Typical Secondary Structure Research Articles

Exploring the Origins of Association of Poly(acrylic acid) Polyelectrolyte with Lysozyme in Aqueous Environment through Molecular Simulations and Experiments.

This study provides a detailed picture of how a protein (lysozyme) complexes with a poly(acrylic acid) polyelectrolyte (PAA) in water at the atomic level using a combination of all-atom molecular dynamics simulations and experiments. The effect of PAA and temperature on the protein's structure is explored. The simulations reveal that a lysozyme's structure is relatively stable except from local conformational changes induced by the presence of PAA and temperature increase. The effect of a specific thermal treatment on the complexation process is investigated, revealing both structural and energetic changes. Certain types of secondary structures (i.e., α-helix) are found to undergo a partially irreversible shift upon thermal treatment, which aligns qualitatively with experimental observations. This uncovers the origins of thermally induced aggregation of lysozyme with PAA and points to new PAA/lysozyme bonds that are formed and potentially enhance the stability in the complexes. As the temperature changes, distinct amino acids are found to exhibit the closest proximity to PAA, resulting into different PAA/lysozyme interactions; consequently, a different complexation pathway is followed. Energy calculations reveal the dominant role of electrostatic interactions. This detailed information can be useful for designing new biopolymer/protein materials and understanding protein function under immobilization of polyelectrolytes and upon mild denaturation processes.

Geometric descriptors for beta turns.

Beta turns, in which the protein backbone abruptly changes direction over four amino acid residues, are the most common type of protein secondary structure after alpha helices and beta sheets and play key structural and functional roles. Previous work has produced classification systems for turn geometry at multiple levels of precision, but these operate in backbone dihedral-angle (Ramachandran) space, and the absence of a local Euclidean-space coordinate system and structural alignment for turns, or of any systematic Euclidean-space characterization of turn backbone shape, presents challenges for the visualization, comparison and analysis of the wide range of turn conformations and the design of turns and the structures that incorporate them. This work derives a turn-local coordinate system that implicitly aligns turns, together with a set of geometric descriptors that characterize the bulk BB shapes of turns and describe modes of structural variation not explicitly captured by existing systems. These modes are shown to be meaningful by the demonstration of clear relationships between descriptor values and the electrostatic energy of the beta-turn H-bond, the overrepresentations of key side-chain motifs, and the structural contexts of turns. Geometric turn descriptors complement Ramachandran-space classifications, and they can be used to select turn structures for compatibility with particular side-chain interactions or contexts. Potential applications include protein design and other tasks in which an enhanced Euclidean-space characterization of turns may improve understanding or performance. The web-based tools ExploreTurns, MapTurns, and ProfileTurn, available at www.betaturn.com, incorporate turn-local coordinates and turn descriptors and demonstrate their utility.

A comprehensive guide for secondary structure and tertiary structure determination in peptides and proteins by circular dichroism spectrometer.

Secondary structure refers to highly regular local sub-structures formed by the polypeptide backbone through hydrogen bonding. The two main types of secondary structures are α-helices and β-strands (which can form β-sheets). The development of a robust circular dichroism (CD) method for structural analysis of biomolecules requires careful consideration of several key factors. Solvent selection plays a crucial role in maintaining the native or desired conformation of the sample while ensuring transparency in the relevant wavelength regions. Aqueous buffers are often preferred for studying proteins in their native state. Optimizing the sample concentration and path length is essential to achieve an optimal absorbance range and maximize the signal-to-noise ratio. Typical concentrations for far-UV CD measurements range from 0.1 to 1mg/ml, with shorter path lengths (1mm) allowing for higher concentrations and longer path lengths (5mm) suitable for dilute solutions. Instrumental parameters, such as scanning speed, accumulations, and nitrogen flow rate, significantly impact the quality and reliability of the acquired CD spectra. Data processing is a critical step in obtaining accurate and interpretable CD spectra. Baseline correction, smoothing, and conversion to mean residue ellipticity are essential for reliable secondary structure analysis.

De novo design of alpha-beta repeat proteins.

