Week 2 HW: DNA Design

Set up in Kernel

I created my project in the HTBAA 2026 workspace under the ‘Living Photographic Material’ repository and the ‘meunier-living photographic material’ file.

Part 1: Define your expression target

From the project I proposed in HW1, to sum up what I want to obtain from the material is a response to light, a physical organisation of this material that would produce a structural colour, and that this organisaton be coherent with the spacial repartition of thu light leading to the creation of a photographic image.

Building on the first asignment, I led a more in-depth literature review, to identify possible relevant candidates. This resulted in the underneath table:

System	What it brings to the project	Material / substrate	Photonic / optical-state control	Light required	Response	Characteristic / compatible timescale	Produces structural colour	Light modifies the state	Response depends on light quantity	Spatially local response / potential spatiality	Compatible with projection	Image measurable	Culture / manipulation	Biosafety	A. Living photonic material → image formation	B. Light → modification of an existing living photonic material
Cellulophaga lytica	Living photonic material + biomanufacturing	Biofilm on agar/support	Growth, salinity, mechanics, cellular organization	Mainly for observation; role as a stimulus to be tested	Structural colour not shown to be directly controlled by light	Hours–days for growth; SC dynamics to be characterized	✓✓	?	?	Potential; spatial organization of the biofilm	✓✓	✓✓	✓✓	✓*	Potential	To be demonstrated
Flavobacterium IR1	Well-characterized living 2D photonic crystal	Colony/biofilm on agar	Motility, cell geometry, environment, genetics	Mainly for observation	Structural colour not controlled by light in examined experiments	Rapid organization; ~30 h to several days	✓✓	?	?	Potential; 2D cellular organization	✓✓	✓✓	✓✓	To be verified	Potential	To be demonstrated
Marinobacter algicola	Bacterial structural colour	Colony	Cellular organization	Unknown	Unknown	Unknown	✓	?	?	Unknown	✓	✓	✓	To be verified	Potential	Unknown
Agrobacterium SC	Potential combination of structural colour + photoreception	Colony/biofilm	Organization + photoreceptors depending on strain	Red/far-red for phytochromes in some strains	Photobiological responses documented; coupling to SC not demonstrated	Unknown for SC	✓ depending on strain	?	?	Unknown	✓	✓	✓	To be verified	Potential	Potential, but not established within the same strain
Pseudomonas aeruginosa	Proof of principle for light → biological organization	Biofilm	BphP photoreceptor / c-di-GMP / biofilm	✓	Light-dependent biological organization documented	Seconds–hours depending on mechanism	✓ / strain-dependent	✓✓ for biological organization, not SC	✓✓	✓✓ for biofilm	✓	✓	✓✓	Unfavorable	Theoretical potential	Yes for biological organization, not SC
Optogenetic E. coli	Direct precedent for bacterial photography	Culture/agar	Genetic circuit + pigments	✓✓	Light-controlled pigment production	Depends on circuit	✗ structural / ✓ pigment	✓✓	✓✓	✓✓	✓✓	✓✓	✓✓	Strain-dependent	Yes, but pigment-based	Yes
Ericaria selaginoides / Cystoseira tamariscifolia	Structural colour directly sensitive to light	Living thallus	Intracellular photonic crystals	✓✓	Light-dependent structural-colour change	Hours	✓✓	✓✓	✓✓	To be tested; spatial response not yet demonstrated	✓✓	✓✓	△	To be verified	Potential	Yes
Neon tetra / iridophores	Reversible structural colour controlled by light	Living tissue	Guanine crystals	✓✓	Reversible light-dependent structural-colour change	Seconds–minutes / adaptation	✓✓	✓✓	✓✓	Unknown for projected patterns	△	✓	✗	—	Potential	Yes
Zebrafish / iridophores	Living photonic-crystal model + genetics	Skin/tissue	Guanine crystals	✓✓	Light-dependent reorganization	Seconds–minutes / protocol-dependent	✓✓	✓✓	✓✓	Potential but not demonstrated for image projection	△	✓	△	—	Potential	Yes
Squid	Extremely rich spatial control of structural colour	Living skin	Iridophores + neural control	Indirect	Dynamic structural-colour control through neural mechanisms	~17–32 s for studied responses	✓✓	Indirect / not direct light response	?	✓✓ naturally	✗	✓	✗	—	Potential	Yes, through neural control rather than direct light
Cuttlefish	Spatial camouflage + structural colour	Living skin	Neural / chromatophores / iridophores	Indirect	Dynamic camouflage and colour control	Very rapid for chromatophores; variable for iridophores	✓✓	Indirect	?	✓✓ naturally	✗	✓	✗	—	Potential	Not necessarily direct light response
Octopus	Camouflage + dynamic structural colour	Living skin	Neural / iridophores	Indirect	Dynamic structural-colour control	Rapid to minutes depending on component	✓✓	Indirect	?	✓✓ naturally	✗	✓	✗	—	Potential	Not necessarily direct light response
Iridescent beetles	Passive structural colour	Cuticle	Fixed structure / sometimes humidity or mechanical stimuli	Generally —	Mostly static structural colour	Variable	✓✓	✗	✗	Low	✓✓	✓✓	△	Low/variable	Low	Low
Morpho	Very strong structural colour	Scales	Fixed structure	—	Mostly static structural colour	—	✓✓	✗	✗	Low	✓✓	✓✓	✗	Low	Low	Low
Structural-colour plants	Living material + growth	Leaf/tissue	Variable depending on species	Variable	Variable	Hours–days	✓	Variable	Variable	Unknown	✓	✓	✓ / △	✓	Potential	Variable
Myxomycetes	Structural colour in non-animal/non-plant organisms	Sporocarps / structures	Unknown	?	Unknown	Variable	✓	?	?	Unknown	✓	✓	△	✓	Potential	Unknown
True fungi	—	—	—	?	No established structural-colour system identified	—	Not established	—	—	—	—	—	✓	Variable	Not established	Not established

