Nonspecific Electrostatic Interactions Research Articles

Multivalent antibacterial agent based on self-assembled glycocluster of mannose-perylene-spermine conjugate for enhanced wound healing

Bacterial infection and the increasing resistance of bacteria to commercially available antibiotics have long become a threat to global human health. Therefore, it is an urgent scientific issue to explore nonantibiotic antibacterials. In this paper, a mannose-decorated spermine derivative (PBI-spm-Man) was synthesized, which formed a self-assembled glycocluster with multivalent mannose moieties and concentrated cations. PBI-spm-Man as a nonantibiotic antibacterial agent showed potent antibacterial activity towards Escherichia coli (E. coli) through both mannose-FimH targeting and non-specific electrostatic interaction and functioned by damaging bacterial membrane. PBI-spm-Man also demonstrated antibacterial activity against representative Gram-positive bacteria Staphylococcus aureus (S. aureus) and intrinsically resistant bacteria Pseudomonas aeruginosa (P. aeruginosa). What is more exciting is that PBI-spm-Man could eliminate three clinical-isolated E. coli strains that are resistant to different antibiotics at around 20 μM. In vivo full-thickness wound healing results showed that the self-assembly of PBI-spm-Man not only reduced the residual bacteria at the wound site, but also promoted wound healing. This work represents a universal design strategy for nonantibiotic antibacterial agents based on multivalent glycoconjugates.

Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages.

Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus' evolution. We analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2200 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment. The data underlying the article are available in the Supplementary material.

Nonspecificity fingerprints for clinical-stage antibodies in solution.

Monoclonal antibodies (mAbs) have successfully been developed for the treatment of a wide range of diseases. The clinical success of mAbs does not solely rely on optimal potency and safety but also require good biophysical properties to ensure a high developability potential. In particular, nonspecific interactions are a key developability parameter to monitor during discovery and development. Despite an increased focus on the detection of nonspecific interactions, their underlying physicochemical origins remain poorly understood. Here, we employ solution-based microfluidic technologies to characterize a set of clinical-stage mAbs and their interactions with commonly used nonspecificity ligands to generate nonspecificity fingerprints, providing quantitative data on the underlying physical chemistry. Furthermore, the solution-based analysis enables us to measure binding affinities directly, and we evaluate the contribution of avidity in nonspecific binding by mAbs. We find that avidity can increase the apparent affinity by two orders of magnitude. Notably, we find that a subset of these highly developed mAbs show nonspecific electrostatic interactions, even at physiological pH and ionic strength, and that they can form microscale particles with charge-complementary polymers. The group of mAb constructs flagged here for nonspecificity are among the worst performers in independent reports of surface and column-based screens. The solution measurements improve on the state-of-the-art by providing a stand-alone result for individual mAbs without the need to benchmark against cohort data. Based on our findings, we propose a quantitative solution-based nonspecificity score, which can be integrated in the development workflow for biological therapeutics and more widely in protein engineering.

Electrostatic-Mediated Binding of DNA to Lysozymes: Evaluation of Aptamer-Based Assays for Highly Positively Charged Targets.

Lysozymes are a highly popular protein target for the development of aptamer-based biosensors. Because a lysozyme is a polycation and DNA is a polyanion, it is essential to separate the contribution of nonspecific electrostatic interactions from specific aptamer binding. In this study, various factors affecting the binding of DNA and lysozymes, including the DNA sequence, DNA length, pH, and salt concentration, were explored using fluorescence polarization. We concluded that direct fluorescence polarization and fluorescence intensity changes are unlikely to be directly applicable for aptamer-based biosensors to detect lysozymes because all of the tested DNA sequences showed binding. These fundamental studies confirm the dominant role of electrostatic binding. We further evaluated three other methods, including label-free fluorescent detection using a DNA staining dye, label-free colorimetric detection using gold nanoparticles, and a fluorescent sensor based on the strand displacement reaction. In each case, we focused on a random DNA sequence that is not expected to bind to the lysozyme as an aptamer. Of all the methods, only the strand displacement strategy can be potentially used to evaluate aptamer binding, as the other methods all responded to nonaptamer sequences. This study provides valuable insights for assaying aptamer binding to cationic proteins that can exhibit a nonspecific attraction to DNA.