Proteins composed of a single structural unit tandemly repeated multiple times carry out a wide range of functions in biology. There has hence been considerable interest in designing such repeat proteins; previous approaches have employed strict constraints on secondary structure types and relative geometries, and most characterized designs either mimic a known natural topology, adhere closely to a parametric helical bundle architecture, or exploit very short repetitive sequences. Here, we describe Rosetta-based and deep learning hallucination methods for generating novel repeat protein architectures featuring mixed alpha-helix and beta-strand topologies, and 25 new highly stable alpha-beta proteins designed using these methods. We find that incorporation of terminal caps which prevent beta strand mediated intermolecular interactions increases the solubility and monomericity of individual designs as well as overall design success rate.

Molecular identification and phylogenetic analysis of the mitogenome in endangered giant nuthatch Sitta magna (Passeriformes, Sittidae)

The Giant Nuthatch Sitta magna (family Sittidae) is a passerine bird, the quantification of the number of habitats and species on a global scale remains low. Most species are restricted to low elevations in southwest China, eastern Myanmar, and northern Thailand. To characterize the mitochondrial genome sequence of S. magna and its phylogenetic relationships with other members within the genus Sitta, the mitochondrial genome of S. magna was sequenced using the whole genome shotgun method. The sequencing results showed that the mitochondrial genome was 16,829 bp long and consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (D-loop). All tRNAs were predicted to form a typical clover secondary structure. Among the 13 PCGs, only the start codon in COI was ATC, the start codon by the remaining 12 PCGs was ATG, and the stop codons were TAG, TAA, AGG, AGA, and TA. Bayesian inference and maximum likelihood phylogenetic analysis of the sequences of 17 species generated consistent well-supported phylogenies. The family Polioptilidae and the family Troglodytidae were closely related, and the family Sittidae was confined to a single branch. The genus Sitta in the family Sittidae was mainly clustered into three branches. Our findings provide new mitochondrial genomic data that could be used for phylogenetic and taxonomic studies; our results also certificate into the phylogenetic relationships within the genus Sitta ((S. himalayensi+(S. nagaensis + S. europaea))+(S. villosa + S. yunnanensis))+(S. carolinensis + S. magna).

Emergence of two distinct spatial folds in a pair of plant virus proteins encoded by nested genes

Virus genomes may encode overlapping or nested open reading frames that increase their coding capacity. It is not known whether the constraints on spatial structures of the two encoded proteins limit evolvability of nested genes. We examine the evolution of a pair of proteins, p22 and p19, encoded by nested genes in plant viruses from the genus Tombusvirus. The known structure of p19, a suppressor of RNA silencing, belongs to the RAGNYA fold from the alpha+beta class. The structure of p22, the cell-to-cell movement protein from the 30K family widespread in plant viruses, is predicted with the AlphaFold approach, suggesting a single jelly-roll fold core from the all-beta class, structurally similar to capsid proteins from plant and animal viruses. The nucleotide and codon preferences impose modest constraints on the types of secondary structures encoded in the alternative reading frames, nonetheless allowing for compact, well-ordered folds from different structural classes in two similarly-sized nested proteins. Tombusvirus p22 emerged through radiation of the widespread 30K family, which evolved by duplication of a virus capsid protein early in the evolution of plant viruses, whereas lineage-specific p19 may have emerged by stepwise increase in the length of the overprinted gene and incremental acquisition of functionally active secondary structure elements by the protein product. This evolution of p19 towards the RAGNYA fold represents one of the first documented examples of protein structure convergence in naturally occurring proteins.

Enhanced chromium and nitrogen removal by constructing a biofilm reaction system based on denitrifying bacteria preferential colonization theory

