Major Groove Of DNA Research Articles

Synthesis, structural elucidation, and DNA binding behavior of a ternary copper(II) complex featuring substituted bipyridyl and dicarboxylate ligands

The present research study is centered around the synthesis, characterization, and biological application of a ternary mixed-ligand based binuclear Cu(II) complex [Cu2(trans-1,4-chdc)(4,4′-Me2-2,2′-bpy)2(5,5′-Me2-2,2′-bpy)2]·2(cis-H21,4-chdc)·2(BF4¯) (1) by meticulous incorporation of 4,4′-dimethyl-2,2′-bipyridine (4,4′-Me2-2,2′-bpy), 5,5′-dimethyl-2,2′-bipyridine (5,5′-Me2-2,2′-bpy) and cis- andtrans- mixture of 1,4-cyclohexanedicarboxylic acid (H21,4-chdc). Hirshfeld analysis is employed to validate non-bonded interactions, demonstrating the existence of widespread π···π stacking interactions between adjacent 4,4′-Me2-2,2′-bpy ligands at a distance of 3.757 Å, forming a one-dimensional (1D) supramolecular polymer chain. The biological activity of complex 1 is explored via docking study, driven by the inherent biological inclination of the Cu(II) complexes. Agreeably, the coordination complex 1 displays a favorable binding to DNA, specifically binds to the major groove of DNA and the aromatic pyridine ring of the ligand partially intercalates into the base pairs with a binding constant (Kb) of 1.98 × 105 M−1.

Cobaltabis(dicarbollide) Interaction with DNA Resolved at the Atomic Scale.

Boron neutron capture therapy represents a promising avenue for cancer treatment that requires nontoxic drugs with a high boron content efficiently distributed into cancerous cells. The metallacarborane o-cobaltabis(dicarbollide) ([COSAN]-) fulfills these requirements and constitutes an attractive candidate. Nevertheless, the interaction of this promising drug with nucleic acids, the assumed target of the biological damage, is poorly understood since contradictory results are reported in the literature. This work establishes the DNA/[COSAN]- interaction strength, mechanism, and time scale at the atomistic level by using a combination of microsecond-molecular dynamics and hybrid quantum mechanics/molecular mechanics simulations and by quantifying the absolute binding free energy. Results show that the DNA/[COSAN]- interaction is highly dependent on the ionic strength of the medium. A relatively weak DNA major groove binding (ΔGbind= -2.49 kcal/mol) driven mostly by dihydrogen B-H···H-N bonding is observed in the simulations only at a high NaCl concentration, whereas DNA intercalation mode is deemed highly unlikely.

Metal-Based Drug-DNA Interactions and Analytical Determination Methods.

DNA structure has many potential places where endogenous compounds and xenobiotics can bind. Therefore, xenobiotics bind along the sites of the nucleic acid with the aim of changing its structure, its genetic message, and, implicitly, its functions. Currently, there are several mechanisms known to be involved in DNA binding. These mechanisms are covalent and non-covalent interactions. The covalent interaction or metal base coordination is an irreversible binding and it is represented by an intra-/interstrand cross-link. The non-covalent interaction is generally a reversible binding and it is represented by intercalation between DNA base pairs, insertion, major and/or minor groove binding, and electrostatic interactions with the sugar phosphate DNA backbone. In the present review, we focus on the types of DNA-metal complex interactions (including some representative examples) and on presenting the methods currently used to study them.

Beyond the "spine of hydration": Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures.

Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for the rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N-H stretch of DNA base pairs and the O-H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, the electric field-induced water structure is symmetric and, therefore, precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove "spine of hydration" is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration.

Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNA.

Triplex DNA structures, formed when a third DNA strand wraps around the major groove of DNA, are key molecular regulators and genomic threats. However, the regulatory network governing triplex DNA dynamics remains poorly understood. Here we reveal the binding and functional repertoire of proteins that interact with triplex DNA through chemoproteomic profiling in living cells. We develop a chemical probe that exhibits exceptional specificity towards triplex DNA. By employing a co-binding-mediated proximity capture strategy, we enrich triplex DNA interactome for quantitative proteomics analysis. This enables the identification of a comprehensive list of proteins that interact with triplex DNA, characterized by diverse binding properties and regulatory mechanisms in their native chromatin context. As a demonstration, we validate DDX3X as an ATP-independent triplex DNA helicase to unwind substrates with a 5' overhang to prevent DNA damage. Overall, our study provides a valuable resource for exploring the biology and translational potential of triplex DNA.

CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes.

Mutations of the SNF2 family ATPase HELLS and its activator CDCA7 cause immunodeficiency, centromeric instability, and facial anomalies syndrome, characterized by DNA hypomethylation at heterochromatin. It remains unclear why CDCA7-HELLS is the sole nucleosome remodeling complex whose deficiency abrogates the maintenance of DNA methylation. We here identify the unique zinc-finger domain of CDCA7 as an evolutionarily conserved hemimethylation-sensing zinc finger (HMZF) domain. Cryo-electron microscopy structural analysis of the CDCA7-nucleosome complex reveals that the HMZF domain can recognize hemimethylated CpG in the outward-facing DNA major groove within the nucleosome core particle, whereas UHRF1, the critical activator of the maintenance methyltransferase DNMT1, cannot. CDCA7 recruits HELLS to hemimethylated chromatin and facilitates UHRF1-mediated H3 ubiquitylation associated with replication-uncoupled maintenance DNA methylation. We propose that the CDCA7-HELLS nucleosome remodeling complex assists the maintenance of DNA methylation on chromatin by sensing hemimethylated CpG that is otherwise inaccessible to UHRF1 and DNMT1.

Graphene Quantum Dots Eradicate Resistant and Metastatic Cancer Cells by Enhanced Interfacial Inhibition.

Drug-resistant and metastatic cancer cells such as a small population of cancer stem cells (CSCs) play a crucial role in metastasis and relapse. Conventional small-molecule chemotherapeutics, however, are unable to eradicate drug-resistant CSCs owing to limited interface inhibitory effects. Herein, it is reported that enhanced interfacial inhibition leading to eradication of drug-resistant CSCs can be dramatically induced by self-insertion of bioactive graphene quantum dots (GQDs) into DNA major groove (MAG) sites in cancer cells. Since transcription factors regulate gene expression at the MAG site, MAG-targeted GQDs exert greatly enhanced interfacial inhibition, downregulating the expression of a collection of cancer stem genes such as ALDH1, Notch1, and Bmi1. Moreover, the nanoscale interface inhibition mechanism reverses cancer multidrug resistance (MDR) by inhibiting MDR1 gene expression when GQDs are used at a nontoxic concentration (1/4 × half-maximal inhibitory concentration (IC50)) as the MDR reverser. Given their high efficacy in interfacial inhibition, CSC-mediated migration, invasion, and metastasis of cancer cells can be substantially blocked by MAG-targeted GQDs, which can also be harnessed to sensitize clinical cytotoxic agents for improved efficacy in combination chemotherapy. These findings elucidate the inhibitory effects of the enhanced nano-bio interface at the MAG site on eradicating CSCs, thus preventing cancer metastasis and recurrence.

Borrelia burgdorferi PlzA is a cyclic-di-GMP dependent DNA and RNA binding protein.

The PilZ domain-containing protein, PlzA, is the only known cyclic di-GMP binding protein encoded by all Lyme disease spirochetes. PlzA has been implicated in the regulation of many borrelial processes, but the effector mechanism of PlzA was not previously known. Here, we report that PlzA can bind DNA and RNA and that nucleic acid binding requires c-di-GMP, with the affinity of PlzA for nucleic acids increasing as concentrations of c-di-GMP were increased. A mutant PlzA that is incapable of binding c-di-GMP did not bind to any tested nucleic acids. We also determined that PlzA interacts predominantly with the major groove of DNA and that sequence length and G-C content play a role in DNA binding affinity. PlzA is a dual-domain protein with a PilZ-like N-terminal domain linked to a canonical C-terminal PilZ domain. Dissection of the domains demonstrated that the separated N-terminal domain bound nucleic acids independently of c-di-GMP. The C-terminal domain, which includes the c-di-GMP binding motifs, did not bind nucleic acids under any tested conditions. Our data are supported by computational docking, which predicts that c-di-GMP binding at the C-terminal domain stabilizes the overall protein structure and facilitates PlzA-DNA interactions via residues in the N-terminal domain. Based on our data, we propose that levels of c-di-GMP during the various stages of the enzootic life cycle direct PlzA binding to regulatory targets.

