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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Observation of early events in the photoactivation of Myxobacterial phytochrome using time-resolved serial femtosecond crystallography

Myxobacteria are non-photosynthetic, soil-dwelling bacteria distinguished by a multicellular stage in their life cycle known as fruiting bodies that are stimulated by light. Myxobacterial phytochromes are candidates for the perception of red-light. The mechanism how light is perceived and converted to a physiological response is unknown. Here, time-resolved serial femtosecond crystallographic (TR-SFX) experiments were conducted on microcrystals of the photosensory core module of the Stigmatella aurantiaca bacteriophytochrome 2 (SaBphP2). Initial events of the Z to E isomerization reaction of the covalently bound, open-chain tetrapyrrole biliverdin (BV) chromophore were determined. At 3 ps after light activation, the BV ring-D assumes a configuration needed for the isomerization. At 100 ps, a mixture of BV in the Z or E configuration is observed in subunit A, while in the other subunit the chromophore remains in the Z configuration. In conjunction with prior results, these structures reveal the molecular mechanism of phytochrome activation in the photomorphogenesis of the myxobacteria and provide the molecular foundation for physiological responses to red light in other bacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Tolyporphins A–R, unusual tetrapyrrole macrocycles in a cyanobacterium from Micronesia, assessed quantitatively from the culture HT-58-2

The ‘pigments of life’ family has been enlarged by the discovery of the tetrapyrrole macrocycles dubbed tolyporphins, which are present in a cyanobacterial culture (HT-58-2). Of the 18 known tolyporphins, fourteen (A–J and L–O) are dioxobacteriochlorins, three (K, Q and R) are oxochlorins, and one (P) is a porphyrin. The members with a given chromophore absorb similarly but not identically with each other, presenting the problem of absorption spectral aliasing. Tolyporphins G and H are isomers, as are tolyporphins L–O, given the nature of the peripheral ( C -glycoside, –OH, or –OAc) substituents, presenting the (isobaric) problem of mass spectrometric analysis. The distribution of tolyporphin members is known to change over time and under different growth conditions, however, the complexity of the tolyporphins mixture presents challenges toward characterization of the underlying factors that alter such distributions. Liquid chromatography-mass spectrometry with dynamic multiple reaction monitoring (LC-MS-dMRM) was employed to characterize the distribution of tolyporphins under distinct growth media, using two semisynthetic standards, tolyporphin A O,O -dibutyrate and tolyporphin D O,O,O,O -tetrabutyrate. Growth in media containing both ammonium and nitrate salts versus nitrate alone affords increased production of tolyporphins. The absorption spectra of tolyporphins A–R have been reevaluated with regards to molar absorption coefficients, are compared with those of selected tetrapyrrole macrocycles to better understand the effects of chromophores and substituents, and are made available here in print and digital forms for comparison with isolated tolyporphins and mixtures thereof. Together, the work provides the foundation for quantitative assessment of these unusual natural products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Resolving Electron Injection from Singlet Fission-Borne Triplets into Mesoporous Transparent Conducting Oxides

Photoinduced electron transfer from a molecular chromophore into mesoporous metal oxide substrates occurs efficiently from both singlet and triplet excited states for traditional metal-to-ligand charge transfer (MLCT) dyes. All organic molecules that undergo singlet fission (SF), the process of generating two triplet excitons with photoexcitation of one singlet exciton, offers a promising method of generating two charges per one absorbed photon. However, the singlet-triplet energy balance required to drive SF often places the driving force for triplet electron injection into metal oxides too low. As such, the dynamics of singlet vs. triplet electron transfer for SF in dye-sensitized solar cell configurations has not been elucidated. Here, we use applied bias transient absorption spectroscopy to modulate the driving force for triplet electron transfer from an anthradithiophene-based SF chromophore (ADT-COOH) adsorbed to mesoporous indium tin oxide (nanoITO).

CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SU↗
DOE OSTI2022

An energetics assessment of benzo[ a ]tetracene and benzo[ a ]pyrene as triplet–triplet annihilation emitters

Optical upconversion (UC) of low energy photons into high energy photons enables solar cells to harvest photons with energies below the band gap of the absorber, reducing the transmission loss. UC based on triplet–triplet annihilation (TTA) in organic chromophores can upconvert photons from sunlight, albeit with low conversion efficiency. We utilize three energy-based criteria to assess the UC potential of TTA emitters in terms of the quantum yield (QY) and the anti-Stokes shift. The energy loss in the singlet pathway of an emitter encounter complex, where a high energy photon is emitted, determines whether a chromophore may undergo TTA. The energy loss in the triplet pathway, which is the main competing process, impacts the TTA QY. The energy difference between the lowest singlet and triplet excitation states in TTA emitters sets an upper bound for the anti-Stokes shift of TTA-UC. Using the energetic criteria evaluated by time-dependent density functional theory (TDDFT) calculations, we find that benzo[a]tetracene, benzo[a]pyrene, and their derivatives are promising TTA emitters. The energetics assessment and computer simulations could be used to efficiently discover and design more candidate high-performance TTA emitters.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Highly-destabilized ligand field excited states of iron carbene complexes and their relation to charge transfer state lifetimes

Lifetimes of photoexcited charge transfer (CT) states in transition metal chromophores are influenced by low-lying ligand field (LF) excited states, especially for 3d metal complexes. To manipulate interactions between LF and CT states, it is important to be able to control LF excited state energies using tunable synthetic variables. In this report, we use Fe 2p3d L 3 -edge resonant inelastic X-ray scattering (RIXS) to measure LF excited state energies of three homoleptic iron chromophores coordinated by strong-field N-heterocyclic carbenes (NHCs). We investigate the effect of oxidation state and ligand scaffold on LF energies and covalency parameters. A cyclometalated bis(NHC) ligand affords both high LF excited state energies (and thus high 10 Dq) as well as high metal–ligand covalency compared to other iron complexes with very strong-field ligands. However, for the set of complexes investigated, we do not observe meaningful correlation between the LF excited state energies and the CT excited state lifetimes. These results illustrate that targeting long-lived CT excited states necessitates control of multiple molecular excited state properties, with destabilization of the LF excited state energies proving necessary, but insufficient, to control the CT excited state lifetime in Fe carbene complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue

Modeling linear absorption spectra of solvated chromophores is highly challenging as contributions are present both from coupling of the electronic states to nuclear vibrations and from solute–solvent interactions. In systems where excited states intersect in the Condon region, significant non-adiabatic contributions to absorption line shapes can also be observed. Here, we introduce a robust approach to model linear absorption spectra accounting for both environmental and non-adiabatic effects from first principles. This model parameterizes a linear vibronic coupling (LVC) Hamiltonian directly from energy gap fluctuations calculated along molecular dynamics (MD) trajectories of the chromophore in solution, accounting for both anharmonicity in the potential and direct solute–solvent interactions. The resulting system dynamics described by the LVC Hamiltonian are solved exactly using the thermalized time-evolving density operator with orthogonal polynomials algorithm (T-TEDOPA). The approach is applied to the linear absorption spectrum of methylene blue in water. We show that the strong shoulder in the experimental spectrum is caused by vibrationally driven population transfer between the bright S1 and the dark S2 states. The treatment of the solvent environment is one of many factors that strongly influence the population transfer and line shape; accurate modeling can only be achieved through the use of explicit quantum mechanical solvation. The efficiency of T-TEDOPA, combined with LVC Hamiltonian parameterizations from MD, leads to an attractive method for describing a large variety of systems in complex environments from first principles.

