Single-Beam Acoustic Tweezers for Cell Biology: Molecular to In Vivo Level

Acoustic tweezers have attracted attention in various fields of cell biology, including in vitro single-cell and intercellular mechanics. Compared with other tweezing technologies such as optical and magnetic tweezers, acoustic tweezers possess stronger forces and are safer for use in biological systems. However, due to the limited spatial resolution or limited size of target objects, acoustic tweezers have primarily been used to manipulate cells in vitro. To extend the advantages of acoustic tweezers to other levels (e.g., molecular and in vivo levels), researchers have recently developed various types of acoustic tweezers such as single-beam acoustic tweezers (SBATs), surface acoustic wave (SAW) tweezers, and acoustic-streaming tweezers. Among these, SBATs utilize a single-focused beam, making the transducer and system simple, noninvasive, and capable of producing strong forces compared with other types of tweezers. Depending on the acoustic beam pattern, SBATs can be classified into Rayleigh regime, Mie regime, and acoustic vortex with different trapping dynamics and application levels. In this review, we provide an overview of the principles and configuration of each type of SBAT, their applications ranging from molecular to in vivo studies, and their limitations and prospects. Thus, this review demonstrates the significance and potential of SBAT technology in biophysics and biomedical engineering.

A nanonewton force sensor using a U-shape tapered microfiber interferometer

Nanomechanical measurements, especially the detection of weak contact forces, play a vital role in many fields, such as material science, micromanipulation, and mechanobiology. However, it remains a challenging task to realize the measurement of ultraweak force levels as low as nanonewtons with a simple sensing configuration. In this work, an ultrasensitive all-fiber nanonewton force sensor structure based on a single-mode-tapered U-shape multimode-single-mode fiber probe is proposed and experimentally demonstrated with a limit of detection of ~5.4 nanonewtons. The use of the sensor is demonstrated by force measurement on a human hair sample to determine the spring constant of the hair. The results agree well with measurements using an atomic force microscope for the spring constant of the hair. Compared with other force sensors based on optical fiber in the literature, the proposed all-fiber force sensor provides a substantial advancement in the minimum detectable force possible, with the advantages of a simple configuration, ease of fabrication, and low cost.

The Plasma Membrane and Mechanoregulation in Cells

Cells inhabit a mechanical microenvironment that they continuously sense and adapt to. The plasma membrane (PM), serving as the boundary of the cell, plays a pivotal role in this process of adaptation. In this Review, we begin by examining well-studied processes where mechanoregulation proves significant. Specifically, we highlight examples from the immune system and stem cells, besides discussing processes involving fibroblasts and other cell types. Subsequently, we discuss the common molecular players that facilitate the sensing of the mechanical signal and transform it into a chemical response covering integrins YAP/TAZ and Piezo. We then review how this understanding of molecular elements is leveraged in drug discovery and tissue engineering alongside a discussion of the methodologies used to measure mechanical properties. Focusing on the processes of endocytosis, we discuss how cells may respond to altered membrane mechanics using endo- and exocytosis. Through the process of depleting/adding the membrane area, these could also impact membrane mechanics. We compare pathways from studies illustrating the involvement of endocytosis in mechanoregulation, including clathrin-mediated endocytosis (CME) and the CLIC/GEEC (CG) pathway as central examples. Lastly, we review studies on cell-cell fusion during myogenesis, the mechanical integrity of muscle fibers, and the reported and anticipated roles of various molecular players and processes like endocytosis, thereby emphasizing the significance of mechanoregulation at the PM.

