRRinDNAwithSSB

Identificador del acuerdo de subvención: 101028365

DOI

10.3030/101028365

Proyecto cerrado

Fecha de la firma de la CE 14 Abril 2021

Fecha de inicio 1 Septiembre 2021

Fecha de finalización 31 Agosto 2023

Financiado con arreglo a

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Coste total

€ 184 707,84

Aportación de la UE

€ 184 707,84

Coordinado por

ECOLE NORMALE SUPERIEURE
France

Periodic Reporting for period 1 - HRRinDNAwithSSB (Unraveling nanosecond motions in nucleic acids with high-resolution relaxometry: how dynamic is nicked DNA?)

Período documentado: 2021-09-01 hasta 2023-08-31

Resumen del contexto y de los objetivos generales del proyecto

Nucleic acids are vital for cellular life and have been shown to have a variety of functions ranging from information storage and transmission to catalysis. Central to their activity are the structures and dynamics they undergo. Understanding these processes is vital for characterising diseased states and the development of new therapeutics for a wide range of conditions from cancer to viral infections.
Typically, nucleic acids are structurally characterized using X-ray crystallography, Cryo-Electron Microscopy (Cryo-EM), and high-field Nuclear Magnetic Resonance (NMR). However, none of these approaches are suitable for studying nanosecond time-scale motions.
To address this issue, we will introduce a new method called High Resolution Relaxometry (HRR) to characterise dynamics in nucleic acids and apply it to a DNA helix. We expect that this will be the first general approach to obtain both time-scales and amplitudes for motions in both RNAs and DNAs. In conjunction to this we will carry our long molecular dynamics simulations to interpret our low field relaxation rates and provide an atomistic picture.

Trabajo realizado desde el comienzo del proyecto hasta el final del período abarcado por el informe y los principales resultados hasta la fecha

This project has been divided into three phases. In the first phase, we explored biochemical strategies for nucleic acid synthesis and prepared unlabeled samples for our relaxometry experiments.

In the second phase we developed experiments to measure longitudinal carbon relaxation rates in nucleic acids by shuttling the sample to different locations in the stray field. Here we showed that we could measure longitudinal relaxation rates for fields as low as 2 T in a site specific manner in a natural abundance sample. These measurements complimented by traditional R1, R2 and heteronuclear NOE experiments carried out at 500 MHz, 600 MHz, 800 MHz and 1GHz. In addition to this we developed a theoretical framework to interpret the entire experimental dataset using a model free formalism.

In the final phase these relaxation rates were interpreted using molecular dynamics simulations totalling over 68 microseconds. In this phase we were able to assess how well each other 3 force fields and 3 water models were able to reproduce the relaxation rates we recorded and allowed to evaluate how well each forcefield reproduced the kinetics and thermodynamic properties of the DNA helix. By doing so we gained insight into which motions give rise to relaxation processes.

Avances que van más allá del estado de la técnica e impacto potencial esperado (incluida la repercusión socioeconómica y las implicaciones sociales más amplias del proyecto hasta la fecha)

This project goes beyond the state of the art by developing new approaches to characterise fast motions in nucleic acids and covering a range of timescales that are mostly missed by common techniques in structural biology. By developing these new methods for characterising motions in nucleic acids we hope to provide a deeper understanding of fundamental biological processes and open new routes targeting these systems with future therapeutics.

Graphic abstract representing this project's aim to develop high resolution experiments