Understanding the developmental characteristics of microbial communities in biofilms is crucial for designing targeted functional microbial enhancements for the remediation of complex contamination scenarios. The strong prioritization effect of microorganisms confers the ability to colonize strains that arrive first dominantly. In this study, the auto-aggregating denitrifying bacterial Pseudomonas stutzeri strain YC-34, which has both nitrogen and chromium removal characteristics, was used as a biological material to form a stable biofilm system based on the principle of dominant colonization and biofortification. The effect of the biofilm system on nitrogen and chromium removal was characterized by measuring the changes in the quality of influent and effluent water. The pattern of biofilm changes was analyzed by measuring biofilm content and thickness and characterizing extracellular polymer substances (EPS). Further analysis of the biofilm microbiota characteristics and potential functions revealed the mechanism of strain YC-34 biofortified biofilm. The results revealed that the biofilm system formed could achieve 90.56% nitrate-nitrogen removal with an average initial nitrate-nitrogen concentration of 51.9 mg/L and 40% chromium removal with an average initial hexavalent chromium Cr(VI) concentration of 7.12 mg/L. The biofilm properties of the system were comparatively analyzed during the biofilm formation period, the fluctuation period of Cr(VI)-stressed water quality, and the stabilization period of Cr(VI)-stressed water quality. The biofilm system may be able to increase the structure of hydrogen bonds, the type of protein secondary structure, and the abundance of amino acid-like components in the EPS, which may confer biofilm tolerance to Cr(VI) stress and allow the system to maintain a stable biofilm structure. Furthermore, microbial characterization indicated an increase in microbial diversity in the face of chromium stress, with an increase in the abundance of nitrogen removal-associated functional microbiota and an increasing trend in the abundance of nitrogen transfer pathways. These results demonstrate that the biofilm system is stable in nitrogen and chromium removal. This bioaugmentation method may provide a new way for the remediation of heavy metal-polluted water bodies and also provides theoretical and application parameters for the popularization and application of biofilm systems.

In vivo detection of DNA secondary structures using permanganate/S1 footprinting with direct adapter ligation and sequencing (PDAL-Seq).

DNA secondary structures are essential elements of the genomic landscape, playing a critical role in regulating various cellular processes. These structures refer to G-quadruplexes, cruciforms, Z-DNA or H-DNA structures, amongst others (collectively called 'non-B DNA'), which DNA molecules can adopt beyond the B conformation. DNA secondary structures have significant biological roles, and their landscape is dynamic and can rearrange due to various factors, including changes in cellular conditions, temperature, and DNA-binding proteins. Understanding this dynamic nature is crucial for unraveling their functions in cellular processes. Detecting DNA secondary structures remains a challenge. Conventional methods, such as gel electrophoresis and chemical probing, have limitations in terms of sensitivity and specificity. Emerging techniques, including next-generation sequencing and single-molecule approaches, offer promise but face challenges since these techniques are mostly limited to only one type of secondary structure. Here we describe an updated version of a technique permanganate/S1 nuclease footprinting, which uses potassium permanganate to trap single-stranded DNA regions as found in many non-B structures, in combination with S1 nuclease digest and adapter ligation to detect genome-wide non-B formation. To overcome technical hurdles, we combined this method with direct adapter ligation and sequencing (PDAL-Seq). Furthermore, we established a user-friendly pipeline available on Galaxy to standardize PDAL-Seq data analysis. This optimized method allows the analysis of many types of DNA secondary structures that form in a living cell and will advance our knowledge of their roles in health and disease.

A self-assembling peptide nanofiber hydrogel for biomaterials with rapid stimulation response to naturally positively charged group substances

Peptides as unique supramolecular nanofibrous materials are favored choices to fabricate hydrogel for artificial extracellular matrices. Herein, we devised an amphiphilic polypeptide that could be motivated by multiple substances with positively charged group at physiological temperature and pH to assemble supramolecular nanofiber hydrogels since the electrostatic repulsion between monomers was attenuated. The hydrogelation phenomenon and spectroscopy were compatible with molecular dynamics simulations (MDs) results for revealing the assembly mechanism of this peptide, confirming that the behavior of assembling and the typical secondary structure of the assemblies was β-sheet. The impact of peptide concentration on the mechanical properties of hydrogels were described using rheology. We found that the peptide formed elastic gels from 0.3 wt% onwards in practical use and that these recovered by themselves after shear thinning that indicated they were injectable hydrogels. The successful establishment of cell spheres with high cell viability during 15 days culture in 3D space demonstrated the nanofiber hydrogels had potential in cell model construction and microtissue culture. Overall, the superior biologically friendly gel-forming conditions and excellent biological properties of this supramolecular assembly peptide material have invigorated the progress of biomedical fields such as tissue regeneration based on in vitro 3D culture.