System	Biological system type	Photonic material / structure	What it brings to the project	Optical-state control	Light required	Biological response	Timescale	Structural colour	Light modifies optical state	Light-dose dependence	Spatial response	Projection compatibility	Image measurable	Culture / manipulation	Biosafety / practical constraints	Main limitation	A — Living material → image	B — Light → existing living material
Cellulophaga lytica	Bacterium / biofilm	Ordered bacterial biofilm / 2D cellular organization	Living material that naturally manufactures an iridescent photonic structure	D — growth, cell morphology and environment affect optical structure	D — illumination used for optical observation; light during growth studied	D — colour linked to cell density, morphology and environment	D — days to several days for biofilm formation	D	U / negative evidence — light exposure during growth did not alter iridescence in one study	U	I — spatial organization exists, but no spatial light-addressed response demonstrated	I — physically exposable, but photographic use untested	D — colour/reflectance measurable	D	D* — strain-dependent; some laboratory strains are RG1	No demonstrated light-addressable control of structural colour	I	U
Flavobacterium IR1	Bacterium / 2D colony	Ordered bacterial colony / 2D photonic crystal	Highly organized living bacterial photonic material with genetic and environmental control	D — cell geometry, motility, genetics and environment influence colour	D — light primarily for optical readout	D — biological organization determines structural colour	D — colony development over days	D	U — no demonstrated light → structural-colour mechanism	U	I — highly spatially organized colony, but spatial optical addressing untested	I	D	D — genetically studied/cultivable	U — strain-specific biosafety	No demonstrated light-controlled optical-state change	I	U
Marinobacter algicola HM-28	Bacterium / colony	Ordered bacterial colony / photonic organization	Additional bacterial structural-colour system outside the Flavobacteria model	D — photonic organization associated with cellular arrangement	D — illumination for optical detection	U — relevant biological control mechanisms insufficiently characterized	U — HM-28-specific optical kinetics not established	D	U	U	U	I — physically exposable	D — optical structure measurable	D* — experimentally cultured	U	Very limited mechanistic information; no demonstrated light-addressable response	I	U
Agrobacterium SC-positive strain	Bacterium / colony	Structural-colour-producing bacterial colony	Potential combination of structural colour and photoreception	D — structural colour documented in some isolates; photoreceptors documented in some strains	D* — wavelength sensitivity documented for some photoreceptors	U — coupling between photoreception and structural colour not demonstrated	U	D — in SC-positive isolates	U	U	U	I	D	D* — strain dependent	U	Exact strain must be identified; cannot assume structural colour + photoreception coexist in the same strain	I	U
Pseudomonas aeruginosa	Bacterium / biofilm	Biofilm architecture; structural colour documented separately	Strong precedent for spatial optical control of bacterial organization	D — optogenetic control of biological organization; SC separately documented	D	D* — strong light-controlled biological response	D — experimental responses over hours/days depending on system	D	D* — light modifies biological state; not established for structural colour	D* — engineered optogenetic response	D* — spatial optogenetic patterning demonstrated	D* — spatial light patterns can control biofilm organization	D*	D — highly tractable	D — opportunistic pathogen; unsuitable as first experimental candidate	Structural colour and light-control systems have not been demonstrated together	I	D* for biological organization / U for SC
Optogenetic E. coli	Bacterium / engineered culture	Pigment-producing bacterial culture	Direct precedent for turning spatially patterned light into bacterial photographs	D — genetic circuit controls pigment production	D	D — light → gene expression → pigment	D* — circuit-dependent	N/A — pigmentary, not structural colour	D	D	D — spatial colour images demonstrated	D	D	D	D* — engineered strain/circuit dependent	Does not solve the structural-colour problem	D	D
Ericaria selaginoides	Brown alga / multicellular thallus	Intracellular 3D photonic crystals	Strong precedent for a living structural-colour material whose optical state changes with light	D	D	D — light intensity/duration alter colour	D — hours	D	D	D	U — global response demonstrated, projected spatial response not demonstrated	I	D — reflectance/time-lapse measurement	D*	U	Spatial image inscription has not been demonstrated	I	D* globally / U spatially