Nanomechanoelectrical approach to highly sensitive and specific label-free DNA detection

Electronic detection of DNA oligomers offers the promise of rapid, miniaturized DNA analysis across various biotechnological applications. However, known all-electrical methods, which solely rely on measuring electrical signals in transducers during probe-target DNA hybridization, are prone to nonspecific electrostatic and electrochemical interactions, subsequently limiting their specificity and detection limit. Here, we demonstrate a nanomechanoelectrical approach that delivers ultra-robust specificity and a 100-fold improvement in detection limit. We drive nanostructural DNA strands tethered to a graphene transistor to oscillate in an alternating electric field and show that the transistor-current spectra are characteristic and indicative of DNA hybridization. We find that the inherent difference in pliability between unpaired and paired DNA strands leads to the spectral characteristics with minimal influence from nonspecific electrostatic and electrochemical interactions, resulting in high selectivity and sensitivity. Our results highlight the potential of high-performance DNA analysis based on miniaturized all-electronic settings.

SH3 binding pathway and kinetics in the presence of salt.

Protein-protein interactions are involved in a wide range of cellular processes, like cell signaling, in which these interactions often bind to intrinsically disordered proteins. SH3 domains are common protein interaction domains which are typically negatively charged and typically bind proline-rich disordered segments, which are positively charged. This project focuses on the role of electrostatics in the binding pathway of the yeast protein Abp1 SH3 domain (AbpSH3) and the intrinsically disordered peptide ArkA. We are investigating the binding pathway by simulating ArkA-AbpSH3 binding using molecular dynamics in the presence of sodium chloride, which serves to screen electrostatic interactions. Previous simulations in the absence of salt showed that ArkA initially forms a disordered encounter complex with AbpSH3 before reaching the fully bound state. In the absence of salt, the encounter complex, characterized by many transient non-specific electrostatic interactions, forms rapidly followed by a slower transition to the fully bound state. The addition of 800 mM sodium chloride leads to a slower encounter complex formation and a decrease in electrostatic contacts. Screening of long-range electrostatic interactions could also disrupt electrostatic steering to the binding surface during the initial encounter complex formation. Simulating the binding between ApbSH3 and ArkA in the presence of salt can provide insight into the role of electrostatics in SH3 binding in general and can be compared to experimental data on AbpSH3 binding at different salt concentrations.

Investigation of Charged Small Molecule-Aptamer Interactions with Surface Plasmon Resonance.

Investigating the interactions between small, charged molecules and aptamers using surface plasmon resonance (SPR) is limited by the inherent low response of small molecules and difficulties with nonspecific electrostatic interactions between the aptamer, analyte, and sensor surface. However, aptamers are increasingly being used in sensors for small molecule detection in critical areas like healthcare and environmental safety. The ability to probe these interactions through simple, direct SPR assays would be greatly beneficial and allow for the development of improved sensors without the need for complicated signal enhancement. However, these assays are nearly nonexistent in the current literature and are instead surpassed by sandwich or competitive binding techniques, which require additional sample preparation and reagents. In this work, we develop a method to characterize the interaction between the charged small molecule serotonin (176 Da) and an aptamer with SPR using streptavidin-biotin capture and a high-ionic-strength buffer. Additionally, other methods, such as serotonin immobilization and thiol-coupling of the aptamer, were investigated for comparison. These techniques give insight into working with small molecules and allow for quickly adapting a binding affinity assay into a direct SPR sensor.

Ciprofloxacin peptide-based nanoparticles confer antimicrobial efficacy against multidrug-resistant bacteria

Positively charged PAC-NPs destroy the membrane potential through nonspecific electrostatic interactions. Hydrophobic ciprofloxacin also exerts synergistic antibacterial effects. The physical and chemical sterilization methods of PAC-NPs could prevent bacteria from developing drug-resistance.