On the interactions involving serine proteases obtained from Monacrosporium thaumasium (Ascomycota: Orbiliomycetes) and deoxyribonucleic acid (DNA): biological macromolecules in action

The use of force spectroscopy approaches performed with optical tweezers can be very useful in determining the binding modes and the physical chemistry of DNA interactions with ligands, from small drugs to proteins. Helminthophagous fungi, on the other hand, have important enzyme secretion mechanisms for various purposes, and the interactions between such enzymes and nucleic acids are very poorly studied. Therefore, the main goal of the present work was to investigate, at the molecular level, the mechanisms of interaction between fungal serine proteases and the double-stranded (ds) DNA molecule. Experimental assays performed with this single molecule technique consist in exposing different concentrations of the protease of this fungus to dsDNA until saturation while monitoring the changes on the mechanical properties of the macromolecular complexes formed, from where the physical chemistry of the interaction can be deduced. It was found that the protease binds strongly to the double-helix, forming aggregates and changing the persistence length of the DNA molecule. The present work thus allowed us to infer information at the molecular level on the pathogenicity of these proteins, an important class of biological macromolecules, when applied to a target specimen.

Distribution Behavior of Single-Stranded DNA Molecules in an Amino-Group-Functionalized Silica Microparticle

In this study, we investigated the distribution behavior of single-stranded DNA molecules with 20 bases in silica particles (particle size: ∼30 μm) using confocal fluorescence microspectroscopy. The distribution kinetics was investigated under various conditions, such as the type of base (adenine, thymine, guanine, and cytosine), pore size of the particle (30 and 50 nm), and salt concentration (100, 200, and 500 mM), which changed the distribution behavior. At high salt concentrations, we observed sigmoidal kinetic behavior, which does not occur in the general distribution of small organic molecules but is often observed in protein aggregation and nuclear growth. An analytical model based on DNA aggregation explained the sigmoidal distribution behavior well, and this model also worked well when the number of DNA molecules involved in DNA aggregation was greater than two. The intraparticle diffusion of DNA molecules was analyzed using the pore and surface diffusion model. As a result, the intraparticle diffusion of DNA aggregates mainly occurs according to surface diffusion, and the surface diffusion coefficient has the same value ((2.4-6.7) × 10^-9 cm² s^-1) independent of the pore size and type of base.

Imidazolium-based ionic liquids binding to DNA: Mechanical effects and thermodynamics of the interactions

We performed a robust characterization of the molecular interactions between the DNA molecule and two imidazolium-based ionic liquids (ILs): 1-Butyl-3-methylimidazolium chloride ([bmim]Cl) and 1-Octyl-3-methylimidazolium chloride ([omim]Cl), using single molecule approaches (optical and magnetic tweezers) and bulk techniques (isothermal titration calorimetry and conductivity measurements). Optical and magnetic tweezers allowed us to obtain the changes on the mechanical properties of the DNA complexes formed with both ILs, as well as the relevant physicochemical (binding) parameters of the interaction. Despite the weak binding measured between DNA and the two ILs, we identify a transition on the regime of polymer elasticity of the complexes formed, which results in a relevant DNA compaction for high IL concentrations. In addition, isothermal titration calorimetry and conductivity complemented the single molecule investigation, giving a complete thermodynamic characterization of the interactions and allowing the identification of the most relevant driving forces at various different concentration ranges of the ILs. Based on the results obtained with all the employed techniques, we propose a model for the binding schemes involving DNA and both [bmim]Cl and [omim]Cl.

New Insights into the Mechanism of Action of the Drug Chloroquine: Direct Interaction with DNA and Cytotoxicity

Chloroquine (CLQ) and hydroxychloroquine (HCLQ) are compounds largely employed in the treatment of various human diseases for decades. Nevertheless, a number of intrinsic details concerning their mechanisms of action, especially at the molecular level, are still unknown or have presented controversial results in the literature. Using optical tweezers, here, we investigate at the single-molecule level the molecular mechanism of action of the drug CLQ in its intrinsic interaction with the double-stranded (ds)DNA molecule, one of its targets inside cells, determining the binding modes and the physicochemical (binding) parameters of the interaction. In particular, we show that the ionic strength of the surrounding medium strongly influences such interaction, changing even the main binding mode. In addition, the cytotoxicity of CLQ against three different cell lines was also investigated here, allowing one to evaluate and compare the effect of the drug on the cell viability. In particular, we show that CLQ is highly cytotoxic at a very low (a few micromolar) concentration range for all cell lines tested. These results were rigorously compared to the equivalent ones obtained for the closely related compound hydroxychloroquine (HCLQ), allowing a critical comparison between the action of these drugs at the molecular and cellular levels.

