Physiological Conditions Of Ionic Strength Research Articles

Multicomponent Peptide-Based Hydrogels Containing Chemical Functional Groups as Innovative Platforms for Biotechnological Applications.

Multicomponent hydrogels (HGs) based on ultrashort aromatic peptides have been exploited as biocompatible matrices for tissue engineering applications, the delivery of therapeutic and diagnostic agents, and the development of biosensors. Due to its capability to gel under physiological conditions of pH and ionic strength, the low molecular-weight Fmoc-FF (Nα-fluorenylmethoxycarbonyl-diphenylalanine) homodimer is one of the most studied hydrogelators. The introduction into the Fmoc-FF hydrogel of additional molecules like protein, organic compounds, or other peptide sequences often allows the generation of novel hydrogels with improved mechanical and functional properties. In this perspective, here we studied a library of novel multicomponent Fmoc-FF based hydrogels doped with different amounts of the tripeptide Fmoc-FFX (in which X= Cys, Ser, or Thr). The insertion of these tripeptides allows to obtain hydrogels functionalized with thiol or alcohol groups that can be used for their chemical post-derivatization with bioactive molecules of interest like diagnostic or biosensing agents. These novel multicomponent hydrogels share a similar peptide organization in their supramolecular matrix. The hydrogels' biocompatibility, and their propensity to support adhesion, proliferation, and even cell differentiation, assessed in vitro on fibroblast cell lines, allows us to conclude that the hybrid hydrogels are not toxic and can potentially act as a scaffold and support for cell culture growth.

Dilated cardiomyopathy mutation E525K in human beta-cardiac myosin stabilizes the interacting-heads motif and super-relaxed state of myosin.

The auto-inhibited, super-relaxed (SRX) state of cardiac myosin is thought to be crucial for regulating contraction, relaxation, and energy conservation in the heart. We used single ATP turnover experiments to demonstrate that a dilated cardiomyopathy (DCM) mutation (E525K) in human beta-cardiac myosin increases the fraction of myosin heads in the SRX state (with slow ATP turnover), especially in physiological ionic strength conditions. We also utilized FRET between a C-terminal GFP tag on the myosin tail and Cy3ATP bound to the active site of the motor domain to estimate the fraction of heads in the closed, interacting-heads motif (IHM); we found a strong correlation between the IHM and SRX state. Negative stain electron microscopy and 2D class averaging of the construct demonstrated that the E525K mutation increased the fraction of molecules adopting the IHM. Overall, our results demonstrate that the E525K DCM mutation may reduce muscle force and power by stabilizing the auto-inhibited SRX state. Our studies also provide direct evidence for a correlation between the SRX biochemical state and the IHM structural state in cardiac muscle myosin. Furthermore, the E525 residue may be implicated in crucial electrostatic interactions that modulate this conserved, auto-inhibited conformation of myosin.

Impact of Degree of Ionization and PEGylation on the Stability of Nanoparticles of Chitosan Derivatives at Physiological Conditions.

Nowadays, the therapeutic efficiency of small interfering RNAs (siRNA) is still limited by the efficiency of gene therapy vectors capable of carrying them inside the target cells. In this study, siRNA nanocarriers based on low molecular weight chitosan grafted with increasing proportions (5 to 55%) of diisopropylethylamine (DIPEA) groups were developed, which allowed precise control of the degree of ionization of the polycations at pH 7.4. This approach made obtaining siRNA nanocarriers with small sizes (100–200 nm), positive surface charge and enhanced colloidal stability (up to 24 h) at physiological conditions of pH (7.4) and ionic strength (150 mmol L−1) possible. Moreover, the PEGylation improved the stability of the nanoparticles, which maintained their colloidal stability and nanometric sizes even in an albumin-containing medium. The chitosan-derivatives displayed non-cytotoxic effects in both fibroblasts (NIH/3T3) and macrophages (RAW 264.7) at high N/P ratios and polymer concentrations (up to 0.5 g L−1). Confocal microscopy showed a successful uptake of nanocarriers by RAW 264.7 macrophages and a promising ability to silence green fluorescent protein (GFP) in HeLa cells. These results were confirmed by a high level of tumor necrosis factor-α (TNFα) knockdown (higher than 60%) in LPS-stimulated macrophages treated with the siRNA-loaded nanoparticles even in the FBS-containing medium, findings that reveal a good correlation between the degree of ionization of the polycations and the physicochemical properties of nanocarriers. Overall, this study provides an approach to enhance siRNA condensation by chitosan-based carriers and highlights the potential of these nanocarriers for in vivo studies.

