DNA Base Stack Research Articles

Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase γ.

The mitochondrial single-stranded DNA (ssDNA)binding protein, mtSSB or SSBP1, binds to ssDNA to prevent secondary structures of DNA that could impede downstream replication or repair processes. Clinical mutations in the SSBP1 gene have been linked to a range of mitochondrial disorders affecting nearly all organs and systems. Yet, the molecular determinants governing the interaction between mtSSB and ssDNA have remained elusive. Similarly, the structural interaction between mtSSB and other replisome components, such as the mitochondrial DNA polymerase, Polγ, has been minimally explored. Here, we determined a 1.9-Å X-ray crystallography structure of the human mtSSB bound to ssDNA. This structure uncovered two distinct DNA binding sites, a low-affinity site and a high-affinity site, confirmed through site-directed mutagenesis. The high-affinity binding site encompasses a clinically relevant residue, R38, and a highly conserved DNA base stacking residue, W84. Employing cryo-electron microscopy, we confirmed the tetrameric assembly in solution and capture its interaction with Polγ. Finally, we derived a model depicting modes of ssDNA wrapping around mtSSB and a region within Polγ that mtSSB binds.

MLDSPP: Bacterial Promoter Prediction Tool Using DNA Structural Properties with Machine Learning and Explainable AI.

Bacterial promoters play a crucial role in gene expression by serving as docking sites for the transcription initiation machinery. However, accurately identifying promoter regions in bacterial genomes remains a challenge due to their diverse architecture and variations. In this study, we propose MLDSPP (Machine Learning and Duplex Stability based Promoter prediction in Prokaryotes), a machine learning-based promoter prediction tool, to comprehensively screen bacterial promoter regions in 12 diverse genomes. We leveraged biologically relevant and informative DNA structural properties, such as DNA duplex stability and base stacking, and state-of-the-art machine learning (ML) strategies to gain insights into promoter characteristics. We evaluated several machine learning models, including Support Vector Machines, Random Forests, and XGBoost, and assessed their performance using accuracy, precision, recall, specificity, F1 score, and MCC metrics. Our findings reveal that XGBoost outperformed other models and current state-of-the-art promoter prediction tools, namely Sigma70pred and iPromoter2L, achieving F1-scores >95% in most systems. Significantly, the use of one-hot encoding for representing nucleotide sequences complements these structural features, enhancing our XGBoost model's predictive capabilities. To address the challenge of model interpretability, we incorporated explainable AI techniques using Shapley values. This enhancement allows for a better understanding and interpretation of the predictions of our model. In conclusion, our study presents MLDSPP as a novel, generic tool for predicting promoter regions in bacteria, utilizing original downstream sequences as nonpromoter controls. This tool has the potential to significantly advance the field of bacterial genomics and contribute to our understanding of gene regulation in diverse bacterial systems.

Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy.

Atomic force microscopy (AFM) is widely used to image and study biological molecules. As an example, we have utilized AFM to investigate how the mechanical properties of DNA polymers depend on electrostatics and the strength of DNA base stacking by studying double-stranded DNA molecules incorporating several different neutral and charged base modifications. Here we describe ten complementary approaches for determining DNA persistence length by AFM imaging. The combination of different approaches provides increased confidence and statistical reliability over existing methods utilizing only a single approach.

Transition metal salphen DNA complexes as biosensor application for detecting various mosquito viruses

