Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

Structural Study of DNA in Simulated Crowded Fluids

This work studied the structure and hybridization properties of DNA in simulated crowded media containing polyethylene glycol 10,000 and sucrose. Synchrotron radiation circular dichroism revealed that the overall CD profiles of a 21-mer and a d(CG)9 duplex remain similar in the simulated crowded fluids compared with those in Tris buffer, but the amplitude ratios of individual maxima and minima vary with the concentration of DNA and the media, suggesting possible conformational changes. Using fluorescence resonance energy transfer, this work confirmed that hairpin and duplex formations are not affected by the crowding condition. On the other hand, the duplex dynamics is affected by the crowding condition, where strand exchanges were promoted by the presence of PEG, but unaffected by sucrose.

Potential Bioactivities, Chemical Composition, and Conformation Studies of Exopolysaccharide-Derived Aspergillus sp. Strain GAD7

This research identified a marine fungal isolate, Aspergillus sp. strain GAD7, which produces an acidic and sulfated extracellular polysaccharide (EPS) with notable anticoagulant and antioxidant properties. Six fungal strains from the Egyptian Mediterranean Sea were screened for EPS production, with Aspergillus sp. strain GAD7 (EPS-AG7) being the most potent, yielding ~5.19 ± 0.017 g/L. EPS-AG7 was characterized using UV-Vis and FTIR analyses, revealing high carbohydrate (87.5%) and sulfate (24%) contents. HPLC and GC-MS analyses determined that EPS-AG7 is a heterogeneous acidic polysaccharide with an average molecular weight (Mw¯) of ~7.34 × 103 Da, composed of mannose, glucose, arabinose, galacturonic acid, galactose, and lyxose in a molar ratio of 6.6:3.9:1.8:1.3:1.1:1.0, linked through α- and β-glycosidic linkages as confirmed by NMR analysis. EPS-AG7 adopted a triple helix-like conformation, as evidenced by UV-Vis (Congo Red experiment) and circular dichroism (CD) studies. This helical arrangement demonstrated stability under various experimental conditions, including concentration, ionic strength, temperature, and lipid interactions. EPS-AG7 exhibited significant anticoagulant activity, doubling blood coagulation time at a concentration of 3.0 mg/mL, and showed significant antioxidant activity, with scavenging activities reaching up to 85.90% and 58.64% in DPPH and ABTS+ assays at 5.0 mg/mL, and EC50 values of 1.40 mg/mL and 3.80 mg/mL, respectively. These findings highlight the potential of EPS-AG7 for therapeutic applications due to its potent biological activities.

Exploring enantioselective recognition of dTMP-Co-bpe coordination polymer for natural amino acids using molecular simulations and circular dichroism

The 1D homochiral coordination polymer (CP-1) {[Co(dTMP)(bpe)2(H2O)3]·9H2O}n was constructed by using 2'-deoxy thymidine 5'-monophosphate disodium salt (dTMP·2Na), and auxiliary ligand bpe (1,2-bis(4-pyridyl)ethene) and characterized by single-crystal XRD, PXRD, IR, UV-visible, CD and TGA analyses. Molecular simulations revealed the selective chiral behaviour of CP-1 towards phenylalanine and histidine, as indicated by their higher binding free energies compared to other amino acids. Theoretical parameters were also compared with experimental UV-visible verdicts. Notably, the D-enantiomers of phenylalanine and histidine demonstrated strong bonding abilities and optimal configurations for probing and distinguishing them from their L-counterparts. These findings led to propositions suggesting that the dissimilarities between these D and L amino acid forms and their binding orientations with CP-1 may contribute to alterations in the CD signal. CP-1 exhibited a robust inherent circular dichroism (CD) signal in aqueous solutions, modulated by the presence of specific amino acids, namely D/L phenylalanine and D/L histidine. Leveraging the measurement of CD signal intensity, a sensor capable of detecting unmodified amino acids has been developed. Unlike previously reported approaches that relied on complex chemical reactions between initially CD-silent molecules and probed amino acids, this new method offers a more straightforward means of amplifying the CD signal. Consequently, this change facilitates a more accurate differentiation between the enantiomers of these specific amino acids compared to others.

DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources

Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.