Titanium dioxide nanoparticle-based hydroxyl and superoxide radical production for oxidative stress biological simulations

The present study introduces a TiO2 nanoparticle-based (TiO2-NP) system for the generation of •OΗ and O2•− upon visible photo-excitation, in order to be used for high oxidative stress biological simulations in vitro. The main novelties of TiO2-NP system are: It is set to produce •OΗ and O2•− alone or both (in contrast to •OΗ-based common use of TiO2), as these options cover all possible generation means of these radicals in biological systems in vivo. Moreover, the known non-specific electrostatic interactions of TiO2-NP with H2O and various biological systems (e.g., cells, membrane proteins, even drugs) simulate direct/distant interactions of any in vivo•OΗ, O2•− source with extra/intracellular biological targets taking place in a densely packed biomolecular environment. The TiO2-NP system can use any commercially available TiO2-NP source (dispersion, nanopowder, crystal type), as long as TiO2-NPs’ concentrations in use meet the critical criterion to produce •OΗ levels linearly proportional to irradiation time, set for a given simulation study. The TiO2-NP system is calibrated by a standardized protocol developed to be applicable to most biological systems, offering the option of TiO2-NP removal via coagulation when needed. The production rates of •OΗ and O2•− by the TiO2-NP system are specifically calibrated with the respective specific probes terephthalic acid (TPA) and hydroethidine (HE), and tested in comparison to the •OΗ-producing Fenton system. The reaction kinetics of •OΗ and O2•− with TPA and HE is found to be in competition with their generating source, the TiO2-NP system. Similar ROS source competition phenomena with biological targets (simulated by TPA/HE) are very common in biological systems. In contrast, the Fenton system is shown not to exhibit such competition kinetics. The TiO2-NP system can be used to study •OΗ/O2•− dose–response-depended oxidative modifications in biological simulations. This stems from the fact that •OΗ and O2•− linear production rates (60 min and up to 8 min, respectively) can be controlled by varying (i) TiO2 concentration, (ii) light-source photon emission energy (decreasing from 370 to 410 nm), and (iii) light intensity (as a function of the inverse of squared distance from the irradiated sample). In contrast, •OΗ production by the Fenton system reaches steady state in ∼5 s regardless of varying Fe-II concentration, rendering it inappropriate for •OΗ simulation studies on biological systems. The biological simulating potential of the TiO2-NP system, as producer of both •OΗ and O2•−, is also experimentally verified on indicative biological examples selected to structurally represent most biological systems: BSA, a model hydrophilic protein; LDL, structurally resembling most of the biological systems (cells, membranes, organelles, lipoproteins, proteins, lipids). The TiO2-NP system causes a linear increase of all the tested oxidative modifications on both BSA and LDL for irradiation exposure 20 to 40 min, which strongly suggests that they are mainly •OΗ dose-proportional. In contrast, the Fenton system does not display •OΗ dose-associated oxidative modifications on BSA.

All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes.

The spike protein of SARS-CoV-2 is known to interact with the human ACE2 protein via its receptor binding domain (RBD). We have investigated the molecular nature of this interprotein interaction and the associated free energy diagrams for the unbinding of the two proteins for SARS-CoV-2 and some of its known variants through all-atom simulations. The present work involves generation and analysis of 2.5 μs of unbiased and 4.2 μs of biased molecular dynamics trajectories in total for five explicitly solvated RBD-ACE2 systems at full atomic level. First, we have made a comparative analysis of the details of residue-wise specific interactions of the spike protein with ACE2 for SARS-CoV-1 and SARS-CoV-2. It is found that the average numbers of both direct interprotein and water-bridged hydrogen bonds between the RBD and ACE2 are higher for SARS-CoV-2 than SARS-CoV-1. These higher hydrogen bonded interactions are further aided by enhanced nonspecific electrostatic attractions between the two protein surfaces for SARS-CoV-2. The free energy calculations reveal that there is an increase in the free energy barrier by ∼1.5 kcal/mol for the unbinding of RBD from ACE2 for SARS-CoV-2 compared to that for SARS-CoV-1. Subsequently, we considered the RBDs of three variants of SARS-CoV-2, namely N501Y, E484Q/L452R, and N440K. The free energy barrier of protein unbinding for the N501Y variant is found to be ∼4 kcal/mol higher than the wild type SARS-CoV-2 which can be attributed to additional specific interactions involving Tyr501 of RBD and Lys353 and Tyr42 of ACE2 and also enhanced nonspecific electrostatic interaction between the protein surfaces. For the other two mutant variants of E484Q/L452R and N440K, the free energy barrier for protein unbinding increases by ∼2 and ∼1 kcal/mol, respectively, compared with the wild type SARS-CoV-2, which can be attributed to an increase in the number of interprotein hydrogen bonds for the former and also to enhanced positive electrostatic potential on the RBD surfaces for both of the variants. The successive breaking of interprotein hydrogen bonds along the free energy pathway of the unbinding process is also found out for all five systems studied here.

