Analysis of the Structure of 14 Therapeutic Antibodies Using Circular Dichroism Spectroscopy.

Understanding the impact of the manufacturing environment on therapeutic monoclonal antibody (mAb) structures requires new process analytical technology. Here, we describe the creation of a new reference set for the circular dichroism (CD) spectra of mAbs. Data sets of the highest quality were collected by synchrotron radiation CD for 14 different mAbs in both native and acid-stressed states. Deconvolution of far-UV spectra for the mAb cohort identified two current reference sets (SP175 and SMP180) as assigning accurate secondary structures, irrespective of the analysis program employed. Scrutiny of spectra revealed significant variation in the far-UV and especially near-UV CD of the 14 mAbs. Two spectral features were found to be sensitive to changes in solution pH, i.e., the far-UV positive peak at 201-202 nm and the near-UV negative exciton couplet around 230-240 nm. The latter feature offers attractive possibilities for in-line CD-based monitoring of the mAb structure during manufacture.

The ultraviolet and vacuum ultraviolet absorption spectrum of gamma-pyrone; the singlet states studied by configuration interaction and density functional calculations.

A synchrotron based vacuum ultraviolet absorption spectrum for γ-pyrone has been interpreted in terms of singlet excited electronic states using a variety of coupled cluster, configuration interaction, and density functional calculations. The extremely weak spectral onset at 3.557 eV shows eight vibrational peaks, which following previous analyses, are attributed to a forbidden 1A2 state. A contrasting broad peak with a maximum at 5.381 eV has a relatively high cross-section of 30 Mb; this arises from three overlapping states, where a 1A1 state dominates over progressively weaker 1B2 and 1B1 states. After fitting the second band to a polynomial Gaussian function and plotting the regular residuals over 20 vibrational peaks, we have had limited success in analyzing this fine structure. However, the small separation between these three states clearly shows that their vibrational satellites must overlap. Singlet valence and Rydberg state vibrational profiles were determined by configuration interaction using the CAM-B3LYP density functional. Vibrational analysis using both the Franck-Condon and Herzberg-Teller procedures showed that both procedures contributed to the profiles. Theoretical Rydberg states were evaluated by a highly focused CI procedure. The superposition of the lowest photoelectron spectral band on the vacuum ultraviolet spectrum near 6.4 eV shows that the 3s and 3p Rydberg states based on the 2B2 ionic state are present; those based on the other low-lying ionic state (X2B1) are destroyed by broadening; this is a dramatic extension of the broadening previously witnessed in our studies of halogenobenzenes.

Advantages of a synchrotron light source for fluorescence-detected linear dichroism.

Fluorescence-detected linear dichroism (FD-LD) enables one to collect linear dichroism spectra for oriented fluorophores in the presence of other absorbing species and light scattering. The experiment proceeds by scanning the excitation wavelength and using a filter to collect only emitted photons from the fluorophore. Thus, it has the potential to give data with enhanced selectivity and quality. By using a synchrotron radiation light source and fluorescence-detection, we show data for a range of fluorophores in different orienting environments. Film and flow-oriented FD-LD spectra were collected down to 170 nm. Even for flow-oriented liposomes, we have data collected down to 210 nm. For strongly scattering samples, for example, liposomes, FD-LD has the clear advantage that scattering is absent for the longer wavelength fluorescence photons. The collimated and smaller beam size of the synchrotron radiation also gives rise to sharper and more well-defined features in the spectra.

Chiroptical properties of membrane glycerophospholipids and their chiral backbones.

Glycerophospholipid membranes are one of the key cellular components. Still, their species-dependent composition and homochirality remain an elusive subject. In the context of the astrophysical circularly polarized light scenario likely involved in the generation of a chiral bias in meteoritic amino and sugar acids in space, and consequently in the origin of life's homochirality on Earth, this study reports the first measurements of circular dichroism and anisotropy spectra of a selection of glycerophospholipids, their chiral backbones and their analogs. The rather low asymmetry in the interaction of UV/VUV circularly polarized light with sn-glycerol-1/3-phosphate indicates that chiral photons would have been unlikely to directly induce symmetry breaking to membrane lipids. In contrast, the anisotropy spectra of d-3-phosphoglyceric acid and d-glyceraldehyde-3-phosphate unveil up to 20 and 100 times higher maximum anisotropy factor values, respectively. This first experimental report, targeted on investigating the origins of phospholipid symmetry breaking, opens up new avenues of research to explore alternative mechanisms leading to membrane lipid homochirality, while providing important clues for the search for chiral biosignatures of extant and/or extinct life in space, in particular for the ExoMars 2028 mission.

