Gabriel Abrahams

Generative design of synthetic gene circuits for functional and evolutionary properties https://www.biorxiv.org/content/10.1101/2025.09.26.678595v1

🚨 We’re hiring!

The OPIG group is looking for multiple postdocs to join OpenBind, an open science initiative generating foundational structural biology data to power the next era of AI/ML for drug discovery.

opig.stats.ox.ac.uk
openbind.uk

It’s an exciting possibility!

Scientists made a biological quantum bit out of a fluorescent protein Researchers could use quantum effects to develop new types of medical imaging inside cells themselves.

www.sciencenews.org/article/biol...

Has been so cool to follow this fantastic work, congrats! Conclusion mentions “improving the release efficiency by enhancing the specific heat absorption rate of the nanoparticles” could this enable multiplexed control - different frequencies activating different nanoparticles in the same cell?

Magnetic activation of spherical nucleic acids enables the remote control of synthetic cells - Nature Chemistry The programmability of synthetic cells, comprising lipid vesicles that are capable of imitating the structure and function of living cells, facilitates their application as drug delivery devices. Now,...

We’ve developed the first-ever method to control nucleic acid activity and gene-expressing synthetic cells with a deeply tissue penetrating alternating magnetic field 🧬 🧪 🧲!!!

Published in *Nature Chemistry*

Led by Ellen Parkes
@syncelleu.bsky.social #chemsky
www.nature.com/articles/s41...

A. Structure of AsLOV2 PDB~2V1A (Halavaty, 2007) with mutations resulting in MagLOV~2 highlighted. Spin transitions driven by radio-frequency (RF) fields in the presence of a static magnetic field are optically detected via fluorescence measurements on an otherwise standard widefield microscope. Similar effects have recently been observed in other protein systems (Burd 2025, Meng 2025, Feder 2025). B. Simplified photocycle diagram in the case of a large external magnetic field. C. A single cell expressing MagLOV 2 displaying an MFE of ~50% (measured as a change in fluorescence intensity in the presence of an applied field). For MFE measurements, the magnetic field was switched between 0 mT and 10 mT. D. Black dots: data from a single cell expressing MagLOV 2 displaying an ODMR signal with ~10% contrast. The static field B_0 is ~21.6 mT. Blue line (shade): the mean (std) of all single cell data in a field of view (~1000 cells). E. The static magnetic field B_0 was varied by adjusting the magnet's position, and ODMR spectra recorded. Red-lines are Lorentzian fits. Blue line is a theoretical prediction (i.e. is not a fit) of the expected resonance frequency of an electron spin with $\bar\gamma_e$=28 MHz/mT.

Electronics, radio electronics, optical parts, and an animal sized MRI coil are assembled to perform fluorescence MRI measurements using MagLOV.

MagLOV quantum sensing update! Much improved imaging (>10% single cell ODMR contrast), detailed characterisation and simulation, and new experimental demonstrations taking us a step closer to applications.
www.biorxiv.org/content/10.1...

SI: www.biorxiv.org/content/10.1...

Now out in JACS. pubs.acs.org/doi/full/10....
Grateful to thoughtful reviewers who found some errors in our model and encouraged us to make a better one! A renaissance in magnetobiology is coming...

Advertisement for PhD position

My lab at @ethzurich.bsky.social is looking for a motivated PhD student. We develop chemical tools for advanced fluorescence microscopy 🔬 and work at the interface of synthetic chemistry ⚗️ and protein engineering 🦠. Sharing with skilled Master students appreciated. More info at tinyurl.com/2dbjk5ty

NEW PREPRINT! Do you think we can do better when characterising resource competition properties of gene circuit modules? If no, think again; if yes, you’re in for a pitch how exactly we can do that – automated culturing, cybergenetic control and all! 1/
doi.org/10.1101/2025...

Quantum Spin Resonance in Engineered Magneto-Sensitive Fluorescent Proteins Enables Multi-Modal Sensing in Living Cells Quantum mechanical phenomena have been identified as fundamentally significant to an increasing number of biological processes. Simultaneously, quantum sensing is emerging as a cutting-edge technology...

And as we showed MagLOV by itself has a spin resonance dependent fluorescence www.biorxiv.org/content/10.1...

A fluorescent-protein spin qubit Optically-addressable spin qubits form the foundation of a new generation of emerging nanoscale sensors. The engineering of these sensors has mainly focused on solid-state systems such as the nitrogen...