Differential DNA Recognitions of Benzimidazole Based Astemizole, Omeprazole, Lansoprazole, and Thiabendazole

AbstractWell known benzimidazole based drugs – astemizole, omeprazole, lansoprazole, and thiabendazole – are studied whether those can bind with two different oligonucleotides sequences or not. Molecular docking study and further molecular dynamics are employed to find out the capability of these drugs toward different DNA sequences. The substitution at N2 with different atoms/group or heterocyclic moieties favors the binding in the major groove of DNA in most of the cases. The substitutions at N1 beside N2 position clearly increase the binding possibility of astemizole as compared to the rest. Various functional possibilities of known drugs through DNA recognitions may be explored in drug repurposing purposes in virtue of present study.

Decoding the dual recognition mechanism of the glucocorticoid receptor for DNA and RNA: sequence versus shape

Transcription factors (TFs) regulate eukaryotic transcription through selective DNA-binding, can also specifically interact with RNA, which may present another layer of transcriptional control. The mechanisms of the TFs-DNA recognition are often well-characterised, while the details of TFs-RNA complexation are less understood. Here we investigate the dual recognition mechanism of the glucocorticoid receptor (GR), which interacts with similar affinities with consensus DNA and diverse RNA hairpin motifs but discriminates against uniform dsRNA. Using atomic molecular dynamics simulations, we demonstrate that the GR binding to nucleic acids requires a wide and shallow groove pocket. The protein effectively moulds its binding site within DNA major groove, which enables base-specific interactions. Contrary, the GR binding has little effect on the grooves geometry of RNA systems, most notably in uniform dsRNA. Instead, a hairpin motif in RNA yields a wide and shallow major groove pocket, allowing the protein to anchor itself through nonspecific electrostatic contacts with RNA backbone. Addition of a bulge increases RNA hairpin flexibility, which leads to a greater number of GR-RNA contacts and, thus, higher affinity. Thus, the combination of structural motifs defines the GR-RNA selective binding: a recognition mechanism, which may be shared by other zinc finger TFs.

DNA major versus minor groove occupancy of monomeric and dimeric crystal violet derivatives. Toward structural correlations

Six monomeric (1a-1f) and five dimeric (2a-2e) derivatives of the triphenylmethane dye crystal violet (CV) have been prepared. Evaluation of the binding of these compounds to CT DNA by competitive fluorescent intercalator displacement (FID) assays, viscosity experiments, and UV and CD spectroscopy suggest that monomeric derivative 1a and dimeric derivative 2d likely associate with the major groove of DNA, while dimeric derivatives 2a and 2e likely associate with the minor groove of DNA. Additional evidence for the groove occupancy assignments of these derivatives was obtained from ITC experiments and from differential inhibition of DNA cleavage by the major groove binding restriction enzyme BamHI, as revealed by agarose gel electrophoresis. The data indicate that major groove ligands may be optimally constructed from dye units containing a sterically bulky 3,5-dimethyl-N,N-dimethylaniline group; furthermore, the groove-selectivity of olefin-tethered dimer 2d suggests that stereoelectronic interactions (n → π*) between the ligand and DNA are also an important design consideration in the crafting of major-groove binding ligands.

Molecular docking and biological activities of Ni(II), Cu(II) and Co(II) complexes with a new potentially hexadentate polyamine ligand; X-ray crystal structure of the Cu(II) complex

Three new metal complexes have been obtained from the reaction of a new polyamine (L) with Ni(II), Cu(II), and Co(II) ions. The X-ray structural analysis of the Cu(II) complex shows that the copper atom is in a very distorted square pyramidal environment, coordinated by five of the six nitrogen donor atoms of the potentially hexadentate ligand. To evaluate the biological potential of the ligand and the synthesized metal complexes, their binding behavior with DNA was studied by molecular modeling methods. The Molecular docking studies showed that the free ligand and its complexes were bound to the major groove of DNA. The antioxidant activities of the ligand and its metal complexes were also assessed, in vitro, using 2,2-diphenyl-1-picrylhydrazyl. The synthesized compounds were tested for activity against lung carcinoma epithelial cells (A549) using the MTT cell viability assay. A comparative study of the IC50 values indicated that the Cu(II) complex exhibited the highest activity, while the Co(II) and Ni(II) complexes showed more potent antiproliferative activity than the ligand. The antibacterial activities of the synthesized complexes were evaluated using micro-broth dilution and disk diffusion methods. The complexes showed greater antibacterial activity than the free ligand. Communicated by Ramaswamy H. Sarma

Structures of CTCF-DNA complexes including all 11 zinc fingers.