PurposePiperidine side chain-functionalized N, N′-bissalicylidene phenylene di amine di-anion (salphen) consisting of salphen-Zn and salphen-Cu are able to intercalate with nucleic base stacking of DNA and can be applied as an optical DNA hybridization detector. Attaching DNA and salphen to glass surfaces has been done via coating the surface with the silane coupling agents containing 3-aminopropyltriethoxysilane that was synthesized for acting as a high-affinity RNA carrier matrix. The Schiff base salphen-zinc (II) and salphen-Cu (II) complexes-labelled probe to target nucleic acid renders a colour change of the DNA biosensor to a green and red background colour for zinc and copper, respectively. This study aims to indicate that the DNA biosensor data with high efficiency is used for detection of dengue virus serotypes 2 (DENV-2) and Chikungunya virus (CHIKV) concentration via salphen-Zn (II) and salphen-Cu (II), respectively, in human samples.Design/methodology/approach1H-NMR and 13C-NMR have been used via PerkinElmer LAMBDA 35 instrument. The authors also used a double beam spectrophotometer with (CH3)4Si (TMS) as reference and dimethyl sulfoxide as solvent reference in pH = 7.0. Various DNA concentrations have been used for UV spectrophotometry at 300 nm and 400 nm for zinc and copper complexes, respectively. BRUKER mass spectra with DIONEX Ultimate 3000 LC model were used for all measurements. Mettler Teledo model (DSC882e) of differential scanning calorimeter (DSC) was used for measure the melting temperature of metal zinc and copper complexes. The morphology of the silica Nano spheres (SiNs) were scanned by FESEM with Model JSM-6700F from Japan.FindingsThe Cu (II) and Zn (II)-salphen-viruses DNA system for CHIKV and DENV-2, respectively, in different concentration have been investigated via various spectroscopies (Figure 3). CHIKV and DENV-2 DNA were selected from human saliva and urine samples as models for conformations of human G4-DNA. By increasing the amounts of DNAs, and G4, the UV–Vis bands of located above 300 nm, experienced a hypochromic effect. The Cu2+ complex exhibits selectivity towards the G4, and there is a similar affinity for Zn2+ complex binds to the G4. These results collectively suggest that the Cu2+ complex is stronger than the Zn2+ complex. The authors have found copper (II) and zinc (II) compounds and nucleic acid-complexes are strongly fluorescent molecules in the low energy range, from the visible to the near-infrared. Since the fluorescent emission of Zn (II) and Cu (II) complexes are enhanced by the binding to nucleic acids upon visible light exposure when bound to DNA. These complexes are important as selective fluorescent probes for nucleic acids and to highlight their potential application. UV–vis spectroscopy is an accurate for finding the extent of ligand interaction with DNA and metallic complexes–DNA binding. Generally, the binding of intercalative compounds to DNA can be characterized through absorption spectral titrations, where lowering in absorbance (hypochromism) and shift to longer wavelengths (red shift) were observed in this work.Originality/valueThe serum samples have been provided as citrate and collected in tubes after blood is allowed to clot. Then, it has been separated by centrifugation, and the authors have kept serum refrigerated at 4°C or frozen at –20°C. It is notable; specimens have been confirmed by Centres for Disease Control (CDC)-Dengue Branch previously. For the work, these samples have been frozen previously, and the diagnostic practiced tests at the CDC-Dengue Branch have been validated in serum and plasma. Therefore, plasma separated in lavender or heparins are suitable and acceptable for serology testing.

Functional group substitutions influence the binding of benzophenone-type UV filters with DNA

As a class of possible carcinogens, benzophenone-type UV filters (BPs) widely exist in natural environments and organisms. The crucial step of the carcinogenic process induced by cancerous toxins is binding with DNA to form adducts. Here, the binding of 10 typical BPs, i.e., benzophenone (BP1), 2-hydroxyl benzophenone (BP2), 4-hydroxyl benzophenone (BP3), 2,2′-dihydroxyl benzophenone (BP4), 2,4-dihydroxyl benzophenone (BP5), 4,4′-dihydroxyl benzophenone (BP6), 2,4,4′-trihydroxyl benzophenone (BP7), 2,2′,4,4′-tetrahydroxyl benzophenone (BP8), 2-hydroxyl-4-methoxyl benzophenone (BP9), and 2,2′-dihydroxyl-4-methoxyl benzophenone (BP10), with DNA was tested via fluorescence quenching experiments. Only hydroxyl group-substituted BPs could bind to DNA by groove binding mode, and the quenching constants were 0.93 × 103–5.89 × 103 L/mol. Substituted BPs were preferentially bound to thymine. Circular dichroism analysis confirmed that BPs could affect DNA base stacking but could not transform its B-form. Based on molecular electrostatic surface potential analyses, molecular dynamics simulations, and energy decomposition calculations, it could be found that the site and number of hydroxyl substitution changed the molecular polarity of BPs, thereby affecting the number and strength of hydrogen bonds between BPs and DNA. The hydroxyl substitution at site 2 was more conducive to binding than at site 4. This study is beneficial in comprehending the carcinogenic mechanisms of BPs.