Formulation matters! A spectroscopic and molecular dynamics investigation on the peptide CIGB552 as itself and in its therapeutical formulation

Synthetic therapeutic peptides (STP) are intensively studied as new-generation drugs, characterized by high purity, biocompatibility, selectivity and stereochemical control. However, most of the studies are focussed on the bioactivity of STP without considering how the formulation actually used for therapy administration could alter the physico-chemical properties of the active principle. The aggregation properties of a 20-mer STP (Ac-His-Ala-Arg-Ile-Lys-D-Pro-Thr-Phe-Arg-Arg-D-Leu-Lys-Trp-Lys-Tyr-Lys-Gly-Lys-Phe-Trp-NH2 ), showing antitumor activity, were investigated by optical spectroscopy and atomic force microscopy imaging, as itself (CIGB552) and in its therapeutic formulation (CIGB552TF). It has found that the therapeutic formulation deeply affects the aggregation properties of the investigated peptide and the morphology of the aggregates formed on mica by deposition of CIGB552 and CIGB552TF millimolar solutions. Molecular dynamics simulations studied the first steps of CIGB552 aggregation under physiological ionic strength conditions (NaCl 150 mM), showing that peptide oligomers, from dimers to tetramers, are preferentially formed in this environment. Interestingly, cell viability assays performed on H-460 cell lines indicate a major antiproliferative activity of the peptide in its therapeutic formulation with respect to the peptide aqueous solution.

An Oligonucleotide Sensor with Parallel Electrical Pathways

Point-of-care sensors can combat the spread of infectious diseases and inform timely treatments. But in order to be used in this capacity, point-of-care sensors need to combine rapid detection speed with high sensitivity. Detection speed has traditionally been reduced by increasing the sensing surface area of the device, but this can increase noise and reduce sensitivity. In this work we align multiple tube-in-a-tube (Tube^2) nanostructures across a trench between two electrodes. Each Tube^2 consists of a semiconducting carbon nanotube nested within an outer nanotube densely functionalized with oligonucleotide probes. This device design provides a high surface area, while forcing the electrical current through distinct electrical pathways, allowing the binding events to be sensitively detected. Using this device architecture, we demonstrate the selective detection of Lyme disease oligonucleotide biomarkers in physiological ionic strength conditions on the order of seconds.

Adsorption of Human Serum Albumin on Graphene Oxide: Implications for Protein Corona Formation and Conformation.

The influence of solution chemistry on the adsorption of human serum albumin (HSA) proteins on graphene oxide (GO) was investigated through batch adsorption experiments and the use of a quartz crystal microbalance with dissipation (QCM-D). The conformation of HSA layers on GO was also examined with the QCM-D. Our results show that an increase in ionic strength under neutral pH conditions resulted in stronger binding between HSA and GO, as well as more compact HSA layers on GO, emphasizing the key role of electrostatic interactions in controlling HSA-GO interactions. Calcium ions also facilitated HSA adsorption likely through charge neutralization and bridging effect. At physiological ionic strength conditions (150 mM), maximum HSA adsorption was observed at the isoelectric point of HSA (4.7). Under acidic conditions, the adsorption of HSA on GO led to the formation of protein layers with a high degree of fluidity due to the extended conformation of HSA. Finally, the attachment of GO to a supported lipid bilayer that was composed of zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphocholine, a model for cell membranes, was reduced in the presence of protein coronas. This reduction in GO attachment was influenced by the conformation of the protein coronas on GO.

Enhanced Antimicrobial Activity and Structural Transitions of a Nanofibrillated Cellulose-Nisin Biocomposite Suspension.