Dunnett, Angus J. (ORCID:0000000285797826)↗
DOE OSTI2023

Data-driven insights into the fluorescence of asphaltene aggregates using extended Frenkel exciton model

The origin of the fluorescence redshift during asphaltene aggregation remains debated due to the great diversity of asphaltene molecules, while the extended Frenkel exciton model provided a theoretical framework for studying multi-chromophore systems, such as asphaltene aggregates. We investigated the fluorescence energy of hundreds of asphaltene dimers based on 133 experimental revealed asphaltene monomer structures. Our result shows that the dimer's fluorescence energy is always lower than both of its monomers regardless of its intermolecular conformation, with its redshift dominated by superexchange. The dimer oscillator strength predominantly depends on the monomer with the lower fluorescence energy, and the involvement of charge-transfer states and the cancellation between monomer transition dipole moments suppressed the fluorescence especially when two monomers have similar fluorescence energy. The above-mentioned findings hold for all asphaltene dimers despite their diversity, which offers a theoretical interpretation for comprehending the relationship between asphaltene aggregation and its fluorescence variation. Furthermore, this work provides theoretical guidance to other research areas related to organic planar conjugated systems with multiple chromophores.

Chemistry↗
DOE OSTI2024

Spectral broadening and vibronic dynamics of the S2 state of canthaxanthin in the orange carotenoid protein

We have performed a series of broadband multidimensional electronic spectroscopy experiments to probe the electronic and vibrational dynamics of the canthaxanthin chromophore of the Orange Carotenoid Protein (OCP) from Synechocystis sp. PCC 6803 in its photoactivated red state, OCPR. Cross-peaks observed below the diagonal of the two-dimensional electronic spectrum indicate that absorption transitions prepare the bright S2 state of the ketocarotenoid canthaxanthin near to a sequence of conical intersections, allowing passage to the dark S1 state via the Sx intermediate in <50 fs. Rapid damping of excited-state coherent wavepacket motions suggests that the branching coordinates of the conical intersections include out-of-plane deformation and C=C stretching coordinates of the π-conjugated isoprenoid backbone. The unusual proximity of the Franck–Condon S2 state structure to the conical intersections with Sx and S1 suggests that the protein surroundings of canthaxanthin prepare it to function as an excitation energy trap in the OCPR–phycobilisome complex. Numerical simulations using the multimode Brownian oscillator model demonstrate that the ground-state absorption spectrum of OCPR overlaps with the fluorescence emission spectrum of allophycocyanin due to spectral broadening derived especially from the intramolecular motions of the canthaxanthin chromophore in its binding site.

Yang, Kunwei↗
DOE OSTI2020

Control of the optical properties of gum and dentin tissue of a human tooth at laser spectral lines in the range of 200 – 800 nm

A change in the optical properties of the tissue of the gums and dentin of a human tooth is experimentally investigated in vitro with the application of a 99.5 % glycerol solution. The kinetics of the total transmittance in the spectral range of 200 – 800 nm on characteristic laser lines is studied. It is shown that the effectiveness of optical clearing, expressed as a relative increase in the total transmittance, for gum tissue in the laser radiation range of 200 – 800 nm can vary significantly (by an order of magnitude). In this case, the absolute values of optical transmittance in the UV region are relatively small due to the strong absorption by the endogenous chromophores of the studied tissues, and in the visible and NIR regions, on the contrary, they are significant, which is due to the absence of strongly absorbing chromophores. The effectiveness of dentin clearing in the entire visible and NIR spectral regions is on average 25 % for 300 minutes of immersion of the sample in a 99.5 % glycerol solution. The presented results are necessary for increasing the efficiency of laser therapy and methods for optical monitoring of morphological changes in biological tissues for the purpose of early diagnosis of diseases. (paper)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Charge transfer as a mechanism for chlorophyll fluorescence concentration quenching