Solvent effects on the NMR shieldings of stacked DNA base pairs.

Stacking effects are among the most important effects in DNA. We have recently studied their influence in fragments of DNA through the analysis of NMR magnetic shieldings, firstly in vacuo. As a continuation of this line of research we show here the influence of solvent effects on the shieldings through the application of both explicit and implicit models. We found that the explicit solvent model is more appropriate for consideration due to the results matching better in general with experiments, as well as providing clear knowledge of the electronic origin of the value of the shieldings. Our study is grounded on a recently developed theoretical model of our own, by which we are able to learn about the magnetic effects of given fragments of DNA molecules on selected base pairs. We use the shieldings of the atoms of a central base pair (guanine-cytosine) of a selected fragment of DNA molecules as descriptors of physical effects, like π-stacking and solvent effects. They can be taken separately and altogether. The effect of π-stacking is introduced through the addition of some pairs above and below of the central base pair, and now, the solvent effect is considered including a network of water molecules that consist of two solvation layers, which were fixed in the calculations performed in all fragments. We show that the solvent effects enhance the stacking effects on the magnetic shieldings of atoms that belong to the external N-H bonds. The net effect is of deshielding on both atoms. There is also a deshielding effect on the carbon atoms that belong to CO bonds, for which the oxygen atom has an explicit hydrogen bond (HB) with a solvent water molecule. Solvent effects are found to be no higher than a few percent of the total value of the shieldings (between 1% and 5%) for most atoms, although there are few for which such an effect can be higher. There is one nitrogen atom, the acceptor of the HB between guanine and cytosine, that is more highly shielded (around 15 ppm or 10%) when the explicit solvent is considered. In a similar manner, the most external nitrogen atom of cytosine and the hydrogen atom that is bonded to it are highly deshielded (around 10 ppm for nitrogen and around 3 ppm for hydrogen).

Structural origins of Escherichia coli RNA polymerase open promoter complex stability

The first step in gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In Escherichia coli, promoter DNA sequence fundamentally determines how fast the RNA polymerase (RNAP) forms "open" complexes (RPo), whether RPo persists for seconds or hours, and how quickly RNAP transitions from initiation to elongation. These rates control promoter strength in vivo, but their structural origins remain largely unknown. Here, we use cryoelectron microscopy to determine the structures of RPo formed de novo at three promoters with widely differing lifetimes at 37 °C: λPR (t1/2 ∼10 h), T7A1 (t1/2 ∼4 min), and a point mutant in λPR (λPR-5C) (t1/2 ∼2 h). Two distinct RPo conformers are populated at λPR, likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA-RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate strand "scrunches" inside the active site cleft; the template strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and affect the subsequent steps of the transcription cycle.

Interaction of aflatoxin G1 with free DNA in vitro and possibility of its application in removing aflatoxin G1

The present study sought to evaluate the interaction between aflatoxin G1 and free DNA in vitro through different analytical techniques. The UV–visible spectra results showed that the structure of DNA might be changed with a new aflatoxin G1-DNA complex forming, which indicated that the interacting mode between them was the intercalating mode. The DNA melting temperature increased by 12.80 °C, suggesting that the DNA double helix structure was more compact and stable through intercalation. The circular dichroism (CD) spectra results indicated that the interaction of aflatoxin G1 with DNA induced the DNA base stacking changes. The results of agarose gel electrophoresis and fluorescence microscope further verified that the interacting mode between aflatoxin G1 and DNA was intercalation mode. According to the fluorescence spectrum data, the binding constant was calculated 6.24 × 104 L·mol−1. The thermodynamic results demonstrated that the reaction of aflatoxin G1 intercalating to DNA was a spontaneous reaction. The elimination results suggested that aflatoxin G1 could be enriched and removed by DNA intercalation through magnetic beads separation, with the removal efficiency of 93.73%. The study results would provide a theoretical basis for establishing a new aflatoxin removal method based on DNA intercalation.