Resistance to antibiotics has posed a high demand for novel strategies to fight bacterial infections. Antimicrobial peptides (AMPs) are a promising alternative to conventional antibiotics. However, their poor solubility in water and sensitivity to degradation has limited their application. Here, we report the design of a smart, pH-responsive antimicrobial nanobiocomposite material based on the AMP nisin and 2,2,6,6-tetramethyl-1-piperidinyloxyl-oxidized nanofibrillated cellulose (TONFC). Morphological transformations of the nanoscale structure of nisin functionalized-TONFC fibrils were discovered at pH values between 5.8 and 8.0 using small-angle X-ray scattering. Complementary ζ potential measurements indicate that electrostatic attractions between the negatively charged TONFC surface and the positively charged nisin molecules are responsible for the integration of nisin. Modification of the pH level or increasing the ionic strength reduces the nisin binding capacity of TONFC. Biological evaluation studies using a bioluminescence-based reporter strain of Bacillus subtilis and a clinically relevant strain of Staphylococcus aureus indicated a significantly higher antimicrobial activity of the TONFC-nisin biocomposite compared to the pure nisin against both strains under physiological pH and ionic strength conditions. The in-depth characterization of this new class of antimicrobial biocomposite material based on nanocellulose and nisin may guide the rational design of sustainable antimicrobial materials.

Interactions between fluorescein isothiocyanate and star-shaped polymer carriers studied by isothermal titration calorimetry (ITC)

Isothermal titration calorimetry (ITC) technique was used to determine the thermodynamic parameters of reaction between fluorescein isothiocyanate (FITC) and novel star-shaped copolymers. Measurements were taken at 310.15K using 0.64g dm−3 NaCl, 0.5g dm−3 Na2B4O7·10H2O in deionized water/methanol (60/40v/v). Tested polymers belong to the innovative group of star-shaped copolymers with sugar core. Fluorescent FITC was chosen as one of the most reactive dye, which allowed monitoring the polymer behavior in physiological ionic strength conditions, as well as it was treated as the model biologically active substance. Analysis of the obtained calorimetric data allowed to determine the standard molar enthalpy of binding (ΔH○), the stoichiometry (n), the equilibrium constant (K), the standard Gibbs free energy change (ΔG○) and the standard entropy change (ΔS°), whose values allowed to obtain a wealth of information for the polymer-FITC binding, and identified the best carrier for the dye.

Understanding the non-catalytic behavior of human butyrylcholinesterase silent variants: Comparison of wild-type enzyme, catalytically active Ala328Cys mutant, and silent Ala328Asp variant

Conformational dynamics of wild-type human butyrylcholinesterase (BChE), two mutants of residue Ala328, the catalytically active Ala328Cys, and the catalytically inactive (silent) Ala328Asp, and their interactions with butyrylcholine were studied. The aim was to understand the molecular mechanisms by which point mutations may lead to silent BChE variant or alter catalytic activity. Importance of BChE natural variants is due to medical consequences, i.e. prolonged apnea, following administration of the myorelaxant esters, succinylcholine and mivacurium.Comparison of molecular dynamics (MD) simulations for the three model systems showed that: 1) the active mutant Ala328Cys mutant has some changes in configuration of catalytic residues, which do not prevent binding of butyrylcholine to the active site; 2) in the naturally-occurring silent variant Ala328Asp, the Asp328 carboxylate may either form a salt bridge with Lys339 or a H-bond with His438. In the first case, the Ω-loop swings off the gorge, disrupting the π-cation binding site and the catalytic triad. In the second case, binding of cationic substrates in the catalytic center is also impaired. MD simulations carried out in 0.15 M NaCl, close to physiological ionic strength conditions, favored the second situation. It was seen that Asp328 forms a H-bond with the catalytic triad His438, which in turn disrupts the catalytic machinery. Therefore, we concluded that the Ala328Asp variant is not catalytically active because of that dramatic event. Computational results, consistent with in vitro biochemical data and clinical observations, validate our MD approach.

Calcium binding to beta-2-microglobulin at physiological pH drives the occurrence of conformational changes which cause the protein to precipitate into amorphous forms that subsequently transform into amyloid aggregates.

Using spectroscopic, calorimetric and microscopic methods, we demonstrate that calcium binds to beta-2-microglobulin (β2m) under physiological conditions of pH and ionic strength, in biological buffers, causing a conformational change associated with the binding of up to four calcium atoms per β2m molecule, with a marked transformation of some random coil structure into beta sheet structure, and culminating in the aggregation of the protein at physiological (serum) concentrations of calcium and β2m. We draw attention to the fact that the sequence of β2m contains several potential calcium-binding motifs of the DXD and DXDXD (or DXEXD) varieties. We establish (a) that the microscopic aggregation seen at physiological concentrations of β2m and calcium turns into actual turbidity and visible precipitation at higher concentrations of protein and β2m, (b) that this initial aggregation/precipitation leads to the formation of amorphous aggregates, (c) that the formation of the amorphous aggregates can be partially reversed through the addition of the divalent ion chelating agent, EDTA, and (d) that upon incubation for a few weeks, the amorphous aggregates appear to support the formation of amyloid aggregates that bind to the dye, thioflavin T (ThT), resulting in increase in the dye's fluorescence. We speculate that β2m exists in the form of microscopic aggregates in vivo and that these don't progress to form larger amyloid aggregates because protein concentrations remain low under normal conditions of kidney function and β2m degradation. However, when kidney function is compromised and especially when dialysis is performed, β2m concentrations probably transiently rise to yield large aggregates that deposit in bone joints and transform into amyloids during dialysis related amyloidosis.