Cystoseira tamariscifolia	Brown alga / multicellular thallus	Intracellular 3D photonic crystals	Particularly strong precedent for dynamic light-controlled structural colour	D	D	D — light level changes structural colour	D — hours	D	D	D	U	I	D — reflectance measurable	D*	U	Global light response is demonstrated, but spatial light addressing is not	I	D* globally / U spatially
Neon tetra / iridophores	Fish / specialized tissue	Iridophores containing guanine-crystal photonic arrays	Reversible living photonic crystal whose optical state changes with light	D	D	D — light-induced reversible colour change	D* — minutes	D	D	D	U	I	D	N/A — whole-animal system	Animal husbandry / ethics; difficult experimental manipulation	No demonstrated projected-pattern control	I	U
Zebrafish / iridophores	Fish / specialized tissue	Iridophore guanine-crystal arrays	Mechanistically well-characterized living photonic structure	D	D*	D* — biological state modifies structural colour; direct light → SC coupling less established	D* — some changes on minute scale	D	D* / U — biological modification documented, direct optical control uncertain	U	U	I	D	D* — established model organism	D* — requires animal facility	No demonstrated spatial light → iridophore patterning	I	U
Squid	Cephalopod / living skin	Iridophore structural-colour system within skin	Very strong dynamic and spatial biological control of structural colour	D — neural/cholinergic control	D* — indirect neural/physiological stimulation	D — neural control changes iridescence	D — tens of seconds in studied responses	D	D* — neural stimulation changes optical state	U	D* — natural spatial control	U — direct projected-light inscription untested	D	N/A — whole animal	N/A — complex animal system / husbandry	Control is neural rather than direct optical control	I	U
Cuttlefish	Cephalopod / living skin	Iridophores + chromatophores in skin	Extremely sophisticated natural spatial pattern formation	D — neural control	D* — visual environment involved	D — dynamic skin patterning	D* — rapid responses, especially chromatophores	D	D* — neural control; direct light → SC not established	U	D* — natural spatial patterning	U	D	N/A	N/A — complex animal system	No direct projected-light control; biological system is highly complex	I	U
Octopus	Cephalopod / living skin	Iridophores + chromatophores in skin	Dynamic biological colour and spatial patterning	D — neural skin control	D* — visual environment relevant	D — dynamic coloration	D* — rapid overall skin response	D	D* — neural control; direct light → SC not established	U	D* — natural spatial patterning	U	D	N/A	N/A — complex animal system	No demonstrated direct optical addressing	I	U
Iridescent beetles	Insect / cuticle or elytra	Fixed multilayer / helicoidal photonic structures	Excellent natural structural-colour material	D — primarily fixed architecture	D — illumination for viewing	D — little evidence of dynamic biological reorganization	U / effectively static	D	U	U	U	D* — can simply be illuminated	D	N/A — non-living optical structure after formation	D* — species-dependent	No demonstrated biological light-controlled reorganization	N/A / low relevance	U
Morpho butterflies	Insect / wing scales	Multilayer nanostructure in wing scales	Highly developed natural structural-colour architecture	D — fixed nanostructure	D — illumination	D — essentially passive optical response	N/A / static	D	U	U	U	D* — passive illumination	D	N/A	D* — species-dependent	No biological mechanism for light-addressed modification	N/A / low relevance	U
Structural-colour plants	Plant / tissue	Species-dependent nanostructures in leaves/other tissues	Broad unexplored biological-material category	D — species dependent	D — illumination	U — insufficient evidence for a general light-controlled structural-colour response	U	D	U	U	U	I	D	D* — species-dependent	D* — species-dependent	Category is too broad; no specific image-addressable candidate identified	I	U
Myxomycetes	Slime mould / reproductive structure	Thin-film/interference structures in sporocarp peridium	Demonstrates structural colour outside the usual animal/plant/bacterial systems	D	D — illumination	U	U	D	U	U	U	I	D	D* — species-dependent	D* — species-dependent	No demonstrated light-controlled reorganization of photonic structure	I	U
True fungi	Fungus / multicellular mycelial organism	—	Potentially interesting biological material category, but no established natural SC system identified	—	—	—	—	N/A — no established natural SC system identified	—	—	—	—	—	D* — many fungi culturable	U	No established natural structural-colour system to manipulate	N/A	N/A