Synthesis, characterization, DFT calculation, DNA binding and antimicrobial activities of metal complexes of dimedone arylhydrazone

The diazotization, coupling and metallization process was employed to create hydrazone chelating ligand (HL) and its Co(II), Cu(II) and Ni(II) complexes. Elemental analysis, FT-IR, UV–visible, thermal analysis, 1H NMR, and 13C NMR were utilized to propose their structures. The reaction between metal (II) with HL produced mononuclear complexes and the molar conductivity results demonstrated that the complexes are all non-electrolytes that fall within a certain range 8–12 Ω−1 cm2 mol−1. Co(II) and Ni(II) complexes have pseudooctahedral coordination geometry, whereas Cu(II) complexes have square planar coordination geometry. The metal ion interacts with the ligand. as a monobasic bidentate by (CO) as well as deprotonating hydrazone moiety (NH). Besides, the optimized structure, bond lengths, and angles of the ligand and its complexes determined quantum chemical parameters were estimated by molecular modeling. Electronic absorption dilution and viscosity analysis techniques were used to study the compounds' DNA binding activities. With a binding constant in the 5.13 × 105 M−1 range. The results revealed that the complexes bind to CT-DNA in grooves followed by partial incorporation of the ligand between the DNA base stacks. The cytotoxicity of the new complexes was examined versus human carcinoma cell lines, HepG-2 & MCF-7, and compared to positive controls as vinblastine and colchicine. The DPPH free radical-scavenging assay was used to evaluate the anti-oxidant capacity of all compounds in-vitro. Finally, the antimicrobial activities of the complexes against fungal (Candida albicans), gram negative bacteria (Escherichia coli), and gram positive bacteria (Escherichia coli) were investigated using the disc-diffusion process (Staphylococcus aureus).

DNA Ring-Opening Polymerization Driven by Base Stacking.

Supramolecular polymers, relying on reversible intermolecular interactions, promise a wide range of applications, including optoelectronic materials, self-healing materials, and biomedical delivery materials. Among potential molecular candidates, DNA strands act as an excellent platform. DNA has a well-established secondary structure (double helix), and its intermolecular interactions can be readily thermodynamically engineered and kinetically controlled. Extensive studies have demonstrated that various DNA motifs can polymerize/assemble into large polymers with different topology, geometry, and dimensionalities. Most of the reported polymerization is driven by hybridization of DNA strands. Herein, we report a novel system of DNA supramolecular polymerization that is driven by DNA base stacking. The polymerization has been confirmed by native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM). We believe that this work will expand the toolbox for DNA supramolecular polymerization and would, with further development, increase further control of DNA supramolecular polymerization.

Opposite Effects of Flexible Single-Stranded DNA Regions and Rigid Loops in DNAzyme on Colloidal Nanoparticle Stability for "Turn-On" Plasmonic Detection of Lead Ions.

Strains in biomolecules greatly restrict their structural flexibility. The effects of DNA's structural flexibility on nanoparticle stability have remained less explored in the field of plasmonic biosensors. In the present study, we discover the opposite effects of a rigid loop and a flexible single-stranded DNA (ssDNA) region in DNAzyme on the colloidal stability of gold nanoparticles (AuNPs), which afford "turn-on" plasmonic detection of Pb2+. In specific, DNAzyme-functionalized AuNPs undergo spontaneous assembly at high ionic strength upon hybridization to their substrate sequence because of a DNA base stacking interaction. In the presence of Pb2+, however, the DNAzyme grafted on the AuNP cleaves the substrate and forms an ssDNA region in the middle of the rigid loop. The induced structural flexibility of the surface-grafted DNAzyme by the ssDNA region in the middle helps elevate interparticle entropic repulsion, thereby bringing AuNP assemblies back to dispersion. We discover that this process can afford a dramatic increase of the AuNPs' plasmon resonance for determination of Pb2+ concentration. Under optimized conditions, a detection limit of 8.0 nM can be achieved for Pb2+ by this method with high selectivity. Its applicability to Pb2+ analysis in tap water samples has also been demonstrated.