Preparation of size tunable giant vesicles from cross-linked dextran(ethylene glycol) hydrogels

We present a novel chemically cross-linked dextran-poly(ethylene glycol) hydrogel substrate for the preparation of dense vesicle suspensions under physiological ionic strength conditions. These vesicles can be easily diluted for individual study. Modulating the degree of cross-linking within the hydrogel network results in tuning of the vesicle size distribution.

Post-translational S-Nitrosylation Is an Endogenous Factor Fine Tuning the Properties of Human S100A1 Protein

S100A1 protein is a proposed target of molecule-guided therapy for heart failure. S-Nitrosylation of S100A1 is present in cells, increases Ca(2+) binding, and tunes the overall protein conformation. Thiol-aromatic molecular switch is responsible for NO-related modification of S100A1 properties. Post-translational S-nitrosylation may provide functional diversity and specificity to S100A1 and other S100 protein family members. S100A1 is a member of the Ca(2+)-binding S100 protein family. It is expressed in brain and heart tissue, where it plays a crucial role as a modulator of Ca(2+) homeostasis, energy metabolism, neurotransmitter release, and contractile performance. Biological effects of S100A1 have been attributed to its direct interaction with a variety of target proteins. The (patho)physiological relevance of S100A1 makes it an important molecular target for future therapeutic intervention. S-Nitrosylation is a post-translational modification of proteins, which plays a role in cellular signal transduction under physiological and pathological conditions. In this study, we confirmed that S100A1 protein is endogenously modified by Cys(85) S-nitrosylation in PC12 cells, which are a well established model system for studying S100A1 function. We used isothermal calorimetry to show that S-nitrosylation facilitates the formation of Ca(2+)-loaded S100A1 at physiological ionic strength conditions. To establish the unique influence of the S-nitroso group, our study describes high resolution three-dimensional structures of human apo-S100A1 protein with the Cys(85) thiol group in reduced and S-nitrosylated states. Solution structures of the proteins are based on NMR data obtained at physiological ionic strength. Comparative analysis shows that S-nitrosylation fine tunes the overall architecture of S100A1 protein. Although the typical S100 protein intersubunit four-helix bundle is conserved upon S-nitrosylation, the conformation of S100A1 protein is reorganized at the sites most important for target recognition (i.e. the C-terminal helix and the linker connecting two EF-hand domains). In summary, this study discloses cysteine S-nitrosylation as a new factor responsible for increasing functional diversity of S100A1 and helps explain the role of S100A1 as a Ca(2+) signal transmitter sensitive to NO/redox equilibrium within cells.

Ureido-Derivatized Polymers Based on Both Poly(allylurea) and Poly(l-citrulline) Exhibit UCST-Type Phase Transition Behavior under Physiologically Relevant Conditions

There are few examples of polymers that exhibit upper critical solution temperature (UCST) behavior under physiological conditions of temperature, pH, and ionic strength. In this study, we demonstrated that polymers with ureido groups undergo UCST-type phase transitions under physiologically relevant conditions. Poly(allylurea) copolymers showed UCST behavior at pH 7.5 in 150 mM NaCl even at the low polymer concentration of 0.13 mg/mL. Their phase separation temperatures (T(p)) could be controlled up to 65 °C. Similar thermosensitivity was observed with copolypeptides consisting of L-citrulline having an ureido group. This is the first demonstration of a non-vinyl polymer that shows UCST behavior under physiologically relevant conditions. We suggest that the ureido modification will be useful for production of polymer materials with UCST behavior in aqueous media.

