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Photophysics and photochemistry of “non-natural” DNA building blocks

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

Over the last decade, a number of alternative nucleobase units have been developed that have allowed expansion of the genetic alphabet.1 For some of these “non-natural” nucleobases which form into unique base pairs, it has even been possible to introduce them into living bacteria.2 Currently, there are a huge number of scientific questions surrounding the fundamental properties of “non-natural” nucleobases. One such question relates to the photostability of non-natural nucleobases. While the native nucleobases are well known for their intrinsic photostability and their ability to convert harmful UV radiation into benign heat energy, the behaviour of non-native nucleobases in the presence of UV radiation is much more poorly understood.3

In this project, we propose to introduce the non-native nucleobases into the gas-phase and characterise their UV absorption properties by measuring the electronic absorption spectra away from the complications of the solution-phase environment. Similar measurements have been conducted previously in our group for the natural nucleotide, ATP.4 In addition to allowing us to measure the intrinsic UV absorption spectra of the non-natural nucleotide, our experimental approach allows us to measure all of the photodecay channels of the nucleobase, thus providing us with a broad overview of the photophysics, photostability and photodegradation pathways for the system. Initial measurements will focus on the thiouracil family of RNA-base mimics, and will then move to the NaM and 5SICS pair of units,1 and studies will be conducted or the bare nucleobase as well as the nucleoside and nucleotide analogues to investigate how the photophysics and photochemistry evolve with derivatisation. There will be excellent opportunities to perform quantum chemical calculations to support the experimental work, depending on the interests of the student.

Methods
Laser photodissociation measurements will be conducted in a novel laser-interfaced mass spectrometer (LIMS) which includes an ESI source that can be used to transfer a wide range of molecular ions directly into the gas-phase.4,5 For this project, we will introduce the non-natural nucleobases into the gas-phase as either their protonated or deprotonated forms, or we will study the neutral analogues through electrospray of the nucleobases with charge tags (e.g. Cs+ cations). Ions will be mass selected and isolated in an ion trap prior to CID and/or laser excitation. Electronic spectra will be recorded via action spectroscopy, and all photofragmentation pathways will be monitored. The geometries of the systems studied will be optimized using high-level ab intio quantum chemistry or density functional methods, and the excited state spectra of the systems will be studied via time-dependent density functional theory.

All research students follow our innovative Doctoral Training in Chemistry (iDTC): cohort-based training to support the development of scientific, transferable and employability skills. All research students take the core training package which provides both a grounding in the skills required for their research, and transferable skills to enhance employability opportunities following graduation. Core training is progressive and takes place at appropriate points throughout a student’s higher degree programme, with the majority of training taking place in Year 1. In conjunction with the Core training, students, in consultation with their supervisor(s), select training related to the area of their research.

The project will provide a very broad range of student training in the experimental and theoretical work conducted in the Dessent group. For the experimental part of the project, training will include mass spectrometry, (soft ionization techniques, CID, and mass spectral analysis), laser spectroscopy (use of class 4 laser systems and diode lasers), as well as routine handling of gas and vacuum systems. Full training in data analysis, data storage, and data presentation will also be provided. For the theoretical part of the project, full training in computational chemistry techniques (ab initio and DFT) will be given. Mass spectrometry and computational chemistry are both highly-valuable, transferrable skills. The great majority of this training will be provided by research group members, who have extensive experience in the techniques involved. The student will participate in Dessent group meetings, as well as the broader physical chemistry group, providing excellent opportunities to develop wide-ranging contemporary physical chemistry knowledge . The student will be strongly encouraged to participate in national and international conferences (https://twitter.com/dessentlab?lang=en), allowing them to develop oral and presentation skills.

The Department of Chemistry holds an Athena SWAN Gold Award and is committed to supporting equality and diversity for all staff and students. The Department strives to provide a working environment which allows all staff and students to contribute fully, to flourish, and to excel.


Funding Notes

This project is open to students who can fund their own studies or who have been awarded a scholarship separate from this project. The Chemistry Department at York is pleased to offer Wild Fund Scholarships to those from countries outside the UK. Wild Fund Scholarships offer up to full tuition fees for those from countries from outside the European Union. EU students may also be offered £6,000 per year towards living costs. For further information see: View Website

References

1. https://www.nature.com/news/chemical-biology-dna-s-new-alphabet-1.11863:
2. Zhang et al., PNAS, 114, 1317, 2017:
3. B. Ashwood, et al. J. P. C. Lett, 8, 2387, 2017:
4. R. Cercola et al. J. P. C. B, 121, 5553, 2017:
5. E. Matthews et al, PCCP, 19, 17434, 2017.

Related Subjects

How good is research at University of York in Chemistry?

FTE Category A staff submitted: 47.06

Research output data provided by the Research Excellence Framework (REF)

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