Synchrotron Radiation Circular Dichroism Spectroscopy of Oligonucleotides at Millimolar Concentrations

Circular dichroism spectroscopy of nucleic acids has been traditionally performed at sample concentrations orders of magnitude lower than what occur in biological systems. While recent work from us demonstrated the flexibility of an adjustable sample cell that allowed for successful recording of CD spectra of an 18- and a 21-mer double stranded DNA sequences at around 1 mM, sample concentrations beyond 1 mM present a challenge for standard benchtop CD spectrometers. In the present work, the synchrotron radiation circular dichroism (SRCD) spectra were recorded for d(CG)₉ and a mixed 18-mer double stranded DNA at 1, 5, and 10 mM in 100 mM or 4 M NaCl. SRCD of low molecular weight salmon DNA was also measured at a 10 mg/ml concentration. These results represent the first report of CD spectra of DNA samples measured at concentrations comparable to those found in the nucleus. The results suggest that dsDNA maintain very similar structures at concentrations up to 10s of mg/ml, as evident by the very similar CD patterns in this concentration range. Furthermore, the SRCD allowed for the recording of CD patterns of DNA in the far UV region, which is not readily accessible by standard benchtop CD spectropolarimeters. These far UV signals appear to be quite characteristic of DNA structures and are sensitive to sample conditions.

Lipid-membranes interaction, structural assessment, and sustainable production of polyhydroxyalkanoate by Priestia filamentosa AZU-A6 from sugarcane molasses

This study presented for the first time the PHA-lipid interactions by circular dichroism (CD) spectroscopy, besides a sustainable PHA production strategy using a cost-effective microbial isolate. About 48 bacterial isolates were selected from multifarious Egyptian sites and screened for PHAs production. The Fe(AZU-A6) was the most potent isolate, and identified genetically as Priestia filamentosa AZU-A6, while the intracellular PHA granules were visualized by TEM. Sugarcane molasses (SCM) was used an inexpensive carbon source and the production conditions were optimized through a Factor-By-Factor strategy and a Plackett-Burman statistical model. The highest production (6.84 g L^-1) was achieved at 8.0 % SCM, pH 8.0, 35 °C, 250 rpm, and 0.5 g L^-1 ammonium chloride after 72 h. The complementary physicochemical techniques (e.g., FTIR, NMR, GC-MS, DSC, and TGA) have ascertained the structural identity as poly-3-hydroxybutyrate (P3HB) with a characteristic melting temperature of 174.5 °C. The circular dichroism analysis investigated the existence of interactions between the PHB and the different lipids, particularly 1,2-dimyristoyl-sn-glycero-3-phosphocholine. The ATR technique for the lipid-PHB films suggested that both the hydrophobic and electrostatic forces control the lipid-PHB interactions that might induce changes in the structuration of PHB.

Complementary spectroscopy studies and potential activities of levan-type fructan produced by Bacillus paralicheniformis ND2

This study aimed at the production of marine bacterial exopolysaccharides (EPS) as biodegradable and nontoxic biopolymers, competing the synthetic derivatives, with detailed structural and conformational analyses using spectroscopy techniques. Twelve marine bacterial bacilli were isolated from the seawater of Mediterranean Sea, Egypt, then screened for EPS production. The most potent isolate was identified genetically as Bacillus paralicheniformis ND2 by16S rRNA gene sequence of ~99 % similarity. Plackett-Burman (PB) design identified the optimization conditions of EPS production, which yielded the maximum EPS (14.57 g L^-1) with 1.26-fold increase when compared to the basal conditions. Two purified EPSs namely NRF1 and NRF2 with average molecular weights (Mw¯) of 15.98 and 9.70 kDa, respectively, were obtained and subjected for subsequent analyses. FTIR and UV-Vis reflected their purity and high carbohydrate contents while EDX emphasized their neutral type. NMR identified the EPSs as levan-type fructan composed of β-(2-6)-glycosidic linkage as a main backbone, and HPLC explained that the EPSs composed of fructose. Circular dichroism (CD) suggested that NRF1 and NRF2 had identical structuration with a little variation from the EPS-NR. The EPS-NR showed antibacterial activity with the maximum inhibition against S. aureus ATCC 25923. Furthermore, all the EPSs revealed a proinflammatory action through dose-dependent increment of expression of proinflammatory cytokine mRNAs, IL-6, IL-1β and TNFα.

Controlling the Orbital Alignment in Atoms Using Cross-Circularly Polarized Extreme Ultraviolet Wave Packets

We report on the use of pairs of 10-cycle extreme ultraviolet wave packets with attosecond-controlled spacing emitted by individual relativistic electrons within an electron bunch passing through a tandem undulator. Based on the temporal coherent control technique with circular polarization, we succeeded in controlling the excited state alignment in the photoexcitation of helium atoms, which we verified through the observation of oscillation in fluorescence yield depending on the attosecond-controlled delay time. Our work demonstrates the potential of undulator radiation for the generation of longitudinally coherent wave packets suitable for attosecond coherent control, an application which has hitherto been hidden in the incoherent nature of the radiation pulse emitted by a bunch of electrons.