Target Search Dynamics of Sox Transcription Factors

Here we investigate the impact of regions outside of the DNA‐binding domain (DBD) on target search efficiency of transcription factors (TFs). In living organisms, TFs are key for gene regulation by binding sequence DNA‐binding sites. The facilitated diffusion theory proposes a search process combining TF 1D sliding on DNA and 3D diffusion in the nucleus. Moreover, the local non‐specific TF‐DNA interactions mediated by electrostatic forces enhance the target search efficiency to reach on‐rates faster than allowed by free diffusion. While such theoretical models fit TF behaviors in prokaryotes, how TFs search the chromatinized eukaryotic genome is poorly understood. More importantly, the relevance of regions outside of the DNA‐binding domain for the search process remains to be clarified.We hypothesize that positive charges flanking the DBD accelerate TF target search by interacting non‐specifically with negatively charged DNA. We tackle this hypothesis with a comparative study between Sox2 and Sox17. While recognizing the same DNA motif, Sox2 displays higher non‐specific binding affinity, which we think is caused by a higher content in positive charges close to the DBD.To probe the kinetics of in vivo Sox‐DNA interactions in living mouse embryonic stem cells, we used highly inclined and laminated optical sheet (HiLo) microscopy. We determined that Sox2 and Sox17 have similar profiles of residence time with specific binding of ~ 12 s and non‐specific binding of ~ 0.7 s. We then quantified the search efficiency of Sox2 and Sox17 by determining their pseudo on‐rate, which we define as the time‐averaged number of specifically bound particles per time interval and per TF concentration. Since Sox2 and Sox17 bind to the same DNA motifs, they thus have the same number of targets in the mouse genome. Therefore, the pseudo on‐rate scales linearly with association rate at a given TF concentration. We found that Sox2 has a two‐fold higher pseudo on‐rate than Sox17. We also generated a Sox2 mutant in which its DBD flanking region was swapped with the one from Sox17. This led to a two‐fold decrease in pseudo on‐rate as compared to the wild‐type Sox2. These results thus directly support the hypothesis that non‐specific electrostatic interactions of positively charged residues in regions flanking the DBD enhance their DNA association rates.One limitation of in vivo experiments is that the chromatin context in which TF‐DNA interactions are observed is unknown. To dissect the differential interactions of Sox2 and Sox17 with naked versus nucleosomal DNA, we are using chemically‐synthesized in vitro chromatin combined with single‐molecule tracking via total internal reflection (TIRF) microscopy. Since Sox2 but not Sox17 is known as a pioneer factor, quantifying their interactions with chromatinized DNA will shed light on search mechanisms of pioneer TFs in compact chromatin. In that sense, we foresee that more positively‐charged DBD flanking regions may stabilize specific binding of TF to nucleosomal DNA and help TFs to invade and remodel chromatin.Taken together, our combination of in vivo and in vitro single‐molecule imaging techniques allows dissecting how the charge distribution of DBD flanking regions modulates TF target search on chromatin.

Caging Cationic Polymer Brush-Coated Plasmonic Nanostructures for Traceable Selective Antimicrobial Activities.

Cationic polymers are under intense research to achieve prominent antimicrobial activity. However, the cellular and in vivo toxicity caused by nonspecific electrostatic interaction has become a major challenge for their practical applications. Here, the development of a "caging" strategy based on the use of a block copolymer consisting of a stealth block and an anionic block that undergoes degradation in presence of enzymes secreted by selective bacterial pathogens of interest is reported. The results have shown that antimicrobial cationic polymer brushes-coated gold nanorods (AuNRs) can be caged by the block polymer of poly(ethylene glycol) and anionic, lipase-degradable block of ε-caprolactone and methacrylic acid copolymer to afford neutrally charged surfaces. The caged AuNRs are activated by lipase released by bacteria of interest to endow an excellent bactericidal effect but show minimal binding and toxicity against mammalian cells and nonspecific bacteria that do not produce lipase. In this design, AuNRs play multifunctional roles as the scaffolds for polymer brushes, photothermal transducers, and imaging probes for traceable delivery of the activation and delivery of bactericidal cationic polymer brushes. The caging strategy opens new opportunities for the safe delivery of antimicrobial materials for the treatment of bacterial infections.