Mechanical properties of hierarchical lattice via strain gradient homogenization approach

With the advancement of 3D printing technology, manufacturing metamaterials with extreme mechanical properties is becoming more feasible. Hierarchical lattices appear to be ideal candidates for obtaining desirable lightweight, high specific stiffness, and enhanced specific energy absorption. They can be constructed by architected substructures at multiple length scales. The interpretations of the underlying deformation mechanisms are necessary in order to manipulate with expected mechanical properties. In this paper, experiments were conducted to examine the effective mechanical behaviors of hierarchical lattice metamaterials. A strain gradient homogenization approach has been employed to correlate their morphological characteristics to the resulting material properties. The effective stiffness tensors are identified including the fourth-, fifth-, and sixth-order stiffness tensors. The higher-order inertial parameters are determined by a fitting procedure. Comparisons between direct finite element analyses and the homogenized strain gradient continua have been made for hierarchical lattice materials under static and dynamic loads. It is found that strain gradient homogenization approach can be an accurate, efficient and reliable way of predicting the mechanical behaviors of hierarchical lattice. A systematic analysis of geometrical parameters was conducted to uncover the underlying mechanisms responsible for the enhancement of effective properties. This work offers a novel approach for designing the mechanical properties of hierarchical metamaterials through precise control of secondary structure types and distributions.

DichroIDP: a method for analyses of intrinsically disordered proteins using circular dichroism spectroscopy

Intrinsically disordered proteins (IDPs) are comprised of significant numbers of residues that form neither helix, sheet, nor any other canonical type of secondary structure. They play important roles in a broad range of biological processes, such as molecular recognition and signalling, largely due to their chameleon-like ability to change structure from unordered when free in solution to ordered when bound to partner molecules. Circular dichroism (CD) spectroscopy is a widely-used method for characterising protein secondary structures, but analyses of IDPs using CD spectroscopy have suffered because the methods and reference datasets used for the empirical determination of secondary structures do not contain adequate representations of unordered structures. This work describes the creation, validation and testing of a standalone Windows-based application, DichroIDP, and a new reference dataset, IDP175, which is suitable for analyses of proteins containing significant amounts of disordered structure. DichroIDP enables secondary structure determinations of IDPs and proteins containing intrinsically disordered regions.

Complete mitogenomes characterization and phylogenetic analyses of Ceratophyllus anisus and Leptopsylla segnis.

Fleas are one of the most common ectoparasites in warm-blooded mammals and an important vector of zoonotic diseases with serious medical implications. We sequenced the complete mitochondrial genomes of Ceratophyllus anisus and Leptopsylla segnis for the first time using high-throughput sequencing and constructed phylogenetic relationships. We obtained double-stranded circular molecules of lengths 15,875 and 15,785 bp, respectively, consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and two control regions. AT-skew was negative in both C. anisus (-0.022) and L. segnis (-0.231), while GC-skew was positive in both (0.024/0.248), which produced significant differences in codon usage and amino acid composition. Thirteen PCGs encoding 3,617 and 3,711 codons, respectively, isoleucine and phenylalanine were used most frequently. The tRNA genes all form a typical secondary structure. Construction of phylogenetic trees based on Bayesian inference (BI) and maximum likelihood (ML) methods for PCGs. The results of this study provide new information for the mitochondrial genome database of fleas and support further taxonomic studies and population genetics of fleas.

The complete mitogenome of blue sheep (Pseudois nayaur) from the Indian Himalayan Region and its comparative phylogenetic relationship with other related species

The ‘Bharal’ or ‘Himalayan Blue Sheep’ (Pseudois nayaur) is endemic to the Himalayan and Tibetan Regions. There are gaps in the available database for the blue sheep mitogenome sequencing from the Indian region. We sequenced and characterized the whole mitogenome of one blue sheep individual using the Illumina Nova-seq 6000 platform, which was 16,718 bp in length. It included 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding control region (D loop). It was compared with other complete mitochondrial DNA sequences of blue sheep from the NCBI database. The whole mitogenome of blue sheep was found to be highly AT-biased (60%) and had a positive AT skew (0.121) and a negative GC skew (−0.341). In 13 PCGs of blue sheep, Leucine (15.58%) and tryptophan (2.72%) occurred most frequently. A typical secondary cloverleaf structure was observed for all tRNA genes except for tRNA-Ser, where a stable structure of dihydrouridine did not develop. The phylogenetic analysis showed Indian blue sheep population formed a separate clade with a genetic distance of 3.7 to 4.1% from the Chinese blue sheep population, suggesting it to be of a different lineage and genetically qualifies the status of distinct subspecies. The results of this study will help in further phylogenetic analysis of Indian blue sheep populations in the Western and Eastern Himalayan regions and in understanding lineage identification and evolution for further research.