Inhibition of porcine kidney betaine aldehyde dehydrogenase by hydrogen peroxide

Renal hyperosmotic conditions may produce reactive oxygen species, which could have a deleterious effect on the enzymes involved in osmoregulation. Hydrogen peroxide was used to provoke oxidative stress in the environment of betaine aldehyde dehydrogenase in vitro. Enzyme activity was reduced as hydrogen peroxide concentration was increased. Over 50% of the enzyme activity was lost at 100 μM hydrogen peroxide at two temperatures tested. At pH 8.0, under physiological ionic strength conditions, peroxide inhibited the enzyme. Initial velocity assays of betaine aldehyde dehydrogenase in the presence of hydrogen peroxide (0–200 μM) showed noncompetitive inhibition with respect to NAD+ or to betaine aldehyde at saturating concentrations of the other substrate at pH 7.0 or 8.0. Inhibition data showed that apparent Vmax decreased 40% and 26% under betaine aldehyde and NAD+ saturating concentrations at pH 8.0, while at pH 7.0 Vmax decreased 40% and 29% at betaine aldehyde and NAD+ saturating concentrations. There was little change in apparent KmNAD at either pH, while KmBA increased at pH 7.0. Ki values at pH 8 and 7 were calculated. Our results suggest that porcine kidney betaine aldehyde dehydrogenase could be inhibited by hydrogen peroxide in vivo, thus compromising the synthesis of glycine betaine.

Effects of phosphorylation on the self-assembly of native full-length porcine amelogenin and its regulation of calcium phosphate formation in vitro

The self-assembly of the predominant extracellular enamel matrix protein amelogenin plays an essential role in regulating the growth and organization of enamel mineral during early stages of dental enamel formation. The present study describes the effect of the phosphorylation of a single site on the full-length native porcine amelogenin P173 on self-assembly and on the regulation of spontaneous calcium phosphate formation in vitro. Studies were also conducted using recombinant non-phosphorylated (rP172) porcine amelogenin, along with the most abundant amelogenin cleavage product (P148) and its recombinant form (rP147). Amelogenin self-assembly was assessed using dynamic light scattering (DLS) and transmission electron microscopy (TEM). Using these approaches, we have shown that self-assembly of each amelogenin is very sensitive to pH and appears to be affected by both hydrophilic and hydrophobic interactions. Furthermore, our results suggest that the phosphorylation of the full-length porcine amelogenin P173 has a small but potentially important effect on its higher-order self-assembly into chain-like structures under physiological conditions of pH, temperature, and ionic strength. Although phosphorylation has a subtle effect on the higher-order assembly of full-length amelogenin, native phosphorylated P173 was found to stabilize amorphous calcium phosphate for extended periods of time, in sharp contrast to previous findings using non-phosphorylated rP172. The biological relevance of these findings is discussed.

Kinetic and thermodynamic analysis of 9‐nitrocamptothecin hydrolysis at physiological pH in the presence and absence of human serum albumin

AbstractKinetic and thermodynamic analysis of the 9‐nitrocamptothecin (9NC) hydrolysis reaction in the presence and absence of human serum albumin (HSA) in phosphate‐buffered saline (PBS) of pH 7.4 was carried out by first derivative absorption spectroscopy. The thermodynamic parameters determined in these studies provided a mechanistic explanation toward the endothermic but yet thermodynamically favorable hydrolysis of 9NC at physiological temperature and pH. In the presence of HSA, the apparent rate constant of 9NC hydrolysis was 3–3.5 times higher than in 9NC solutions alone, whereas the apparent equilibrium constant of 9NC hydrolysis was found to increase at a higher extent in the presence of HSA than in PBS with increasing temperature, reaching almost complete hydrolysis of the 9NC to the 9NC‐carboxylate at 315.15 K. Importantly, the Ea of the 9NC hydrolysis reaction in the presence of HSA was determined to be on average 17 kJ mol−1 lower than the Ea determined in plain PBS. Moreover, analysis of binding isotherms constructed for the HSA interaction with 9NC, using infinitely cooperative and independent binding models, demonstrated an incredibly higher binding constant for the 9NC‐carboxylate form as compared to the very weak and concentration‐dependent binding for the 9NC‐lactone species at 310.15 K. Taken together, the preferential association of the carboxylate form with HSA and the lower Ea of 9NC hydrolysis in the presence of HSA provide a mechanistic explanation for the shift of lactone–carboxylate equilibria toward the carboxylate product under physiological conditions of pH and ionic strength. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 693–703, 2010