Host glycocalyx captures HIV proximal to the cell surface via oligomannose-GlcNAc glycan-glycan interactions to support viral entry.

Here, we present ultrastructural analyses showing that incoming HIV are captured near the lymphocyte surface in a virion-glycan-dependent manner. Biophysical analyses show that removal of either virion- or cell-associated N-glycans impairs virus-cell binding, and a similar glycan-dependent relationship is observed between purified HIV envelope (Env) and primary Tcells. Trimming of N-glycans from either HIV or Env does not inhibit protein-protein interactions. Glycan arrays reveal HIV preferentially binds to N-acetylglucosamine and mannose. Interfering with these glycan-based interactions reduces HIV infectivity. These glycan interactions are distinct from previously reported glycan-lectin and non-specific electrostatic charge-based interactions. Specific glycan-glycan-mediated attachment occurs prior to virus entry and enhances efficiency of infection. Binding and fluorescent imaging data support glycan-glycan interactions as being responsible, at least in part, for initiating contact between HIV and the host cell, prior to viral Env-cellular CD4 engagement.

Phase separation studies of anionic lipids and tau in biologically relevant conditions

Tau, is an important microtubule-associated protein (MAP) essential in regulating microtubule (MT) dynamics in neuronal axons. A central role of tau is the stabilization of MTs through the suppression of dynamic instability in a tau-concentration dependent manner. Tau-MT associations are made possible through Tau’s MT binding domains and non-specific electrostatic interactions driven in part by the polyampholytic nature of tau and the lack of a stable tertiary structure. In fact it is known that tau is a surface active molecule that, upon chemical alterations, can interact pathologically with itself to promote neurodegenerative tauopathies such as Alzheimer’s and frontotemporal dementia with parkinsonism-17 (FTDP-17).

Motif-pattern dependence of biomolecular phase separation driven by specific interactions.

Eukaryotic cells partition a wide variety of important materials and processes into biomolecular condensates—phase-separated droplets that lack a membrane. In addition to nonspecific electrostatic or hydrophobic interactions, phase separation also depends on specific binding motifs that link together constituent molecules. Nevertheless, few rules have been established for how these ubiquitous specific, saturating, motif-motif interactions drive phase separation. By integrating Monte Carlo simulations of lattice-polymers with mean-field theory, we show that the sequence of heterotypic binding motifs strongly affects a polymer’s ability to phase separate, influencing both phase boundaries and condensate properties (e.g. viscosity and polymer diffusion). We find that sequences with large blocks of single motifs typically form more inter-polymer bonds, which promotes phase separation. Notably, the sequence of binding motifs influences phase separation primarily by determining the conformational entropy of self-bonding by single polymers. This contrasts with systems where the molecular architecture primarily affects the energy of the dense phase, providing a new entropy-based mechanism for the biological control of phase separation.

Nucleosomes enter cells by clathrin- and caveolin-dependent endocytosis.

DNA damage and apoptosis lead to the release of free nucleosomes—the basic structural repeating units of chromatin—into the blood circulation system. We recently reported that free nucleosomes that enter the cytoplasm of mammalian cells trigger immune responses by activating cGMP-AMP synthase (cGAS). In the present study, we designed experiments to reveal the mechanism of nucleosome uptake by human cells. We showed that nucleosomes are first absorbed on the cell membrane through nonspecific electrostatic interactions between positively charged histone N-terminal tails and ligands on the cell surface, followed by internalization via clathrin- or caveolae-dependent endocytosis. After cellular internalization, endosomal escape occurs rapidly, and nucleosomes are released into the cytosol, maintaining structural integrity for an extended period. The efficient endocytosis of extracellular nucleosomes suggests that circulating nucleosomes may lead to cellular disorders as well as immunostimulation, and thus, the biological effects exerted by endocytic nucleosomes should be addressed in the future.

60-nt DNA Direct Detection without Pretreatment by Surface-Enhanced Raman Scattering with Polycationic Modified Ag Microcrystal Derived from AgCl Cube.