Photoactive Yellow Protein Adsorption at Hydrated Polyethyleneimine and Poly-l-Glutamic Acid Interfaces.

Chiral and achiral vibrational sum-frequency generation (VSFG) spectroscopy was performed in the 1400-1700 and 2800-3800 cm-1 range to study the interfacial structure of photoactive yellow protein (PYP) adsorbed on polyethyleneimine (PEI) and poly-l-glutamic acid (PGA) surfaces. Nanometer-thick polyelectrolyte layers served as the substrate for PYP adsorption, with 6.5-pair layers providing the most homogeneous surfaces. When the topmost material was PGA, it acquired a random coil structure with a small number of β2-fibrils. Upon adsorption on oppositely charged surfaces, PYP yielded similar achiral spectra. However, the VSFG signal intensity increased for PGA surfaces with a concomitant redshift of the chiral Cα-H and N-H stretching bands, suggesting increased adsorption for PGA compared to PEI. At low wavenumbers, both the backbone and the side chains of PYP induced drastic changes to all measured chiral and achiral VSFG spectra. Decreasing ambient humidity led to the loss of tertiary structure with a re-orientation of α-helixes, evidenced by a strongly blue-shifted chiral amide I band of the β-sheet structure with a shoulder at 1654 cm-1. Our observations indicate that chiral VSFG spectroscopy is not only capable of determining the main type of secondary structure of PYP, i.e., β-scaffold, but is also sensitive to tertiary protein structure.

Apoptosis induction in leukemic cells by L-asparaginase preparation from Bacillus indicus: bench-scale production, purification and therapeutic application.

With the emergence of multiple side effects on the usage of commercial L-asparaginase formulations, keen interest is provoked to investigate new sources of L-asparaginases that possess antileukemic properties with minimal side effects. The present study reports the cost-effective bench-scale production, homogeneity purification and apoptosis induction potential of a new L-asparaginase preparation from Bacillus indicus against human leukemia cells. The enzyme is highly specific toward the natural substrate L-asparagine. The study initiated with the enzyme production using cost-effective substrates in which a 3.28-fold enhancement of enzyme activity was achieved in comparison with an unoptimized medium using the central composite experimental design approach. The scale-up of the process in a 3.7-L batch bioreactor resulted in 16.42 ± 0.17IU/mL of L-asparaginase activity in 24h. The crude extracellular enzyme was purified to homogeneity using anion exchange chromatography followed by gel filtration chromatography. A single band of approximately 35kDa molecular weight was obtained on SDS-PAGE, while native PAGE analysis confirmed it to be a tetramer of four identical subunits. The circular dichroism spectroscopic study revealed the α + β mixed type of secondary structure with 38.7% α-helices and 27.4% β pleated sheets. The antitumor toxicity exhibited on the MOLT-4 leukemia cells by the new L-asparaginase was revealed using the MTT assay and acridine orange/propidium iodide dual staining for live/dead cells. The flow cytometry analysis established the potential of the purified L-asparaginase to induce the apoptotic cell death mechanism in MOLT-4 leukemia cells. Conclusively, the L-asparaginase of Bacillus indicus is a highly promising candidate that can be introduced as a new enzyme therapeutic against various leukemia disorders.

Implications of differential transcription start site selection on chronic myeloid leukemia and prostate cancer cell protein expression.

The relevance of minor transcription start sites in broad promoters is not well understood. We have studied AGAP2 expression in prostate cancer and chronic myeloid leukemia (CML), showing transcription is initiated from alternative transcription start sites (TSSs) within a single TSS cluster, producing cancer-type-specific AGAP2 mRNAs with small differences in their 5' UTR length. Interestingly, in the CML cell lines where the 5' UTR is longer, AGAP2 protein levels are lower. We demonstrate that the selection of an upstream TSS involved the formation of a G quadruplex in the 5' UTR, decreasing polysome formation. After developing a bioinformatics pipeline to query data from the FANTOM project and the NCl-60 human tumor cell lines screen, we found HK1 expression can also be regulated by the same mechanism. Overall, we present compelling data supporting TSS selection within a TSS cluster play a role in protein expression and should not be ignored.