Maurer et al. showed EYFP can be driven into a metastable state arxiv.org/abs/2411.16835

Mechanism of giant magnetic field effect in fluorescence of mScarlet3, a red fluorescent protein Several fluorescent proteins, when expressed in E. coli , are sensitive to weak magnetic fields1. We found that mScarlet3 fluorescence in E. coli reversibly decreased by 21% in the presence of a 60 mT...

Hot on the heels of @adamezracohen.bsky.social and @kxiang.bsky.social work, unpacking the flavin-fluorescent protein mechanism in detail www.biorxiv.org/content/10.1...

Magnetic resonance control of reaction yields through genetically-encoded protein:flavin spin-correlated radicals in a live animal Radio-frequency (RF) magnetic fields can influence reactions involving spin-correlated radical pairs. This provides a mechanism by which RF fields can influence living systems at the biomolecular leve...

@nahal75bagheri.bsky.social and @scburd.bsky.social rd.bsky.social show MagLOV resonance can be transferred to mScarlet www.biorxiv.org/content/10.1...

New spin resonance measurements with fluorescent proteins out this month from Burd et al., following the still mind-blowing result from @andrewgyork.bsky.social and @mariaingaramo.bsky.social that if you create a selection pressure for a quantum system, nature will oblige! 🧪

DNA-programmable Protein Degradation: Dynamic Control of PROTAC Activity via DNA Hybridization and Strand Displacement Targeted protein degradation is a powerful therapeutic approach: expanding the druggable proteome, providing enhanced selectivity, and having the ability to overcome conventional resistance mechanisms...

New preprint 🎇 We developed oligonucleotide PROTACs (OligoPROTACs), which show comparable activity to small molecule equivalents - but can be *switched off*, using DNA nanotech, to restore protein levels!

Last of Disha's trilogy!
#chemsky 🧪 @uclchemistry.bsky.social chemrxiv.org/engage/chemr...

Mechanism of giant magnetic field effect in fluorescence of mScarlet3, a red fluorescent protein Several fluorescent proteins, when expressed in E. coli, are sensitive to weak magnetic fields1. We found that mScarlet3 fluorescence in E. coli reversibly decreased by 21% in the presence of a 60 mT ...

How do tiny magnetic fields affect biochemistry? Overflowing with pride over Katherine Xiang's study on a giant magnetic field effect in a red fluorescent protein, www.biorxiv.org/content/10.1...

Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!

PLOS statement on recent US Executive Orders and scientific integrity - The Official PLOS Blog Since its founding over twenty five years ago PLOS has been dedicated to advancing open science, ensuring that knowledge is accessible to…

Bravo @plos.org!

US exec orders "stand in direct conflict with our core values, our mission, edit policies"

"PLOS will not compromise on issues of scientific rigor & editorial integrity... we seek diversity because more expert voices make for better science"

theplosblog.plos.org/2025/02/plos...

Experimental evolution of evolvability Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains...

Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...

Red colored protein model of the Avena sativa LOV2 domain (PDBID: 7PGY)

This Valentine's day I want to share the LOV2 with you! ❤️

Roses are red,
the light is blue,
stimuli are read
by the domain LOV2.

My lab does cool stuff 👇

Looking for a #PhD that is at the intersection of #biodesign, #synbio, #openendedness, #evolution? Look no further. Great supervisory team too 😉

How to Apply and Funding

Two weeks to go until the application deadline for ILESLA. If you or anyone you know would benefit from full funding to carry out a PhD in Life and/or Environmental Science please visit/refer to our website page iles.web.ox.ac.uk/how-apply where you can see open day videos and get full guidance.

A profile picture of Douglas Prasher from Martin Chalfie's Nobel Lecture

Do you know who Douglas Prasher is? Many don't, even though he is the person who cloned the original #GFP gene in the late 1980s. In my short history of plant light #microscopy I also cover a bit of his story - & why he is relatively unknown today, despite the importance of his work. See this 🧵👇

The one time @theguardian.com could rightly use a left-handed DNA image... and they choose right-handed 🤦🏻‍♂️🤦🏻‍♂️🤦🏻‍♂️
@iansample.bsky.social

Thanks! Yeah I don't know why he is unsearchable, same for me. (@support.bsky.team)

👋 also @mariaingaramo.bsky.social and @andrewgyork.bsky.social

Much of the cloning overall, as well as experimental work and computational analysis for this figure was brilliantly carried out by @vincentspreng.bsky.social, who is currently interning in our lab. MagLOV can only be studied through deep interdisciplinary collaboration! 🧪

Reflecting on the two days of #sbuk24 talks on the very slow journey home, I think my favourite was Scott Stacey from Harrison Steel's group.

Lovely demonstration of complexity built from simple biology that needs modelling to fully understand an unexpected result