DNA scaffold supports long-lived vibronic coherence in an indodicarbocyanine (Cy5) dimer.

Vibronic coupling between pigment molecules is believed to prolong coherences in photosynthetic pigment–protein complexes. Reproducing long-lived coherences using vibronically coupled chromophores in synthetic DNA constructs presents a biomimetic route to efficient artificial light harvesting. Here, we present two-dimensional (2D) electronic spectra of one monomeric Cy5 construct and two dimeric Cy5 constructs (0 bp and 1 bp between dyes) on a DNA scaffold and perform beating frequency analysis to interpret observed coherences. Power spectra of quantum beating signals of the dimers reveal high frequency oscillations that correspond to coherences between vibronic exciton states. Beating frequency maps confirm that these oscillations, 1270 cm−1 and 1545 cm−1 for the 0-bp dimer and 1100 cm−1 for the 1-bp dimer, are coherences between vibronic exciton states and that these coherences persist for ∼300 fs. Our observations are well described by a vibronic exciton model, which predicts the excitonic coupling strength in the dimers and the resulting molecular exciton states. The energy spacing between those states closely corresponds to the observed beat frequencies. MD simulations indicate that the dyes in our constructs lie largely internal to the DNA base stacking region, similar to the native design of biological light harvesting complexes. Observed coherences persist on the timescale of photosynthetic energy transfer yielding further parallels to observed biological coherences, establishing DNA as an attractive scaffold for synthetic light harvesting applications.

Understanding Rad51 function is a prerequisite for progress in cancer research.

The human protein Rad51 is double-edged in cancer contexts: on one hand, preventing tumourigenesis by eliminating potentially carcinogenic DNA damage and, on the other, promoting tumours by introducing new mutations. Understanding mechanistic details of Rad51 in homologous recombination (HR) and repair could facilitate design of novel methods, including CRISPR, for Rad51-targeted cancer treatment. Despite extensive research, however, we do not yet understand the mechanism of HR in sufficient detail, partly due to complexity, a large number of Rad51 protein units being involved in the exchange of long DNA segments. Another reason for lack of understanding could be that current recognition models of DNA interactions focus only on hydrogen bond-directed base pair formation. A more complete model may need to include, for example, the kinetic effects of DNA base stacking and unstacking ('longitudinal breathing'). These might explain how Rad51 can recognize sequence identity of DNA over several bases long stretches with high accuracy, despite the fact that a single base mismatch could be tolerated if we consider only the hydrogen bond energy. We here propose that certain specific hydrophobic effects, recently discovered destabilizing stacking of nucleobases, may play a central role in this context for the function of Rad51.

Relation between DNA ionization potentials, single base substitutions and pathogenic variants

BackgroundIt is nowadays clear that single base substitutions that occur in the human genome, of which some lead to pathogenic conditions, are non-random and influenced by their flanking nucleobase sequences. However, despite recent progress, the understanding of these "non-local" effects is still far from being achieved.ResultsTo advance this problem, we analyzed the relationship between the base mutability in specific gene regions and the electron hole transport along the DNA base stacks, as it is one of the mechanisms that have been suggested to contribute to these effects. More precisely, we studied the connection between the normalized frequency of single base substitutions and the vertical ionization potential of the base and its flanking sequence, estimated using MP2/6-31G* ab initio quantum chemistry calculations. We found a statistically significant overall anticorrelation between these two quantities: the lower the vIP value, the more probable the substitution. Moreover, the slope of the regression lines varies. It is larger for introns than for exons and untranslated regions, and for synonymous than for missense substitutions. Interestingly, the correlation appears to be more pronounced when considering the flanking sequence of the substituted base in the 3’ rather than in the 5’ direction, which corresponds to the preferred direction of charge migration. A weaker but still statistically significant correlation is found between the ionization potentials and the pathogenicity of the base substitutions. Moreover, pathogenicity is also preferentially associated with larger changes in ionization potentials upon base substitution.ConclusionsWith this analysis we gained new insights into the complex biophysical mechanisms that are at the basis of mutagenesis and pathogenicity, and supported the role of electron-hole transport in these matters.