Stability of Aβ (1-42) peptide fibrils as consequence of environmental modifications

β-Amyloid peptide (Aβ) plays a key role in the pathogenesis of Alzheimer disease (AD). Monomeric Aβ undergoes aggregation, forming oligomers and fibrils, resulting in the deposition of plaques in the brain of AD patients. A widely used protocol for fibril formation in vitro is based on incubation of the peptide at low pH and ionic strength, which generates Aβ fibrils several microns long. What happens to such fibrils once they are brought to physiological pH and ionic strength for biological studies is not fully understood. In this investigation, we show that these changes strongly affect the morphology of fibrils, causing their fragmentation into smaller ones followed by their aggregation into disordered structures. We show that an increase in pH is responsible for fibril fragmentation, while increased ionic strength is responsible for the aggregation of fibril fragments. This behavior was confirmed on different batches of peptide either produced by the same company or of different origin. Similar aggregates of short fibrils are obtained when monomeric peptide is incubated under physiological conditions of pH and ionic strength, suggesting that fibril morphology is independent of the fibrillation protocol but depends on the final chemical environment. This was also confirmed by experiments with cell cultures showing that the toxicity of fibrils with different initial morphology is the same after addition to the medium. This information is of fundamental importance when Aβ fibrils are prepared in vitro at acidic pH and then diluted into physiological buffer for biological investigations.

Recognition of left-handed Z-DNA of short unmodified oligonucleotides under physiological ionic strength conditions

The left-handed Z-DNA form of the short unmodified alternating guanine–cytosine oligonucleotides, 5′-(dGdC)24 and 5′-(dGdC)18, was selectively detected under physiological ionic strength and pH conditions using the anionic nickel(II) porphyrin, NiTPPS. No spectroscopic signal was observed for NiTPPS with any right-handed oligonucleotides under identical conditions. The 48mer 5′-(dGdC)24 Z-form was detected at concentrations as low as 100nM. The binding of NiTPPS to the B- and Z-oligonucleotides was studied quantitatively by UV–vis absorption and circular dichroism spectroscopies. NiTPPS was found to be a universal DNA binder, with binding affinity and geometry depending on the ionic composition of the solution, rather than on the DNA helical twist. This is the first example of a successful spectroscopic detection of the Z-DNA of short unmodified oligonucleotides under physiological pH and ionic strength conditions.

PH-Mediated Fluorescence and G-Quadruplex Binding of Amido Phthalocyanines

A new family of G-quadruplex ligands termed "amido phthalocyanines" (APcs) was synthesized by reacting variable amino acids with tetraamino zinc phthalocyanine. Variation in the number of methylene units separating the APc scaffold from terminal ammonium groups systematically modulated ammonium pK(a) values that, in turn, mediated APc aggregation and DNA binding. Certain APcs exhibited nearly 1000-fold enhancements in fluorescence quantum yield upon binding G-quadruplex DNA under physiological conditions of pH and ionic strength. G-quadruplexes derived from the c-myc and c-kit promoters and the human telomeric repeat were evaluated for APc affinity and specificity using two complementary and direct fluorescence binding assays that revealed apparent dissociation constants ranging from 20 to 200 nM. Approximately 500-fold lower affinities for duplex and single-stranded DNAs were observed. Interestingly, APc-quadruplex binding was relatively insensitive to ionic strength (0.03-1 M KCl) but highly dependent on the pH of the solution. Our results provide a mechanism for the "turn-on" fluorescence properties exhibited by these compounds that will assist in future rational design of new G-quadruplex-specific fluorescent probes and drug candidates.

The human ATR-mediated DNA damage checkpoint in a reconstituted system

DNA damage checkpoints are signal transduction pathways that coordinate the cell cycle with other cellular responses to DNA damage in order to maintain genomic integrity. The ATR kinase is responsible for initiating the DNA damage checkpoint in response to UV-damaged DNA and incompletely replicated DNA. We have recently established an in vitro system that recapitulates most but not all features of the human ATR-mediated DNA damage checkpoint response. With this system we have shown that damaged DNA can be a direct signal for ATR activation, and that TopBP1 specifically stimulates ATR in the presence of damaged DNA under physiological ionic strength conditions. This system provides a powerful tool to gain insight into the molecular mechanism of the ATR pathway. Here we describe preparation of the checkpoint components and our specific kinase assay in more detail.