The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12-15-bp CORE sequence, some of the CTCF binding sites contain 5' upstream and/or 3' downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1-ZF7 and ZF3-ZF11 in complex with DNA that incorporatesthe CORE sequence together with either 3' downstream or 5' upstream motifs. Like conventional tandem ZF array proteins, ZF1-ZF7 followthe right-handed twist of the DNA, with each finger occupying and recognizing one triplet of three basepairs in the DNA major groove. ZF8 plays a unique role, acting as a spacer across the DNA minor groove and positioning ZF9-ZF11 to make cross-strand contacts with DNA. We ascribe the difference between the two subgroups of ZF1-ZF7 and ZF8-ZF11 to residues at the two positions -6 and -5 within each finger, with small residues for ZF1-ZF7 and bulkier and polar/charged residues for ZF8-ZF11. ZF8 is also uniquely rich in basic amino acids, which allows salt bridges to DNA phosphates in the minor groove. Highly specific arginine-guanine and glutamine-adenine interactions, used to recognize G:C or A:T base pairs at conventional base-interacting positions of ZFs, also apply to the cross-strand interactions adopted by ZF9-ZF11. The differences between ZF1-ZF7 and ZF8-ZF11 can be rationalized structurally and may contribute to recognition of high-affinity CTCF binding sites.

Electrostatic Interactions in the Formation of DNA Complexes with Cis- and Trans-Isomers of Azobenzene-Containing Surfactants in Solutions with Di- and Trivalent Metal Ions.

The effect of the presence of divalent and trivalent metal ions in solutions upon DNA packaging induced by the photosensitive azobenzene-containing surfactant is considered. It has been shown that the addition of divalent and trivalent metal ions does not affect the DNA-surfactant interaction for both the cis- and the trans-isomers of the surfactant. At the same time, the ionic strength of the solution, which is provided by a certain concentration of the salt, has a huge impact. It affects the association of surfactant molecules with each other and their binding to DNA. It has been shown by computer simulation that cobalt hexamine is attracted to the N7 atom of guanine in the major groove of DNA and does not penetrate into grooves near the AT base pairs.

Glycerol group substituted bis(2-pyridylimino)isoindoline (BPI) complexes: synthesis, characterization and investigation of their biological properties.

In this study, a glycerol group substituted bis(2-pyridylamino)isoindoline (BPI-OH) ligand and its metal complexes (M = Pt, Cu and Co) were synthesized. Characterization of all new compounds was carried out using FT-IR, NMR, UV-Vis, and mass spectroscopy. Various biological activities of BPI derivatives were also tested. The antioxidant activities of BPI-OH, Pt-BPI-OH, Cu-BPI-OH, and Co-BPI-OH were 87.52 ± 4.62%, 98.05 ± 5.61%, 92.20 ± 5.12%, and 89.27 ± 4.74%, at 200 mg L-1 concentration respectively. BPI derivatives displayed perfect DNA cleavage activity and plasmid DNA was completely broken at all tested concentrations. The antimicrobial and antimicrobial photodynamic therapy (APDT) activities of the compounds were investigated and BPI derivatives showed good APDT. E. coli cell viability was inhibited at 125 and 250 mg L-1. BPI-OH, Pt-BPI-OH, Cu-BPI-OH, and Co-BPI-OH also successfully inhibited the biofilm formation of S. aureus and P. aeruginosa. Furthermore, the antidiabetic activity of BPI derivatives was studied. This study also evaluates the binding affinities of four compounds (BPI-OH, Pt-BPI-OH, Cu-BPI-OH, and Co-BPI-OH) to various residues of DNA using hydrogen bond distance measurements and binding energies. The results show that the BPI-OH compound forms hydrogen bonds with residues in the major groove of DNA, while BPI-Pt-OH, BPI-Cu-OH, and BPI-Co-OH compounds form hydrogen bonds with residues in the minor groove. The hydrogen bond distances for each compound range from 1.75 to 2.2 Angstroms.

DNA topology regulates PAM-Cas9 interaction and DNA unwinding to enable near-PAMless cleavage by thermophilic Cas9

CRISPR-Cas9-mediated genome editing depends on PAM recognition to initiate DNA unwinding. PAM mutations can abolish Cas9 binding and prohibit editing. Here, we identified a Cas9 from the thermophile Alicyclobacillus tengchongensis for which the PAM interaction can be robustly regulated by DNA topology. AtCas9has a relaxed PAM of N4CNNN and N4RNNA (R= A/G) and is able to bind but not cleave targets with mutated PAMs. When PAM-mutated DNA was in underwound topology, AtCas9 exhibited enhanced binding affinity and high cleavage activity. Mechanistically, AtCas9 has a unique loop motif, which docked into the DNA major groove, and this interaction can be regulated by DNA topology. More importantly, AtCas9 showed near-PAMless editing of supercoiled plasmid in E.coli. In mammalian cells, AtCas9 exhibited broad PAM preference to edit plasmid with up to 72% efficiency and effective base editing at four endogenous loci, representing a potentially powerful tool for near-PAMless editing.

