Professor James (Jim) Tucker

Supervisor Details

Contact Details

Professor James (Jim) Tucker

School of Chemistry, University of Birmingham

Scientific Background

Research Interests

Research Themes

DNA synthesis and DNA sensing
Modified nucleosides and nucleic acids
Supramolecular chemistry including functional receptor design, photochromic systems and interlocked structures
Ferrocene and anthracene chemistry
Molecular motion
Chiral sensing
Bioorganometallic chemistry and medicinal chemistry

Research Activity

Research in the Tucker group is focused primarily on the design and study of functional supramolecular and DNA-based systems, which often contain redox-active or photo-active sub-units. Students and postdocs receive training in a variety of techniques, including molecular synthesis, DNA synthesis, fluorescence spectroscopy and electrochemistry.

Research Groups

The Tucker Group

Supervision Style

In three words or phrases: collaborative, outcome-oriented, supportive.

Provision of Training

Guidance and concepts will be provided by me; technical training will be carried out predominantly by members of my research group. The group works as a team in a collaborative manner, which enables problem solving and exchanging of ideas.

Progression Monitoring and Management

I like to set agreed goals together each month and to be kept up to date with results on a weekly basis. The aim is for you to achieve independence and to improve interpersonal skills; you are encouraged to train others as you become more experienced (e.g. undergraduate project students).

Communication

Most communication with me is done by email and I am normally in informal contact with group members, either by email or in person, most days each week. There is also a WhatsApp group chat for group members for sharing information about day-to-day lab activities.

Meetings

PhD Students can expect scheduled meetings with me at least once per week. These meetings will be face-to-face. I am usually contactable for an instant response on every working day.

Working Patterns

Certain tasks in my lab need to occur at set times, and students need to be able to commit to a rota/timetable shared with other members of the team.

Notice Period for Feedback

I need at least 1 week's notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Primary supervisor for:

Molecular Machines from Adapted Transcription Factor-DNA Complexes

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Molecular Machines from Adapted Transcription Factor-DNA Complexes

Secondary Supervisor(s): Dr Anna Peacock

University of Registration: University of Birmingham

BBSRC Research Themes:

Renewable Resources and Clean Growth (Bio-energy, Industrial Biotechnology)

Project Outline

Scientists are investing significant effort into developing small molecular machines capable of translational or rotational motion at the molecular level in response to an external stimulus, with potential future applications in molecular electronics and data storage.[1] In chemistry, these systems are often based on supramolecular architectures such as catenanes (two mechanically interlocked macrocycles) or rotaxanes (a threaded macrocycle with stoppers) which contain individual components held together by a topological bond. Chemical docking stations which utilise recognition motifs are required in order to control molecular motion. However, most docking stations are not that sophisticated nor selective and can be difficult to make. In contrast, biomolecular recognition in nature is extremely sophisticated, whilst being highly selective. This project therefore sets out to utilise DNA-peptide recognition, using protein and DNA segments as the building blocks, to generate novel molecular machines from biological components.

Proteins such as transcription factors (e.g. the bZIP family) can bind to DNA with a high degree of sequence selectivity.[2] Often direct contact is made between the DNA target site and a relatively short protein segment, commonly an alpha-helix, despite the original protein being much larger. A number of examples now exist which demonstrate that this small protein fragment alone can still display similar sequence-selective DNA binding, and therefore these fragments and DNA represent attractive building blocks for assembling molecular machine-type architectures.[3] In this project the student will therefore study shortened versions of the bZIP family of transcription factor proteins, prepared using automated peptide synthesis. He/she will then assess how their adaptation and cyclisation affects their binding to DNA sequences. Synthetic DNA containing two target sites with different affinities (e.g. double stranded DNA, dsDNA vs single stranded DNA, ssDNA) will also be prepared to assess how selective the adapted transcription factors are in their binding to DNA. This is turn will lead to the design of machines displaying molecular motion in which peptide motion along the DNA axis between docking stations can be controlled using enzymatic synthesis of dsDNA.

References

[1] https://www.nobelprize.org/uploads/2018/06/popular-chemistryprize2016-1.pdf.

[2] M. A. Schumacher et al., The Structure of a CREB bZIPzSomatostatin CRE Complex Reveals the Basis for Selective Dimerization and Divalent Cation-enhanced DNA Binding, J. Biol. Chem., 2000, 275, 35242–35247, https://doi.org/10.1074/jbc.M007293200.

[3] G. A. Bullen, et al., Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding. Chem. Comm., 2015, 51, 8130-8133, https://doi.org/10.1039/C5CC01618E.

APPLY HERE

Development of Rapid Assays for Nucleic Acid-based Disease Targets

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Development of Rapid Nucleic Acid Assays for Potato Plant Pathogens

Secondary Supervisor(s): Professor Tim Dafforn

University of Registration: University of Birmingham

BBSRC Research Themes:

Sustainable Agriculture and Food (Microbial Food Safety, Plant and Crop Science)

Project Outline

Potato virus Y (PVY) is a major and prevalent potato virus, causing necrosis (dead spots in leaves and tubers) that leads to a significant reduction in crop yield. PVY is transmitted by aphids but can also be transmitted by machinery and tools. As symptoms alone cannot distinguish various virus strains, a diagnostic assay that can discern various strains but that is also portable, can be used in the field and give fast results, would be of great benefit to both crop scientists and producers alike.

We previously reported with partner SASA a lab-based method for detecting cDNA from PVY.[1] This project will now allow us to apply and develop a new assay technology called EXPAR for both rapid detection and strain differentiation of PVY and related pathogens. EXPAR is much faster than current gold-standard enzymatic nucleic acid detection methods based on PCR,[2] in that it does not rely on lengthy heating and cooling steps, leading to the prospect of rapid and sensitive field-based assays for crop monitoring.

In this project, the student (from a biology, biochemistry or chemistry background) will first learn the EXPAR protocol and then develop it for PVY and the detection of genetic variants at the single base level (single nucleotide variants or SNVs). They will also vary the sequences and reagents used in the assay to adapt it for other plant pathogens such as Xylella. They will have an interest in applying molecular biology methods to assay development as well as performing a range of biochemical, computational and analytical techniques, including nucleic acid handling and sequencing, gel electrophoresis, polymerase reactions, fluorescence spectroscopy and statistical analysis. They will enjoy working in multi-disciplinary teams in laboratories at Birmingham and at SASA.

[1] A. Ali et al., RSC Chem. Biol., 2020, 1, 449-454, https://doi.org/10.1039/D0CB00135J

[2] J. G. Carter et al., PNAS, 2021, 118, e2100347118, https://doi.org/10.1073/pnas.2100347118

APPLY HERE

Co-supervisor on a project with Professor Neil Champness.