Caffeine Enhances the Toxicity of Platinum-Based Drugs at the Molecular Level Even Outside of the Intracellular Environment: A Single-Molecule Force Spectroscopy Study

It is well reported in the literature that caffeine, the most consumed alkaloid around the world, enhances the anticancer effects of the drug cisplatin by inhibiting DNA repair by the cellular machinery. Here, we perform single-molecule force spectroscopy assays with optical tweezers to show that caffeine enhances the toxicity not only of cisplatin but also of various different platinum-based drugs already at the molecular level, using samples containing only double-stranded (ds)DNA, platinum drugs, and the alkaloid in a simple phosphate buffer, that is, completely out of the complex environment found inside real living cells. In fact, our results show that caffeine acts as an allosteric catalyst which increases the effective equilibrium binding constant between DNA and the platinum drugs, also interfering in the cooperativity of the binding reactions. To the best of our knowledge, this is the first time that such a property of caffeine was demonstrated and characterized from a pure physicochemical perspective, outside the cellular environment. Thus, the present work provides new insights into the use of this alkaloid for current chemotherapeutic applications.

A primer to traction force microscopy

Traction force microscopy (TFM) has emerged as a versatile technique for the measurement of single-cell-generated forces. TFM has gained wide use among mechanobiology laboratories, and several variants of the original methodology have been proposed. However, issues related to the experimental setup and, most importantly, data analysis of cell traction datasets may restrain the adoption of TFM by a wider community. In this review, we summarize the state of the art in TFM-related research, with a focus on the analytical methods underlying data analysis. We aim to provide the reader with a friendly compendium underlying the potential of TFM and emphasizing the methodological framework required for a thorough understanding of experimental data. We also compile a list of data analytics tools freely available to the scientific community for the furtherance of knowledge on this powerful technique.

The Role of Ligand Rebinding and Facilitated Dissociation on the Characterization of Dissociation Rates by Surface Plasmon Resonance (SPR) and Benchmarking Performance Metrics

Surface plasmon resonance (SPR) is a real-time kinetic measurement principle that can probe the kinetic interactions between ligands and their binding sites, and lies at the backbone of pharmaceutical, biosensing, and biomolecular research. The extraction of dissociation rates from SPR-response signals often relies on several commonly adopted assumptions, one of which is the exponential decay of the dissociation part of the response signal. However, certain conditions, such as high density of binding sites or high concentration fluctuations near the surface as compared to the bulk, can lead to non-exponential decays via ligand rebinding or facilitated dissociation. Consequently, fitting the data with an exponential function can underestimate or overestimate the measured dissociation rates. Here, we describe a set of alternative fit functions that can take such effects into consideration along with plasmonic sensor design principles with key performance metrics, thereby suggesting methods for error-free high-precision extraction of the dissociation rates.

Cisplatin fastens chromatin irreversibly even at a high chloride concentration

Cisplatin is one of the most potent anti-cancer drugs developed so far. Recent studies highlighted several intriguing roles of histones in cisplatin's anti-cancer effect. Thus, the effect of nucleosome formation should be considered to give a better account of the anti-cancer effect of cisplatin. Here we investigated this important issue via single-molecule measurements. Surprisingly, the reduced activity of cisplatin under [NaCl] = 180 mM, corresponding to the total concentration of cellular ionic species, is still sufficient to impair the integrity of a nucleosome by retaining its condensed structure firmly, even against severe mechanical and chemical disturbances. Our finding suggests that such cisplatin-induced fastening of chromatin can inhibit nucleosome remodelling required for normal biological functions. The in vitro chromatin transcription assay indeed revealed that the transcription activity was effectively suppressed in the presence of cisplatin. Our direct physical measurements on cisplatin-nucleosome adducts suggest that the formation of such adducts be the key to the anti-cancer effect by cisplatin.