Highly concentrated solutions of chlorophyll display rapid fluorescence quenching. The same devastating energy loss is not seen in photosynthetic light-harvesting antenna complexes, despite the need for chromophores to be in close proximity to facilitate energy transfer. A promising, though unconfirmed mechanism for the observed quenching is energy transfer from an excited chlorophyll monomer to a closely associated chlorophyll pair that subsequently undergoes rapid nonradiative decay to the ground state via a short-lived intermediate charge-transfer state. In this work, we make use of newly emerging fast methods in quantum chemistry to assess the feasibility of this proposed mechanism. We calculate rate constants for the initial charge separation, based on Marcus free-energy surfaces extracted from molecular dynamics simulations of solvated chlorophyll pairs, demonstrating that this pathway will compete with fluorescence (i.e., drive quenching) at experimentally measured quenching concentrations. We show that the rate of charge separation is highly sensitive to interchlorophyll distance and the relative orientations of chromophores within a quenching pair. We discuss possible solvent effects on the rate of charge separation (and consequently the degree of quenching), using the light-harvesting complex II (LH2) protein from rps. acidophila as a specific example of how this process might be controlled in a protein environment. Crucially, we reveal that the LH2 antenna protein prevents quenching, even at the high chlorophyll concentrations required for efficient energy transfer, by restricting the range of orientations that neighboring chlorophyll pairs can adopt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quantum coherent energy transport in the Fenna–Matthews–Olson complex at low temperature

In the primary step of natural light harvesting, the solar photon energy is captured in a photoexcited electron–hole pair, or an exciton, in chlorophyll. Its conversion to chemical potential occurs in the special pair reaction center, which is reached by downhill ultrafast excited-state energy transport through a network of chromophores. Being inherently quantum, transport could in principle occur via a matter wave, with vast implications for efficiency. How long a matter wave remains coherent is determined by the intensity by which the exciton is disturbed by the noisy biological environment. The stronger this is, the stronger the electronic coupling between chromophores must be to overcome the fluctuations and phase shifts. The current consensus is that under physiological conditions, quantum coherence vanishes on the 10-fs time scale, rendering it irrelevant for the observed picosecond transfer. Yet, at low-enough temperature, quantum coherence should in principle be present. Here, we reveal the onset of longer-lived electronic coherence at extremely low temperatures of ∼20 K. Using two-dimensional electronic spectroscopy, we determine the exciton coherence times in the Fenna–Matthew–Olson complex over an extensive temperature range. At 20 K, coherence persists out to 200 fs (close to the antenna) and marginally up to 500 fs at the reaction center. It decays markedly faster with modest increases in temperature to become irrelevant above 150 K. At low temperature, the fragile electronic coherence can be separated from the robust vibrational coherence, using a rigorous theoretical analysis. We believe that by this generic principle, light harvesting becomes robust against otherwise fragile quantum effects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Unraveling excitation energy transfer assisted by collective behaviors of vibrations

Abstract We investigate how collective behaviors of vibrations such as cooperativity and interference can enhance energy transfer in a nontrivial way, focusing on an example of a donor–bridge–acceptor trimeric chromophore system coupled to two vibrational degrees of freedom. Employing parameters selected to provide an overall uphill energy transfer from donor to acceptor, we use numerical calculations of dynamics in a coupled exciton–vibration basis, together with perturbation-based analytics and calculation of vibronic spectra, to identify clear spectral features of single- and multi-phonon vibrationally-assisted energy transfer (VAET) dynamics, where the latter include up to six-phonon contributions. We identify signatures of vibrational cooperation and interference that provide enhancement of energy transfer relative to that obtained from VAET with a single vibrational mode. We observe a phononic analogue of two-photon absorption, as well as a novel heteroexcitation mechanism in which a single phonon gives rise to simultaneous excitation of both the trimeric system and the vibrational degrees of freedom. The impacts of vibrations and of the one- and two-phonon VAET processes on the energy transfer are seen to be quite different in the weak and strong site–vibration coupling regimes. In the weak coupling regime, two-phonon processes dominate, whereas in the strong coupling regime up to six-phonon VAET processes can be induced. The VAET features are seen to be enhanced with increasing temperature and site–vibration coupling strength, and are reduced in the presence of dissipation. We analyze the dependence of these phenomena on the explicit form of the chromophore–vibration couplings, with comparison of VAET spectra for local and non-local couplings.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Selection and development of aptamers for pyoverdine