Electronic State Spectroscopy of Nitromethane and Nitroethane.

High-resolution photoabsorption cross-sections in the 3.7-10.8 eV energy range are reinvestigated for nitromethane (CH3NO2), while for nitroethane (C2H5NO2), they are reported for the first time. New absorption features are observed for both molecules which have been assigned to vibronic excitations of valence, Rydberg, and mixed valence-Rydberg characters. In comparison with nitromethane, nitroethane shows mainly broad absorption bands with diffuse structures, which can be interpreted as a result of the side-chain effect contributing to an increased number of internal degrees of freedom. New theoretical quantum chemical calculations performed at the time-dependent density functional theory (TD-DFT) level were used to qualitatively help interpret the recorded photoabsorption spectra. From the photoabsorption cross-sections, photolysis lifetimes in the terrestrial atmosphere have been obtained for both compounds. Relevant internal conversion from Rydberg to valence character is noted for both molecules, while the nuclear dynamics of CH3NO2 and C2H5NO2 along the C-N reaction coordinate have been evaluated through potential energy curves at the TD-DFT level of theory, showing that the pre-dissociative character is more prevalent in nitromethane than in nitroethane.

Excitation and fragmentation of the dielectric gas C4F7N: Electrons vs photons.

C4F7N is a promising candidate for the replacement of sulfur hexafluoride as an insulating medium, and it is important to understand the chemical changes initiated in the molecule by collision with free electrons, specifically the formation of neutral fragments. The first step of neutral fragmentation is electronic excitation, yet neither the absorption spectrum in the vacuum ultraviolet (VUV) region nor the electron energy loss spectrum have previously been reported. Here, we experimentally probed the excited states by VUV photoabsorption spectroscopy and electron energy loss spectroscopy (EELS). We found that the distribution of states populated upon electron impact with low-energy electrons is significantly different from that following photoabsorption. This difference was confirmed and interpreted with ab initio modeling of both VUV and EELS spectra. We propose here a new computational protocol for the simulation of EELS spectra combining the Born approximation with approximate forms of correlated wave functions, which allows us to calculate the (usually very expensive) scattering cross sections at a cost similar to the calculation of oscillator strengths. Finally, we perform semi-classical non-adiabatic dynamics simulations to investigate the possible neutral fragments of the molecule formed through electron-induced neutral dissociation. We show that the product distribution is highly non-statistical.

The ionic and ground states of gamma-pyrone. The photoionization spectrum studied by synchrotron radiation and interpreted by configuration interaction and density functional calculations.

A synchrotron-based photoionization spectrum up to 27 eV represents a considerable improvement in resolution over early He(I) and He(II) spectra. Symmetry-adapted coupled cluster calculations of the ionic state sequence give the sequence of state vertical ionization energies (VIE) as 12B2 < 12B1 < 12A2 < 22B1 < 12A1. Generally, these symmetry-adapted cluster configuration interactions VIE match reasonably well with the experimental spectrum over this wide energy range. Density functional calculations of the corresponding adiabatic terms (AIE) were also performed. Higher energy ionic states were determined by complete active space self-consistent field methods; these include all π-ionizations and some σ-ionic states. These were analyzed by Franck-Condon (FC) procedures and compared with an experiment. The spectral onset is complex, where two states, later shown to be the 12B2 and 12B1 states, are strongly overlapping. The superposition of the FC vibrational structure in the 12B2 and 12B1 states accounts for most of the peaks arising at the onset of the photoelectron spectra. However, the small separation between these two ionic states makes vibronic interaction fairly inevitable. In the absence of Herzberg-Teller analyses for ionic states, we have sought and determined a transition state between the 12B2 and 12B1 states, showing that vibronic coupling does occur. The lack of degradation in the vibrational envelope of the higher of the two states contrasts with our previous work on the halogenobenzenes, where overlapping state envelopes led to considerable widening of the line width at half-height of the higher energy states.