Thermodynamic and structural profiles of multi-target binding of vinblastine in solution.

Structural information about drug-receptor interactions is paramount in drug discovery and subsequent optimization processes. Drugs can bind to multiple potential targets as they contain common chemical entities in their structures. Understanding the details of such interactions offer possibilities for repurposing and developing potent inhibitors of disease pathways. Vinblastine (VLB) is a potent anticancer molecule showing multiple receptor interactions with different affinities and degrees of structural perturbations. We have investigated the multi-target binding profile of VLB with DNA and human serum albumin (HSA) in a dynamic physiological environment using spectroscopic, molecular dynamics simulations, and quantum mechanical calculations to evaluate the structural features, mode, ligand and receptor flexibility, and energetics of complexation. These results confirm that VLB prefers to bind in the major groove of DNA with some inclination toward Thymidine residue and the TR-5 binding site in HSA with its catharanthine half making important contacts with both the receptors. Spectroscopic investigation at multiple temperatures has also proved that VLB binding is entropy driven indicating the major groove and TR-5 binding site of interaction. Finally, the overall binding is facilitated by van der Waals contacts and a few conventional H-bonds. VLB portrays reasonable conformational diversity on binding with multiple receptors.

Structural determinants of DNA recognition by the NO sensor NsrR and related Rrf2-type [FeS]-transcription factors

Several transcription factors of the Rrf2 family use an iron-sulfur cluster to regulate DNA binding through effectors such as nitric oxide (NO), cellular redox status and iron levels. [4Fe-4S]-NsrR from Streptomyces coelicolor (ScNsrR) modulates expression of three different genes via reaction and complex formation with variable amounts of NO, which results in detoxification of this gas. Here, we report the crystal structure of ScNsrR complexed with an hmpA1 gene operator fragment and compare it with those previously reported for [2Fe-2S]-RsrR/rsrR and apo-IscR/hyA complexes. Important structural differences reside in the variation of the DNA minor and major groove widths. In addition, different DNA curvatures and different interactions with the protein sensors are observed. We also report studies of NsrR binding to four hmpA1 variants, which indicate that flexibility in the central region is not a key binding determinant. Our study explores the promotor binding specificities of three closely related transcriptional regulators.

Structural Characterization of Dendriplexes In Vacuo: A Joint Ion Mobility/Molecular Dynamics Investigation.

The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH4+ from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH4+ or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.

The X-ray crystal structures, molecular docking and biological activities of two novel Cu(II) and Zn(II) complexes with a ligand having a potentially N4O2 donor set and two nitro phenyl rings as pendant arms

A new ligand (L) containing two nitro phenyl rings as side chains was synthesized. The reaction of this ligand with copper(II) and zinc(II) metal ions gave complexes with different coordination environments. The free ligand and the metal complexes were characterized using a number of spectroscopic methods. The crystal structure of [ZnLBr]ClO4 showed that the Zn(II) ion was in a distorted square pyramidal environment. The crystal structure of [CuL](ClO4)2 showed that the Cu(II) ion is in a tetragonally distorted octahedral environment. Molecular docking studies with DNA indicated that the binding of L, [ZnLBr]ClO4 and [CuL](ClO4)2 involved the major groove of DNA, H-bonds and Vander Waals interactions. In contrast, the molecular docking of L, [ZnLBr]ClO4 and [CuL](ClO4)2 with human glutathione reductase (GR) showed that the dominant interactions of these compounds with GR were H-bonding, vander Waals and hydrophobic interactions. The antioxidant activity of the synthesized complexes was analyzed by the free radical scavenging activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay with [CuL](ClO4)2 showing maximum activity. In addition, in vitro anticancer activity of the complexes against human breast MCF-7 cancer cell line was confirmed through 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) assay. All compounds showed a dose-dependent inhibitory effect on the growth of breast cancer cells with the inhibition activity of [CuL](ClO4)2 being more active than the other synthesized compounds. Furthermore, results from the antibacterial activity screening of the compounds against two Gram-positive and Gram-negative pathogenic bacteria by the micro-broth dilution and disk diffusion methods indicated that [CuL](ClO4)2 complex had the strongest antibacterial potential.