Structural and functional studies of scorpine: A channel blocker and cytolytic peptide

Scorpine is an antimicrobial and antimalarial peptide isolated from Pandinus imperator scorpion venom. As there are few functional and structural studies reported on scorpine-like peptides, we investigated the recombinant truncated N- and C-terminal domains as well as complete scorpine using biological assays and determined the N- and C-terminal structures using solution nuclear magnetic resonance. The study was conducted using recombinant N- and C-terminal peptides and complete scorpine expressed in Escherichia coli. The results showed that N-scorpine presented a random coil structure in water and adopted α-helical folding in the presence of 50% trifluoroethanol (TFE). C-scorpine contains three disulfide bonds with two structural domains: an unstructured N-terminal domain in water that can form a typical secondary alpha-helix structure in 50% TFE and a C-terminal domain with the CS-αβ motif. Our findings demonstrate cytolytic activity associated with C-scorpine, N-scorpine, and scorpine, as well as channel blocking activity associated with the C-scorpine domain.

Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections.

Whilst DNA repeat expansions cause numerous heritable human disorders, their origins and underlying pathological mechanisms are often unclear. We collated a dataset comprising 224 human repeat expansions encompassing 203 different genes, and performed a systematic analysis with respect to key topological features at the DNA, RNA and protein levels. Comparison with controls without known pathogenicity and genomic regions lacking repeats, allowed the construction of the first tool to discriminate repeat regions harboring pathogenic repeat expansions (DPREx). At the DNA level, pathogenic repeat expansions exhibited stronger signals for DNA regulatory factors (e.g. H3K4me3, transcription factor-binding sites) in exons, promoters, 5'UTRs and 5'genes but were not significantly different from controls in introns, 3'UTRs and 3'genes. Additionally, pathogenic repeat expansions were also found to be enriched in non-B DNA structures. At the RNA level, pathogenic repeat expansions were characterized by lower free energy for forming RNA secondary structure and were closer to splice sites in introns, exons, promoters and 5'genes than controls. At the protein level, pathogenic repeat expansions exhibited a preference to form coil rather than other types of secondary structure, and tended to encode surface-located protein domains. Guided by these features, DPREx ( http://biomed.nscc-gz.cn/zhaolab/geneprediction/# ) achieved an Area Under the Curve (AUC) value of 0.88 in a test on an independent dataset. Pathogenic repeat expansions are thus located such that they exert a synergistic influence on the gene expression pathway involving inter-molecular connections at the DNA, RNA and protein levels.

Folding Coarse-Grained Oligomer Models with PyRosetta.

Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta's ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.

Photo-Oxidizing Ruthenium(II) Complexes with Enhanced Visible-Light Absorption and G-quadruplex DNA Binding Abilities.

Photosensitizers that gather high photo-oxidizing power and strong visible-light absorption are of great interest in the development of new photo-chemotherapeutics. Indeed, such compounds constitute attractive candidates for the design of type I photosensitizers that are not dependent on the presence of oxygen. In this paper, we report on the synthesis and studies of new ruthenium(II) complexes that display strong visible-light absorption and can oxidize guanine residues under visible-light irradiation, as evidenced by nanosecond transient absorption spectroscopy. The reported compounds also tightly bind to G-quadruplex DNA structures from the human telomeric sequence (TTAGGG repeat). The kinetic and thermodynamic parameters of the interaction of these Ru(II) complexes with G-quadruplex and duplex DNA were studied thanks to luminescence titrations and bio-layer interferometry measurements, which revealed higher affinities towards the non-canonical G-quadruplex architecture. Docking experiments and non-covalent ionic analysis allowed us to gain information on the mode and the strength of the interaction of the compounds towards G-quadruplex and duplex DNA. The different studies emphasize the substantial influence of the position and the number of non-chelating nitrogen atoms on the interaction with both types of DNA secondary structures.