Direct detection of long-strand DNA by surface-enhanced Raman scattering (SERS) is a valuable method for diagnosis of hereditary diseases, but it is currently limited to less than 25-nt DNA strand in pure water, which makes this approach unsuitable for many real-life applications. Here, we report a 60-nt DNA label-free detection strategy without pretreatment by SERS with polyquaternium-modified Ag microcrystals derived from an AgCl cube. Through the reduction-induced decomposition, the size of the about 3 × 3 × 3 μm3 AgCl cube is reduced to Ag, and the surface is distributed with the uniform size of 63 nm silver nanoparticles, providing a large area of a robust and highly electromagnetic enhancement region. The modified polycationic molecule enhances the non-specific electrostatic interaction with the phosphate group, thereby anchoring DNA strands firmly to the SERS enhanced region intactly. As a result, the single-base recognition ability of this strategy reaches 60-nt and is successfully applied to detect thalassemia-related mutation genes.

Solution Structure and Conformational Flexibility of a Polyketide Synthase Module.

Polyketide synthases (PKSs) are versatile C–C bond-forming enzymes that are broadly distributed in bacteria and fungi. The polyketide compound family includes many clinically useful drugs such as the antibiotic erythromycin, the antineoplastic epothilone, and the cholesterol-lowering lovastatin. Harnessing PKSs for custom compound synthesis remains an open challenge, largely because of the lack of knowledge about key structural properties. Particularly, the domains—well characterized on their own—are poorly understood in their arrangement, conformational dynamics, and interplay in the intricate quaternary structure of modular PKSs. Here, we characterize module 2 from the 6-deoxyerythronolide B synthase by small-angle X-ray scattering and cross-linking mass spectrometry with coarse-grained structural modeling. The results of this hybrid approach shed light on the solution structure of a cis-AT type PKS module as well as its inherent conformational dynamics. Supported by a directed evolution approach, we also find that acyl carrier protein (ACP)-mediated substrate shuttling appears to be steered by a nonspecific electrostatic interaction network.

Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity.

Nucleoid-associated proteins (NAPs) are crucial in organizing prokaryotic DNA and regulating genes. Vital to these activities are complex nucleoprotein structures, however, how these form remains unclear. Integration host factor (IHF) is an Escherichia coli NAP that creates very sharp bends in DNA at sequences relevant to several functions including transcription and recombination, and is also responsible for general DNA compaction when bound non-specifically. We show that IHF–DNA structural multimodality is more elaborate than previously thought, and provide insights into how this drives mechanical switching towards strongly bent DNA. Using single-molecule atomic force microscopy and atomic molecular dynamics simulations we find three binding modes in roughly equal proportions: ‘associated’ (73° of DNA bend), ‘half-wrapped’ (107°) and ‘fully-wrapped’ (147°), only the latter occurring with sequence specificity. We show IHF bridges two DNA double helices through non-specific recognition that gives IHF a stoichiometry greater than one and enables DNA mesh assembly. We observe that IHF-DNA structural multiplicity is driven through non-specific electrostatic interactions that we anticipate to be a general NAP feature for physical organization of chromosomes.

Transcription factor stoichiometry in cell fate determination

Transcription factors play very important role in cell fate determination. There are many cell specific transcription factors which when expressed ectopically may lead to cell fate conversion or transdifferentiation. Many of these transcription factors function differently based on their levels and stoichiometry. Many different types of differentiated cells have been generated from other differentiated cell types by expressing different levels and stoichiometry of reprogramming factors. Many methodologies have been developed for efficient cell fate conversion by regulating the levels and stoichiometry of transcription factors in a particular cocktail that have therapeutic values. An approach called phenotypic activation which involves overexpression of putative transcription factors has been developed as a tool to discover new transcription factors and their targets. Transcription factor overexpression may also have toxic effects where nonspecific electrostatic interactions and 'squelching' may lead to inhibition of many genes. Altered levels of transcription factors may have disastrous consequences like cancer. Recent developments like designing of artificial transcription factors, nanotechnology-based transcriptional tools and CRISPR-based transcription modules with capabilities of precise regulation of gene expression patterns hold huge potentials in the field of transcriptional therapeutics.