The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescensPf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA and 2’ F-Y-RNA aptamers with specificity for pyoverdine over other siderophores. Pyoverdines from various strains possess a conserved chromophore along with strain-specific peptide chain. Some of the isolated aptamers bind to chromophore of pyoverdine. These will identify pyoverdines from a variety of pseudomonads. Identification of aptamers that selectively bind the peptide portion of pyoverdine Pf-5 is underway. The identified aptamers that are broadly and narrowly specific for pyoverdines or Pf-5 will be optimized for integration into an electrochemical biosensor to track, in real time, P fluorescens activity and other pseudomonads in and around the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Uncovering dark multichromophoric states in Peridinin–Chlorophyll–Protein

It has long been recognized that visible light harvesting in Peridinin–Chlorophyll–Protein is driven by the interplay between the bright (S 2 ) and dark (S 1 ) states of peridinin (carotenoid), along with the lowest-lying bright (Q y ) and dark (Q x ) states of chlorophyll-a. Here, we analyse a chromophore cluster in the crystal structure of Peridinin–Chlorophyll–Protein, in particular, a peridinin–peridinin and a peridinin–chlorophyll-a dimer, and present quantum chemical evidence for excited states that exist beyond the confines of single peridinin and chlorophyll chromophores. These dark multichromophoric states, emanating from the intermolecular packing native to Peridinin–Chlorophyll–Protein, include a correlated triplet pair comprising neighbouring peridinin excitations and a charge-transfer interaction between peridinin and the adjacent chlorophyll-a. Lastly, we surmise that such dark multichromophoric states may explain two spectral mysteries in light-harvesting pigments: the sub-200-fs singlet fission observed in carotenoid aggregates, and the sub-200-fs chlorophyll-a hole generation in Peridinin–Chlorophyll–Protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Design and synthesis of diazirine‐containing dyes for polypropylene fibre: A study on the effect of alkyl chain

Abstract The dyeing of polypropylene fabrics utilising conventional‐disperse dyes often meets poor colour yield and fastness problems, fundamentally caused by the low affinity between dyes and polypropylene fibres. In this article, a new class of hydrophobic reactive dyes that can react with polypropylene were designed using diazirine moiety as a reactive group, azo structure as a chromophore, and an ester group as a linking bridge. The difference among these dyes was the alkyl chain length on the azo chromophore, which was used to fine‐tune the affinity between the dyes and fibre. The structures of the synthesised dyes and intermediates were characterised and confirmed using nuclear magnetic resonance, mass spectrometry, and infrared spectrometry. The absorption and thermal properties of the dyes were also studied to ensure their feasibility for dyeing application. In addition, the diazirine dyes were successfully applied to dye polypropylene fabrics using a two‐step process by dyeing in a non‐aqueous solvent and fixing it under heating. The dyes and polypropylene fibre were demonstrated to react, where the fixation values were in the range 64.5–76.4%. The systematic study of the structure–property relationship demonstrated the positive effect of the alkyl chain in promoting colour yield, however, accompanied by a slightly reduced fixation value. Due to the chemical bonding of the dye molecules to the fibre, the dyed polypropylene fabrics exhibited excellent colour fastness property, making the dyeing technology very promising for future industrial applications.