Part 2: Design your genetic parts

Part 3: Assemble your construct

Part 4: Optimize and quality-check

Part 5: From design to build

Part 6: What don’t you know yet?

References

Cellulophaga lytica — Sullivan et al., 2023, Scientific Reports, “Iridescent biofilms of Cellulophaga lytica are tunable platforms for scalable, ordered materials.” Article

Cellulophaga — light experiment — étude montrant que l’iridescence n’était pas affectée par l’exposition à la lumière pendant la croissance. Article PMC

Flavobacterium IR1 — Hamidjaja et al., 2020, ISME Journal, organisation cellulaire et couleur structurale. Article

Flavobacterium IR1 — genetic colour control — étude des mutants et modification de la couleur structurale. PMC

Marinobacter / Agrobacterium / Pseudomonas — Zomer et al., 2024, PNAS, “Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype.” Article PMC

E. coli photographic precedent — Fernandez-Rodriguez et al., 2017, Nature Chemical Biology, “Engineering RGB color vision into Escherichia coli.” Article

Cystoseira — Lopez-Garcia et al., 2018, Science Advances, “Light-induced dynamic structural color by intracellular 3D photonic crystals in brown algae.” PubMed

Ericaria — Pettifor et al., 2021, “Dynamic structural colour increases photosynthetic performance in the alga Ericaria selaginoides.” Article

Neon tetra — Gur et al., “The Mechanism of Color Change in the Neon Tetra Fish: a Light-Induced Tunable Photonic Crystal Array.” Article

Zebrafish — work on the physical/cellular mechanism of structural-colour change. PMC

Squid — Wardill et al., 2012, “Neural control of tuneable skin iridescence in squid.” PMC

Beetles — Seago et al., review of beetle structural colour and iridescence. PMC

Plants — Airoldi, Ferria & Glover, 2019, review of cellular/genetic basis of plant structural colour. PubMed

Myxomycetes — Bauernfeind et al., 2024, structural colour in slime molds. PubMed

True fungi — Brodie, Ingham & Vignolini, 2021, “Does Structural Color Exist in True Fungi?” Article

P. aeruginosa optogenetics — light-controlled spatial/temporal biofilm engineering. PubMed

Cellulophaga culture/biosafety — DSMZ strain information. DSMZ