Virus self-assembly proceeds through contact-rich energy minima

Self-assembly of supramolecular complexes such as viral capsids occurs prominently in nature. Nonetheless, the mechanisms underlying these processes remain poorly understood. Here, we uncover the assembly pathway of hepatitis B virus (HBV), applying fluorescence optical tweezers and high-speed atomic force microscopy. This allows tracking the assembly process in real time with single-molecule resolution. Our results identify a specific, contact-rich pentameric arrangement of HBV capsid proteins as a key on-path assembly intermediate and reveal the energy balance of the self-assembly process. Real-time nucleic acid packaging experiments show that a free energy change of ~1.4 k_BT per condensed nucleotide is used to drive protein oligomerization. The finding that HBV assembly occurs via contact-rich energy minima has implications for our understanding of the assembly of HBV and other viruses and also for the development of new antiviral strategies and the rational design of self-assembling nanomaterials.

Caffeine modulates the intercalation of drugs on DNA: A study at the single molecule level

We use optical tweezers to characterize the ability of Caffeine (Caf) to modulate the intercalation of drugs into the DNA double-helix at the single molecule level. When previously bound to the double-helix, Caf hinders ethidium bromide (EtBr) intercalation, decreasing its effective equilibrium binding constant with DNA. The dominant mechanism of such singular ability is a direct binding of Caf to the intercalating drugs in solution, which decreases the effective concentration of such compounds available to interact with DNA. When EtBr intercalation into the DNA double-helix occurs firstly, on the other hand, the measured cooperativity between Caf molecules interacting with DNA can be modulated, a feature also correlated to the Caf-EtBr interaction in solution. The results achieved here unveil many peculiarities about the details of such interactions at the molecular level and provide new insights on the use of Caf in therapeutic applications.

Hydroxychloroquine Exhibits a Strong Complex Interaction with DNA: Unraveling the Mechanism of Action

In the past months, the use of the drug hydroxychloroquine has considerably increased in many countries, associated with a proposed treatment for the COVID-19 disease. Although there is no conclusive evidence about the efficacy of the drug for this purpose, surprisingly there are no conclusive studies in the literature concerning its mechanism of action inside cells, which is related to its interaction with nucleic acids. Here, we performed a robust characterization of the interaction between hydroxychloroquine and double-stranded DNA using single-molecule force spectroscopy and gel electrophoresis. Two different binding modes were identified, namely, minor groove binding for low drug concentrations and intercalation for high drug concentrations, and the sets of binding parameters were determined for each of these modes. Such results have unraveled in detail the molecular mechanism of action of the drug as a DNA ligand.

Dodecyltrimethylammonium bromide surfactant effects on DNA: Unraveling the competition between electrostatic and hydrophobic interactions

We present a new study on the interaction of the DNA molecule with the surfactant dodecyltrimethylammonium bromide (DTAB), performed mainly with optical tweezers. Single-molecule force spectroscopy experiments performed in the low-force entropic regime allowed a robust characterization of the DNA-DTAB interaction, unveiling how the surfactant changes the mechanical properties of the biopolymer, the binding parameters, and the competition of the two mechanisms involved in the interaction: electrostatic attraction between the cationic surfactant heads and the negative phosphate backbone of the DNA and hydrophobic interactions between the tails of the bound DTAB molecules, which can result in DNA compaction in solution depending on the quantity of bound surfactant. Finally, force clamp experiments with magnetic tweezers and gel electrophoresis assays confirm that DTAB compacts DNA depending not only on the surfactant concentration but also on the conformation of the biopolymer in solution. The present study provides new insights on general aspects of the DNA-surfactant complexes formation, contributing to the fundamental knowledge of the physics of such interactions.