Guo, Guangluo↗
DOE OSTI2024

Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation

ABSTRACT The ability to better understand the function of proteins expressed by bacteria has typically relied upon the development of genetic mutant strains. This approach has been especially challenging for plasmid-encoded genes, as most of the previously described allelic replacement vectors are inefficient for plasmid genome mutation as they either rely on plasmid-derived counterselection toxins or depend on other strategies suchsacB,tetA, andrpsLwhich have been proven to be less efficient for mutant selection. Integrative vectors lack chromophore indicators, thus requiring laborious screening or excision of the vector’s backbone relies on the introduction of a flippase (FLP)-expressing plasmid. The allelic replacement vector, designated here as pDG1, expresses an X-Gal hydrolyzing enzyme (BgaB) that can be used for blue/white screening allowing identification of colonies that integrated and successfully removed the mutagenesis plasmid without a bias for those still carrying it. pDG1 was further improved by including the rhamnose-inducible Tse2 toxin as a potent counterselection system. The efficacy of pDG1 was validated by deleting portions of the plasmid-encoded VirB4/D4 type IV secretion system and aerobactin-synthesizing operons inSalmonella enterica. The integrative vectors, which contain an ΦC31attPsite and genes encoding ΦC31 integrase (int), can seamlessly integrate to target ΦC31attBonSalmonellaplasmids or chromosome. These vectors were improved by insertingbgaBand FLP-encoding genes so that, following integration, most of the vector’s backbone encompassingint,bgaB, and FLP genes can be excised by FLP, without the need for another FLP-expressing vector, creating white colonies carrying a stably integrated target gene. As such, we were able to integrate a 9.3-kb DNA fragment toSalmonellachromosome and flipped out most of the integrated vector in one step, leaving the target fragment in the chromosome. IMPORTANCE In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens includingin vivostudies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.

Microbiology↗
DOE OSTI2024

Deciphering between enhanced light emission and absorption in multi-mode porphyrin cavity polariton samples

Abstract It remains unclear how the collective strong coupling of cavity-confined photons to the electronic transitions of molecular chromophore leverages the distinct properties of the polaritonic constituents for future technologies. In this study, we design, fabricate, and characterize multiple types of Fabry-Pérot (FP) mirco-resonators containing copper(II) tetraphenyl porphyrin (CuTPP) to show how cavity polariton formation affects radiative relaxation processes in the presence of substantial non-Condon vibronic coupling between two of this molecule’s excited electronic states. Unlike the prototypical enhancement of Q state radiative relaxation of CuTPP in a FP resonator incapable of forming polaritons, we find the light emission processes in multimode cavity polariton samples become enhanced for cavity-exciton energy differences near those of vibrations known to mediate non-Condon vibronic coupling. We propose the value of this detuning is consistent with radiative relaxation of Herzberg-Teller polaritons into collective molecular states coupled to the cavity photon coherently. We contrast the feature stemming from light emission from the HT polariton state with those that occur due to polariton-enhanced light absorption. Our results demonstrate the landscape of molecular and photonic interactions enabled by cavity polariton formation using complex chromophores and how researchers can design resonators to leverage these interactions to characterize and control polaritonic properties.

Odewale, Elizabeth O.↗
DOE OSTI2024

Pyoverdine binding aptamers and label-free electrochemical detection of pseudomonads

Pyoverdines are iron-chelating siderophores employed by various pseudomonads to promote their growth in iron-limited environments, facilitating both beneficial and detrimental interactions with co-inhabiting microbes or hosts, including plants and animals. The fluorescent pseudomonads produce fluorescent pyoverdines comprised of a conserved central chromophore and a unique strain-specific peptidic side chain produced by non-ribosomal peptide synthetases. Pyoverdine Pf5 (PVD-Pf5) is produced by Pseudomonas protegens Pf-5, a species known for supporting plant growth and its involvement in plant pathogen control. To develop a means of exploring the dynamics of P. protegens activity in soil and in the rhizosphere, we selected DNA aptamers that specifically recognize PVD-Pf5 with high affinities. Two selected aptamers with only 16% identity in sequence were examined for structure and function. We found evidence that both aptamers form structures in their apo-forms and one aptamer has structural features suggesting the presence of a G-quadruplex. Although their tertiary structures are predicted to be different, both aptamers bind the target PVD-Pf5 with similar affinities and do not bind other siderophores, including the related pyoverdine, pseudobactin, produced by Pseudomonas sp. B10. One aptamer binds the pyoverdine peptide component and may also interact with the chromophore. This aptamer was integrated into a nanoporous aluminum oxide biosensor and demonstrated to successfully detect PVD-Pf5 and not to detect other siderophores that do not bind to the aptamer when evaluated in solution. This sensor provides a future opportunity to track the locations of P. protegens around plant roots and to monitor PVD-Pf5 production and movement through the soil.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