High-level studies of the singlet states of quadricyclane, including analysis of a new experimental vacuum ultraviolet absorption spectrum by configuration interaction and density functional calculations.

A synchrotron-based vacuum ultraviolet absorption spectrum (VUV) of quadricyclane (QC) is reported with energies up to 10.8 eV. Extensive vibrational structure has been extracted from the broad maxima by fitting short energy ranges of the VUV spectrum to high level polynomial functions and processing the regular residuals. Comparison of these data with our recent high-resolution photoelectron spectral of QC showed that this structure must be attributed to Rydberg states (RS). Several of these appear before the valence states at higher energies. Both types of states have been calculated by configuration interaction, including symmetry-adapted cluster studies (SAC-CI) and time dependent density functional theoretical methods (TDDFT). There is a close correlation between the SAC-CI vertical excitation energies (VEE) and both Becke 3-parameter hybrid functional (B3LYP), especially Coulomb-attenuating method-B3LYP determined ones. The VEE for several low-lying s-, p, d-, and f-RS have been determined by SAC-CI and adiabatic excitation energies by TDDFT methods. Searches for equilibrium structures for 11,3A2 and 11B1 states for QC led to rearrangement to a norbornadiene structure. Determination of the experimental 00 band positions, which show extremely low cross-sections, has been assisted by matching features in the spectra with Franck-Condon (FC) fits. Herzberg-Teller (HT) vibrational profiles for the RS are more intense than the FC ones, but only at high energy, and are attributed to up to ten quanta. The vibrational fine structure of the RS calculated by both FC and HT procedures gives an easy route to generating HT profiles for ionic states, which usually require non-standard procedures.

The excited states of azulene: A study of the vibrational energy levels for the lower ππ*-valence states by configuration interaction and density functional calculations, and theoretical studies of the Rydberg states.

A new vacuum ultraviolet absorption (VUV) spectrum of azulene vapor has been obtained by using a synchrotron radiation source. The onset of the ultraviolet spectrum, previously reported by Sidman et al., has been analyzed in detail by Franck-Condon (FC) and Herzberg-Teller (HT) methods. The photoelectron spectral profile identifies the 3px-Rydberg state 00 band to be 131 cm-1 from the VUV maximum. Excited state energy levels were calculated by three independent methods: the wide scan VUV spectrum was correlated with symmetry adapted cluster configuration interaction calculations. The low energy portion of the spectrum was studied by both time dependent density functional theoretical methods (TDDFT) and multi-reference multi-root CI (MRD-CI). Equilibrium structures were determined for valence states at the TDDFT level. Rydberg states were determined by both TDDFT and MRD-CI. The FC + HT analyses were performed on the TDDFT wave-functions. The HT intensity profiles are generally low in intensity, relative to the FC ones; however, HT is dominant in the second singlet state (S2, 11A1). As a result, numerous non-symmetric modes, their overtones, and combination bands show considerable intensity in that band. Energies obtained from use of extremely diffuse s-, p-, d-, or f-character functions enabled realistic extrapolation to the IE1 for many Rydberg states (RS). The lowest RS (3b13s) based on IE2 lies at 4.804 eV with a quantum defect of 0.714. Differentiation between valence and RS is readily made using the second moments of the charge distribution.

The ground and ionized states of azulene: A combined study of the vibrational energy levels by photoionization, configuration interaction, and density functional calculations.

A synchrotron-based photoionization spectrum of azulene shows a significant additional vibrational fine structure when compared to previous studies. This spectrum was successfully analyzed by using Franck-Condon (FC) methods. Previously reported zero-kinetic-energy electron spectra for azulene have been reinterpreted in FC terms, leading to some alternative assignments to the earlier work. The sequence of ionic states has been determined by using ab initio configuration interaction (CI) methods, leading to reliable theoretical values for both the calculated adiabatic ionization energy (AIE) and vertical ionization energy (VIE). VIEs were calculated by both symmetry-adapted cluster (SAC-CI), together with Green's function (GF) and Tamm-Dancoff approximation (TDA), and single excitation CI methods; AIEs for highest states of each symmetry were determined by open-shell self-consistent field (SCF) methods at the restricted Hartree-Fock level. Complete active space SCF was used for the pairs of 12A2 + 22A2 and 12B1 + 22B1 states, each of which occurs as antisymmetric and symmetric (higher energy) combinations. The combined ionic state sequences (AIE and VIE) from these methods are 12A2 < 12B1 < 22A2 < 22B1. The photoelectron spectrum (PES) shows a series of broadbands above 11 eV, each of which is attributed to more than one ionization. The calculated PES sequence of states of up to 19 eV shows that the SAC-CI and GF results are in almost exact agreement. The internal spacing of the bands is best reproduced by the simpler GF and TDA methods. States involving simultaneous ionization and electronic excitation are considered by both SAC-CI and TDA methods.