Carbon black induced DNA damage and conformational changes to mouse hepatocytes and DNA molecule: A combined study using comet assay and multi-spectra methods

Carbon black (CB), a carbonaceous nanoparticle, has been widely applied in our daily lives and used as a typical model to study environmental safety and health impacts of airborne particles. Although the potential negative effects of CB to organisms have been reported a lot, very limited work is focused on the genotoxicity of CB on molecular and cellular level simultaneously. Herein, we investigated the interaction mechanism between CB and DNA molecule in depth by multiple spectra measurement, UV–vis absorption and ionic strength measurement. The fluorescence spectroscopy, ironic strength measurement and UV absorption indicated that CB changed the structure of DNA and interacted with DNA in an electrostatic binding mode. CD (circular dichroism) spectra proved no significant effects were caused by CB on the base stacking and helicity bands of DNA, which further verified that electrostatic binding is the main binding mode between CB and DNA. On the cellular level, the comet assay shows that CB exposure could cause a remarkable DNA strand break to the mouse hepatocytes after 24 co-incubation. This combined investigation suggests that CB could cause a serious genotoxicity both on molecular and cellular level.

Development of 13H-benzo[f]chromeno[4,3-b][1,7]naphthyridines and their salts as potent cytotoxic agents and topoisomerase I/IIα inhibitors

A novel series of 35 angularly fused pentacyclic 13H-benzo[f]chromeno[4,3-b][1,7]naphthyridines and 13H-benzo[f]chromeno[4,3-b][1,7]naphthyridin-5-ium chlorides were designed and synthesized. Their cytotoxic activities were investigated against six human cancer cell lines (NCIH23, HCT15, NUGC-3, ACHN, PC-3, and MDA-MB-231). Among all screened compounds; 28, 30, 34, 35, 46, 48, 52, and 53 compounds exhibited potent cytotoxic activities against all tested human cancer cell lines. Further, these potent lead cytotoxic agents were evaluated against human Topoisomerase I and IIα inhibition. Among them, the compound 48 exhibited dual Topoisomerase I and IIα inhibition especially at 20 μM concentrations the compound 48 exhibited 1.25 times more potent Topoisomerase IIα inhibitory activity (38.3%) than the reference drug etoposide (30.6%). The compound 52 also exhibited excellent (88.4%) topoisomerase I inhibition than the reference drug camptothecin (66.7%) at 100 μM concentrations. Molecular docking studies of the compounds 48 and 52 with topo I discovered that they both intercalated into the DNA single-strand cleavage site where the compound 48 have van der Waals interactions with residues Arg364, Pro431, and Asn722 whilst the compound 52 have with Arg364, Thr718, and Asn722 residues. Both the compounds 48 and 52 have π–π stacking interactions with the stacked DNA bases. The docking studies of the compound 48 with topo IIα explored that it was bound to the topo IIα DNA cleavage site where etoposide was situated. The benzo[f]chromeno[4,3-b][1,7]naphthyridine ring of the compound 48 was stacked between the DNA bases of the cleavage site with π–π stacking interactions and there were no hydrogen bond interactions with topo IIα.

Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex.

The preparation of homo- and heterocomplexes composed of the parent perylene diimide (PH) and pyrrolidine-substituted perylene diimide (PN) in DNA and rapid electron transfer in these complexes, which has been analyzed by steady-state fluorescence and femtosecond transient absorption measurements, have been demonstrated. The DNA molecules possessing PH and PN were prepared through a recently developed method that involved the reaction of enzymatically generated abasic sites with the amino groups of the perylene diimide molecules, through which these molecules can be incorporated as base surrogates within the DNA base stack. Melting temperature analysis showed that the PH and PN monomers, and their homo- and heterodimers, contribute to the stabilization of the DNA duplex, and is comparable to that of natural base pairs. Fluorescence measurements showed that PH in a single-stranded oligopyrimidine showed a strong fluorescence, whereas the fluorescence of PH was completely quenched upon pairing with PN (PH/PN) through duplex formation. The transient absorption measurements showed that a rapid electron-transfer reaction in the stacked PH/PN heterodimer occurred on a sub-picosecond timescale, which allowed highly efficient fluorescence quenching. The PH/PN pair, which served as a fluorophore and quencher, were utilized to design molecular beacon probes with a high signal/noise ratio. The PH/PN pair was also capable of forming a stable, stacked dimer structure and induced rapid electron transfer that could serve as a good signal reporter for fluorescent nucleic acid detection.