Transplatin ineffectiveness against cancer from a molecular perspective: A single-molecule force-spectroscopy study

By performing single-molecule force spectroscopy with optical tweezers, we have characterized the interaction between the platinum-based compound transplatin and the DNA molecule, establishing a critical comparison with its isomer cisplatin. While transplatin is ineffective against tumor cells, its isomer is one of the most used drugs in current chemotherapies, and a molecular study on this difference performed at the single-molecule level was lacking until the present work. Our experiments show that transplatin binds DNA under low chloride concentrations (a situation usually found inside many cells) with an equilibrium association binding constant about four orders of magnitude lower than cisplatin. In addition, we have found that, at saturation, transplatin binds preferentially forming interstrand cross links and monoadducts, a situation very different from cisplatin, which forms preferentially intrastrand cross links. Such differences explain the ineffectiveness of transplatin in killing tumor cells. From a physical point of view, the present study advances in using the mechanical properties of the DNA molecule as sensors to evaluate the therapeutic efficiency of drugs.

Single-Molecule Sensing of DNA Intercalating Drugs in Water

The occurrence of pharmaceutical residues in surface water is raising environmental concern. To accompany the evolution of measures for natural resources protection, sensing methods enabling sensitive and rapid water quality monitoring are needed. We recently managed the parallelization of the Tethered Particle Motion (TPM), a single molecule technique, sensitive to the conformational changes of DNA. Here, we investigate the capacity of high throughput TPM (htTPM) to detect drugs that intercalate into DNA. As a proof-of-concept we analyze the htTPM signal for two DNA intercalating dyes, namely, YOYO-1 and SYTOX orange. The efficient detection of intercalating drugs is then demonstrated with doxorubicin. We further evaluate the possibility to detect carbamazepine, an antiepileptic massively prescribed and persistent in water, which had been described to interact with DNA through intercalation. Our results corroborated by other techniques show that, in fact, carbamazepine is not a DNA intercalator. The comparison of the results obtained with different aqueous buffers and solutions allows us to identify optimal conditions for the monitoring of intercalation compounds by htTPM.

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here, we probe, via all-atom molecular dynamics (MD) simulations, the change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, the stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs, i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.

Pixantrone anticancer drug as a DNA ligand: Depicting the mechanism of action at single molecule level

In this work we use single molecule force spectroscopy performed with optical tweezers in order to characterize the complexes formed between the anticancer drug Pixantrone (PIX) and the DNA molecule, at two very different ionic strengths. Firstly, the changes of the mechanical properties of the DNA-PIX complexes were studied as a function of the drug concentration in the sample. Then, a quenched-disorder statistical model of ligand binding was used in order to determine the physicochemical (binding) parameters of the DNA-PIX interaction. In particular, we have found that the PIX molecular mechanism of action involves intercalation into the double helix, followed by a significant compaction of the DNA molecule due to partial neutralization of the phosphate backbone. Finally, this scenario of interaction was quantitatively compared to that found for the related drug Mitoxantrone (MTX), which binds to DNA with a considerably higher equilibrium binding constant and promotes a much stronger DNA compaction. The comparison performed between the two drugs can bring clues to the development of new (and more efficient) related compounds.

Nanomechanical DNA resonators for sensing and structural analysis of DNA-ligand complexes

The effect of direct or indirect binding of intercalant molecules on DNA structure is of fundamental importance in understanding the biological functioning of DNA. Here we report on self-suspended DNA nanobundles as ultrasensitive nanomechanical resonators for structural studies of DNA-ligand complexes. Such vibrating nanostructures represent the smallest mechanical resonator entirely composed of DNA. A correlative analysis between the mechanical and structural properties is exploited to study the intrinsic changes of double strand DNA, when interacting with different intercalant molecules (YOYO-1 and GelRed) and a chemotherapeutic drug (Cisplatin), at different concentrations. Possible implications of our findings are related to the study of interaction mechanism of a wide category of molecules with DNA, and to further applications in medicine, such as optimal titration of chemotherapeutic drugs and environmental studies for the detection of heavy metals in human serum.

Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA

DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Parameter extraction typically relies on the neighbor-exclusion model, in which a bound intercalator prevents intercalation into adjacent sites. Here, we challenge the neighbor-exclusion model by carefully quantifying and modeling the force-extension and twisting behavior of single ethidium-complexed DNA molecules. We show that only an anticooperative ethidium binding that allows for a disfavored but nonetheless possible intercalation into nearest-neighbor sites can consistently describe the mechanical behavior of intercalator-bound DNA. At high ethidium concentrations and elevated mechanical stress, this causes an almost complete occupation of nearest-neighbor sites and almost a doubling of the DNA contour length. We furthermore show that intercalation into nearest-neighbor sites needs to be considered when estimating intercalator parameters from zero-stress elongation and twisting data. We think that the proposed anticooperative binding mechanism may also be applicable to other intercalating molecules.

Optical Trapping and Manipulation of Superparamagnetic Beads Using Annular-Shaped Beams

We propose an optical tweezers setup based on an annular-shaped laser beam that is efficient to trap 2.8 μm-diameter superparamagnetic particles. The optical trapping of such particles was fully characterized, and a direct absolute comparison with a geometrical optics model was performed. With this comparison, we were able to show that light absorption by the superparamagnetic particles is negligible for our annular beam tweezers, differing from the case of conventional Gaussian beam tweezers, in which laser absorption by the beads makes stable trapping difficult. In addition, the trap stiffness of the annular beam tweezers increases with the laser power and with the bead distance from the coverslip surface. While this first result is expected and similar to that achieved for conventional Gaussian tweezers, which use ordinary dielectric beads, the second result is quite surprising and different from the ordinary case, suggesting that spherical aberration is much less important in our annular beam geometry. The results obtained here provide new insights into the development of hybrid optomagnetic tweezers, which can apply simultaneously optical and magnetic forces on the same particles.

Biomechanical Characterization at the Cell Scale: Present and Prospects

The rapidly growing field of mechanobiology demands for robust and reproducible characterization of cell mechanical properties. Recent achievements in understanding the mechanical regulation of cell fate largely rely on technological platforms capable of probing the mechanical response of living cells and their physico–chemical interaction with the microenvironment. Besides the established family of atomic force microscopy (AFM) based methods, other approaches include optical, magnetic, and acoustic tweezers, as well as sensing substrates that take advantage of biomaterials chemistry and microfabrication techniques. In this review, we introduce the available methods with an emphasis on the most recent advances, and we discuss the challenges associated with their implementation.

A cooperative transition from the semi-flexible to the flexible regime of polymer elasticity: Mitoxantrone-induced DNA condensation

We report a high cooperative transition from the semi-flexible to the flexible regime of polymer elasticity during the interaction of the DNA molecule with the chemotherapeutic drug Mitoxantrone (MTX). By using single molecule force spectroscopy, we show that the force-extension curves of the DNA-MTX complexes deviate from the typical worm-like chain behavior as the MTX concentration in the sample increases, becoming straight lines for sufficiently high drug concentrations. The behavior of the radius of gyration of the complexes as a function of the bound MTX concentration was used to quantitatively investigate the cooperativity of the condensation process. The present methodology can be promptly applied to other ligands that condense the DNA molecule upon binding, opening new possibilities in the investigation of this type of process and, more generally, in the investigation of phase transitions in polymer physics.