Concentration and pH effect on the electronic circular dichroism and anisotropy spectra of aqueous solutions of glyceric acid calcium salt.

Electronic circular dichroism (ECD) and anisotropy spectra carry information on differential absorption of left- and right-circularly polarized light (LCPL and RCPL) by optically active compounds. This makes them powerful tools for the rapid determination of enantiomeric excesses (ee) in asymmetric synthetic and pharmaceutical chemistry, as well as for predicting the ee inducible by ultraviolet (UV) CPL. The ECD response of a chiral molecule is, however, critically dependent on the properties of the surrounding medium. Here, we report on the first ECD/anisotropy spectra of aqueous solutions of the calcium salt dihydrate of glyceric acid. A systematic study of the effect of the salt concentration and pH on the chiroptical response revealed significant changes and the appearance of a new ECD band of opposite sign. Based on the literature, this can be rationalized by the increase in the relative proportion of free glyceric acid/glycerate to Ca2+ complexes with glycerate with decreasing salt concentration or pH. Glyceric acid can be readily produced under astrophysical conditions. The anisotropy spectra of the solution containing prevalently the free form of this dihydroxy carboxylic acid resemble the ones of previously investigated aliphatic chain hydroxycarboxylic acids and proteinogenic amino acids. This indicates possible common handedness of stellar CPL-induced asymmetry in the potential comonomers of primitive proto-peptides.

Condensation and Protection of DNA by the Myxococcus xanthus Encapsulin: A Novel Function.

Encapsulins are protein nanocages capable of harboring smaller proteins (cargo proteins) within their cavity. The function of the encapsulin systems is related to the encapsulated cargo proteins. The Myxococcus xanthus encapsulin (EncA) naturally encapsulates ferritin-like proteins EncB and EncC as cargo, resulting in a large iron storage nanocompartment, able to accommodate up to 30,000 iron atoms per shell. In the present manuscript we describe the binding and protection of circular double stranded DNA (pUC19) by EncA using electrophoretic mobility shift assays (EMSA), atomic force microscopy (AFM), and DNase protection assays. EncA binds pUC19 with an apparent dissociation constant of 0.3 ± 0.1 µM and a Hill coefficient of 1.4 ± 0.1, while EncC alone showed no interaction with DNA. Accordingly, the EncAC complex displayed a similar DNA binding capacity as the EncA protein. The data suggest that initially, EncA converts the plasmid DNA from a supercoiled to a more relaxed form with a beads-on-a-string morphology. At higher concentrations, EncA self-aggregates, condensing the DNA. This process physically protects DNA from enzymatic digestion by DNase I. The secondary structure and thermal stability of EncA and the EncA-pUC19 complex were evaluated using synchrotron radiation circular dichroism (SRCD) spectroscopy. The overall secondary structure of EncA is maintained upon interaction with pUC19 while the melting temperature of the protein (Tm) slightly increased from 76 ± 1 °C to 79 ± 1 °C. Our work reports, for the first time, the in vitro capacity of an encapsulin shell to interact and protect plasmid DNA similarly to other protein nanocages that may be relevant in vivo.

The Conformation of the N-Terminal Tails of Deinococcus grandis Dps Is Modulated by the Ionic Strength.

DNA-binding proteins from starved cells (Dps) are homododecameric nanocages, with N- and C-terminal tail extensions of variable length and amino acid composition. They accumulate iron in the form of a ferrihydrite mineral core and are capable of binding to and compacting DNA, forming low- and high-order condensates. This dual activity is designed to protect DNA from oxidative stress, resulting from Fenton chemistry or radiation exposure. In most Dps proteins, the DNA-binding properties stem from the N-terminal tail extensions. We explored the structural characteristics of a Dps from Deinococcus grandis that exhibits an atypically long N-terminal tail composed of 52 residues and probed the impact of the ionic strength on protein conformation using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism and small-angle X-ray scattering. A novel high-spin ferrous iron-binding site was identified in the N-terminal tails, using Mössbauer spectroscopy. Our data reveals that the N-terminal tails are structurally dynamic and alter between compact and extended conformations, depending on the ionic strength of the buffer. This prompts the search for other physiologically relevant modulators of tail conformation and hints that the DNA-binding properties of Dps proteins may be affected by external factors.