Multispectroscopic DNA-Binding studies and antimicrobial evaluation of new mixed-ligand Silver(I) complex and nanocomplex: A comparative study

A novel mixed-ligand Ag(I) complex, , has been synthesized and characterized by the elemental analysis, IR spectroscopy and 1HNMR. In the formula, dian and phen are N-(4,5-diazafluoren-9-ylidene)aniline and 1,10-phenanthroline, respectively. This complex also has been prepared at nano size by sonochemical technique and characterized by the FTIR and scanning electron microscopy (SEM). To evaluate the biological preferences of the Ag(I) complex and nanocomplex and verify the relationships between the structure and biological function, in vitro DNA binding and antibacterial experiments have been carried out. DNA-complex interaction has been pursued by electronic absorption titration, luminescence titration, competitive binding experiment, effect of ionic strength, thermodynamic studies, viscometric evaluation and circular dichroism spectroscopy in the physiological pH. Each compound displays significant binding trend to the CT-DNA. The mode of binding to the CT-DNA probably is a moderate intercalation mode with the partial insertion of the planar ligands between the base stacks of double-stranded DNA. The relative viscosities and circular dichroism spectra of the CT-DNA with the complex solutions, confirm the intense interactions of the Ag(I) complex and nanocomplex with DNA. An in vitro antibacterial test of the complex and nanocomplex on a series of the Gram-positive bacteria (Staphylococcus aureus, Enterococcus faecalis) and the Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa) shows a remarkable antibacterial feature of the Ag(I) complex. The MIC values (minimum inhibitory concentration) of the compounds compare with silver nitrate and silver sulfadiazine. The bacterial inhibitions of the Ag(I) complex and nanocomplex are agreed to their DNA binding affinities.

Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy.

Atomic force microscopy (AFM) is widely used to image and study biological molecules. As an example, we have utilized AFM to investigate how the mechanical properties of DNA polymers depend on electrostatics and the strength of DNA base stacking by studying double-stranded DNA molecules incorporating several different neutral and charged base modifications. Here, we describe ten complementary approaches for determining DNA persistence length by AFM imaging. The combination of different approaches provides increased confidence and statistical reliability over existing methods utilizing only a single approach.

Anticancer activity of new imidazole derivative of 1R,2R-diaminocyclohexane palladium and platinum complexes as DNA fluorescent probes

The aim of this study was synthesis of two new water-soluble fluorescent palladium and platinum complexes with formulas of [Pt(DACH)(FIP)](NO3)2 and [Pd(DACH)(FIP)](NO3)2, respectively, where FIP is 2-(furan-2-yl)-1H-imidazo[4,5-f][1,10] phenanthroline and DACH is 1R,2R-diaminocyclohexane. Fluorescence spectroscopy, circular dichroism (CD), thermal denaturation measurement, ionic strength, and kinetic study displayed groove binding of Pt complex on DNA, while due to binding of Pd complex, B form of DNA convert to Z form. Due to electrostatic interaction of Pd complex with DNA, the DNA form is converted and it provides enough space for Pd complex to insert between base stacking of DNA. UV–vis study shows two complexes could denature the DNA at low concentrations in exothermic process and Pt complex is more active than Pd complex. Finally, the anticancer and growth inhibitory activities of synthesized complexes were investigated against human colon cancer cell line HCT116 after incubation time of 24 h using MTT assay and higher activity was observed for the platinum complex. Interaction of the two metal derivative complexes was studied by molecular docking and molecular dynamics simulation. The results showed that Pt complexes have higher negative docking energy and higher tendency for interaction with DNA, and exert more structural change on DNA.