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

Interactions of DNA with proteins are essential for key biological processes and have both a fundamental and practical significance. In particular, DNA binding to anti-DNA antibodies is a pathogenic mechanism in autoimmune pathology, such as systemic lupus erythematosus. Here we measured at the single-molecule level binding and forced unbinding of surface-attached DNA and a monoclonal anti-DNA antibody MRL4 from a lupus erythematosus mouse. In optical trap-based force spectroscopy, a microscopic antibodycoated latex bead is trapped by a focused laser beam and repeatedly brought into contact with a DNA-coated surface. After careful discrimination of non-specific interactions, we showed that the DNA-antibody rupture force spectra had two regimes, reflecting formation of weaker (20-40 pN) and stronger (>40 pN) immune complexes that implies the existence of at least two bound states with different mechanical stability. The two-dimensional force-free off-rate for the DNA-antibody complexes was ~2.2 × 10^-3 s^-1, the transition state distance was ~0.94 nm, the apparent on-rate was ~5.26 s^-1, and the stiffness of the DNA-antibody complex was characterized by a spring constant of 0.0021 pN/nm, suggesting that the DNA-antibody complex is a relatively stable, but soft and deformable macromolecular structure. The stretching elasticity of the DNA molecules was characteristic of single-stranded DNA, suggesting preferential binding of the MRL4 antibody to one strand of DNA. Collectively, the results provide fundamental characteristics of formation and forced dissociation of DNA-antibody complexes that help to understand principles of DNA-protein interactions and shed light on the molecular basis of autoimmune diseases accompanied by formation of anti-DNA antibodies.

Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking

The interaction of herring sperm DNA with the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) was studied by UV/vis absorption, fluorescence and CD spectroscopic methods. Compared with the 1,8-naphthalimide-spermidine conjugate (NIS), the values of KSV (quenching constant) and Kb (binding constant) of NDIS were larger, and the hypochromic effect in the UV/vis spectra and the quenching effect in the fluorescence of NDIS were more significant. The interaction mode between NDIS and DNA was mainly groove binding. The fluorescence experiments at varying temperatures showed that the binding process of NDIS and DNA was static, as both hydrogen bonds and hydrophobic forces played a major role in the binding of NDIS and DNA. The CD spectrum indicated that NDIS caused a conformational change, like the B to A-DNA transition, and the tests using KI and NaCl and 1H NMR spectroscopy indicated that NDIS was not a classical DNA inserter. All the results demonstrated that both the polyamine side chain and the aromatic rings affect the process of NDIS binding to DNA, which is thus obviously different from that of NIS. The conclusion was confirmed by the in silico molecular docking experiments.

Force spectroscopy unravels the role of ionic strength on DNA-cisplatin interaction: Modulating the binding parameters

In the present work we have gone a step forward in the understanding of the DNA-cisplatin interaction, investigating the role of the ionic strength on the complexes formation. To achieve this task, we use optical tweezers to perform force spectroscopy on the DNA-cisplatin complexes, determining their mechanical parameters as a function of the drug concentration in the sample for three different buffers. From such measurements, we determine the binding parameters and study their behavior as a function of the ionic strength. The equilibrium binding constant decreases with the counterion concentration ([Na]) and can be used to estimate the effective net charge of cisplatin in solution. The cooperativity degree of the binding reaction, on the other hand, increases with the ionic strength, as a result of the different conformational changes induced by the drug on the double-helix when binding under different buffer conditions. Such results can be used to modulate the drug binding to DNA, by appropriately setting the ionic strength of the surrounding buffer. The conclusions drawn provide significant new insights on the complex cooperative interactions between the DNA molecule and the class of platinum-based compounds, much used in chemotherapies.