A study on the secondary structure of the metalloregulatory protein CueR: effect of pH, metal ions and DNA.

The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.

Structural features and stability of apo- and holo-forms of a simple iron-sulfur protein.

Iron-sulfur centers are widespread in living organisms, mostly performing electron transfer functions, either in electron transfer chains or as part of multi-enzymatic complexes, while being also present in enzyme active sites, handling substrate catalysis. Rubredoxin is the simplest iron-sulfur containing protein constituted by a single polypeptide chain of 50 to 60 amino acids, of which four cysteine residues are responsible for metal binding in a tetrahedral coordination sphere. In this manuscript we explore the structure and stability of both apo- and holo-forms of a Rubredoxin from Marinobacter hydrocarbonoclasticus using Synchrotron Radiation Circular Dichroism (SRCD) in combination with other biochemical and spectroscopic techniques. The results are consistent with a holo-protein form containing a monomeric iron center with UV-visible maxima at 760, 578, 494, 386, 356 and 279 nm, an intense EPR resonance with a g value around 4.3 and Mössbauer spectroscopy parameters of δ equal to 0.69 mm/s and ΔEQ equal to 3.25 mm/s, for the ferrous reconstituted state. SRCD data, obtained for the first time for the apo-form, show a quite defined structure with ∆ε maximum at 191 nm and minima at 203 and 231 nm. Most significantly, the presence of isosbestic points at 189 and 228 nm made the interconversion between the two stable apo- and holo-form solution structures clear. SRCD temperature dependence data shows that for both forms the denaturation process proceeds through an intermediate species.

Dps-DNA interaction in Marinobacter hydrocarbonoclasticus protein: effect of a single-charge alteration.

DNA-binding proteins from starved cells (Dps) are members of the ferritin family of proteins found in prokaryotes, with hollow rounded cube-like structures, composed of 12 equal subunits. These protein nanocages are bifunctional enzymes that protect the cell from the harmful reaction of iron and peroxide (Fenton reaction), thus preventing DNA damage by oxidative stress. Ferrous ions are oxidized at specific iron-binding sites in the presence of the oxidant and stored in its cavity that can accommodate up to ca. 500 iron atoms. DNA-binding properties of Dps are associated with the N-terminal, positive charge rich, extensions that can promote DNA binding and condensation, apparently by a cooperative binding mechanism. Here, we describe the binding and protection activities of Marinobacter hydrocarbonoclasticus Dps using Electrophoretic Mobility Shift Essays (EMSA), and synchrotron radiation circular dichroism (SRCD) spectroscopy. While no DNA condensation was observed in the tested conditions, it was possible to determine a Dps-DNA complex formation with an apparent dissociation constant of 6.0 ± 1.0 µM and a Hill coefficient of 1.2 ± 0.1. This interaction is suppressed by the inclusion of a single negative charge in the N-terminal region by point mutation. In Dps proteins containing a ferric mineral core (above 96 Fe/protein), DNA binding was impaired. SRCD data clearly showed that no significant modification existed either in secondary structure or protein stability of WT, Q14E variant and core containing proteins. It was, however, interesting to note that, in our experimental conditions, thermal denaturation induced protein aggregation that caused artifacts in thermal denaturation curves, which were dependent on radiation flux and vertical arrangement of the CD cell.

The vacuum ultraviolet absorption spectrum of norbornadiene: Vibrational analysis of the singlet and triplet valence states of norbornadiene by configuration interaction and density functional calculations.

A synchrotron-based vacuum ultraviolet (VUV) absorption spectrum of norbornadiene (NBD) is reported, and the extensive vibrational structure obtained has been analyzed. The previously known 5b13s-Rydberg state has been reinterpreted by comparison with our recent high-resolution photoelectron spectral analysis of the X2B1 ionic state. Additional vibrational details in the region of this Rydberg state are observed in its VUV spectrum when compared with the photoelectron 2B1 ionic state; this is attributed to the underlying valence state structure in the VUV. Valence and Rydberg state energies have been obtained by configuration interaction and time-dependent density functional theoretical methods. Several low-lying singlet valence states, especially those that arise from ππ* excitations, conventionally termed NV1 to NV4, have been examined in detail. Their Franck-Condon (FC) and Herzberg-Teller (HT) profiles have been investigated and fitted to the VUV spectrum. Estimates of the experimental 00 band positions have been made from these fits. The anomaly of the observed UV absorption by the 1A2 state of NBD is attributed to HT effects. Generally, the HT components are less than 10% of the FC terms. The calculated 5b13s lowest Rydberg state also shows a low level of HT components. The observed electron impact spectra of NBD have been analyzed in detail in terms of triplet states.

Excited States of Bromopyrimidines Probed by VUV Photoabsorption Spectroscopy and Theoretical Calculations.

We report absolute photoabsorption cross sections for gas-phase 2- and 5-bromopyrimidine in the 3.7-10.8 eV energy range, in a joint theoretical and experimental study. The measurements were carried out using high-resolution vacuum ultraviolet synchrotron radiation, with quantum chemical calculations performed through the nuclear ensemble approach in combination with time-dependent density functional theory, along with additional Franck-Condon Herzberg-Teller calculations for the first absorption band (3.7-4.6 eV). The cross sections of both bromopyrimidines are very similar below 7.3 eV, deviating more substantially from each other at higher energies. In the 7.3-9.0 eV range where the maximum cross-section is found, a single and broad band is observed for 5-bromopyrimidine, while more discernible features appear in the case of 2-bromopyrimidine. Several π* ← π transitions account for the most intense bands, while weaker ones are assigned to transitions involving the nitrogen and bromine lone pairs, the antibonding σ*Br orbital, and the lower-lying Rydberg states. A detailed comparison with the available photo-absorption data of bromobenzene is also reported. We have found significant differences regarding the main absorption band, which is more peaked in bromobenzene, becoming broader and shifting to higher energies in both bromopyrimidines. In addition, there is a significant suppression of vibrational structures and of Rydberg states in the pair of isomers, most noticeably for 2-bromopyrimidine.

Supramolecular protein polymers using mini-ferritin Dps as the building block.

A missense mutant of a Dps protein (DNA-binding protein from starved cells) from Marinobacter hydrocarbonoclasticus was used as a building block to develop a new supramolecular assembly complex which enhances the iron uptake, a physiological function of this mini-ferritin. The missense mutation was conducted in an exposed and flexible region of the N-terminal, wherein a threonine residue in position 10 was replaced by a cysteine residue (DpsT10C). This step enabled a click chemistry approach to the variant DpsT10C, where a thiol-ene coupling occurs. Two methods and two types of linker were used resulting in two different mini-ferritin supramolecular polymers, which have maintained secondary structure and native iron uptake physiological function. Electrophoretic assays and mass spectrometry were utilized to confirm that both functionalization and coupling reactions occured as predicted. The secondary structure has been investigated by circular dichroism and synchrotron radiation circular dichroism. Size and morphology were obtained by dynamic light scattering, size exclusion chromatography and atomic force microscopy, respectively. The iron uptake of the synthesized protein polymers was confirmed by UV-Vis spectroscopy loading assays.

On the delocalization length in RNA single strands of cytosine: how many bases see the light?

The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics. Electronic coupling between bases in the excited states of single strands of DNA and RNA may extend over several bases and likely protects nucleic acids from harmful UV damage. Here we report on the coupling between bases in single RNA strands of cytosine and find that the excited state is delocalized over up to five bases at neutral pH, where all bases are non-protonated (i.e. neutral). Delocalization is over four bases at 278 nm excitation, while it involves five bases at shorter wavelengths of 188 nm and 201 nm. This is in contrast to only nearest-neighbour interactions for corresponding DNA strands as previously reported. The current results seemingly corroborate earlier findings of larger spatial communication in RNA than in DNA strands of adenine, but there is no obvious link between the overall structure of strands and delocalization lengths. RNA cytosine strands form a tight helix, while comparatively, adenine strands show less tight packing, also compared to their DNA counterparts, and yet exhibit even higher delocalisation.