β-Cyclodextrin polymer binding to DNA: Modulating the physicochemical parameters

Cyclodextrins and cyclodextrins-modified molecules have interesting and appealing properties due to their capacity to host components that are normally insoluble or poorly soluble in water. In this work, we investigate the interaction of a β-cyclodextrin polymer (poly-β-CD) with λ-DNA. The polymers are obtained by the reaction of β-CD with epichlorohydrin in alkaline conditions. We have used optical tweezers to characterize the changes of the mechanical properties of DNA molecules by increasing the concentration of poly-β-CD in the sample. The physical chemistry of the interaction is then deduced from these measurements by using a recently developed quenched-disorder statistical model. It is shown that the contour length of the DNA does not change in the whole range of poly-β-CD concentration (<300μM). On the other hand, significant alterations were observed in the persistence length that identifies two binding modes corresponding to the clustering of ∼2.6 and ∼14 polymer molecules along the DNA double helix, depending on the polymer concentration. Comparing these results with the ones obtained for monomeric β-CD, it was observed that the concentration of CD that alters the DNA persistence length is considerably smaller when in the polymeric form. Also, the binding constant of the polymer-DNA interaction is three orders of magnitude higher than the one found for native (monomeric) β-CD. These results show that the polymerization of the β-CD strongly increases its binding affinity to the DNA molecule. This property can be wisely used to modulate the binding of cyclodextrins to the DNA double helix.

DNA-doxorubicin interaction: New insights and peculiarities

We have investigated the interaction of the DNA molecule with the anticancer drug doxorubicin (doxo) by using three different experimental techniques: single molecule stretching, single molecule imaging, and dynamic light scattering. Such techniques allowed us to get new insights on the mechanical behavior of the DNA-doxo complexes as well as on the physical chemistry of the interaction. First, the contour length data obtained from single molecule stretching were used to extract the physicochemical parameters of the DNA-doxo interaction under different buffer conditions. This analysis has proven that the physical chemistry of such interaction can be modulated by changing the ionic strength of the surrounding buffer. In particular we have found that at low ionc strengths doxo interacts with DNA by simple intercalation (no aggregation) and/or by forming bound dimers. For high ionic strengths, otherwise, doxo-doxo self-association is enhanced, giving rise to the formation of bound doxo aggregates composed by 3 to 4 molecules along the double-helix. On the other hand, the results obtained for the persistence length of the DNA-doxo complexes is strongly force-dependent, presenting different behaviors when measured with stretching or non-stretching techniques.

Membrane and genomic DNA dual-targeting of citrus flavonoid naringenin against Staphylococcus aureus

Naringenin exerts its antibacterial action by disruption of the cytoplasmic membrane and DNA targeting effects inStaphylococcus aureus.

Looking for the Origin of Allosteric Cooperativity in Metallopolymers

The basic concept of allosteric cooperativity used in biology, chemistry and physics states that any change in the intermolecular host-guest interactions operating in multisite receptors can be assigned to intersite interactions. Using lanthanide metals as guests and linear multi-tridentate linear oligomers of variable lengths and geometries as hosts, this work shows that the quantitative modeling of metal loadings requires the consideration of a novel phenomenon originating from solvation processes. It stepwise modulates the intrinsic affinity of each isolated site in multisite receptors, and this without resorting to allosteric cooperativity. An easy-to-handle additive model predicts a negative power law dependence of the intrinsic affinity on the length of the linear metallopolymer. Applied to lanthanidopolymers, the latter common analysis overestimates cooperativity factors by more than two orders of magnitude.

Unraveling the physical chemistry and the mixed binding modes of complex DNA ligands by single molecule stretching experiments

In this work we present a complete methodology to unravel the physical chemistry and the mixed binding modes of complex DNA ligands.

Controlling Cooperativity in β-Cyclodextrin-DNA Binding Reactions

We have investigated the interaction between the native neutral β-cyclodextrin (CD) and the DNA molecule by performing single-molecule stretching experiments with optical tweezers. In particular, we have monitored the changes of the mechanical properties of the CD-DNA complexes as a function of the CD concentration in the sample. By using a quenched disorder statistical model, we were also capable to extract important physicochemical information (equilibrium binding constants, cooperativity degree) of such interaction from the mechanical data. In addition, we have found that the interaction occurs by two different mechanisms, first with the formation of relatively large CD clusters along the double helix, which thereafter can locally denature the DNA molecule by forming hydrogen bonds with the base pairs that eventually flip out. A prediction of our quenched disorder model was that cooperativity could be controlled by adjusting the surface charge of β-CD molecules. This prediction is confirmed in the present work.