DNA and buffers: are there any noninteracting, neutral pH buffers?

Identification of medium- and mechanism-related pitfalls towards improved performance and applicability of electrochemical mercury(II) aptasensors

The importance of understanding the mercury (II) ion interactions with thymine-rich DNA sequences is the reason for multiple comparative investigations carried out with the use of optical detection techniques directly in the depth of solution. However, the results of such investigations have limited applicability in the interpretation of the Hg2+ binding phenomenon by DNA sequences in thin, interfacial (electrode/solution), self-organized monolayers immobilized on polarizable surfaces, often used for sensing purposes in electrochemical biosensors. Overlooking the careful optimization of the measurement conditions is the source of discrepancies in the interpretation of the registered electrochemical signal. In this study, the chosen effects accompanying the efficiency of surface related recognition of Hg2+ by polyThymine DNA sequences labelled with methylene blue were investigated by voltammetry, QCM and spectro-electrochemical techniques. As was shown, the composition of the biosensing layer and buffers or the analytical procedures have a significant impact on the registered electrochemical readout which translates into signal stability, the biosensor's working parameters or even the mechanism of detection. After elucidation of the above factors, the complete and ready-to-use biosensor-based analytical solution was proposed offering subpicomolar mercury ion determination with high selectivity (also in aqueous real samples), reusability, and high signal stability even after long-term storage. The developed procedures were successfully used during the miniaturization process with self-prepared (PVD) elastic transducers. The obtained sensor, together with the simplicity of its use, low manufacturing cost, and attractive analytical parameters (i.e., LOD < < Hg2+ WHO limit) can present an interesting alternative for on-site mercury ion detection in environmental samples.

Influx of zwitterionic buffer after intracytoplasmic sperm injection (ICSI) membrane piercing alters the transcriptome of human oocytes

PURPOSE/STUDY QUESTION

Does piercing oocyte membranes during ICSI allow the influx of surrounding zwitterionic buffer into human oocytes and result in altered developmental competence?

METHODS

Human oocytes directed to IRB-approved research were used to determine the unrestricted influx of surrounding buffer into the oocyte after piercing of membranes via confocal fluorescence microscopy (n = 80 human MII oocytes) and the influence of the select buffer influx of HEPES, MOPS, and bicarbonate buffer on the oocyte transcriptome using ultra-low input RNA sequencing (n = 40 human MII oocytes).

RESULTS

Piercing membranes of human MII oocytes during sham-ICSI resulted in the unrestricted influx of surrounding culture buffer into the oocyte that was beyond technician control. Transcriptome analysis revealed statistically significant decreased cytoskeletal transcripts in the pierced buffer cohorts, higher levels of embryo competency transcripts (IGF2 and G6PD) in the bicarbonate buffer cohort, higher levels of stress-induced transcriptional repressor transcripts (MAF1) in the HEPES and MOPS cohorts, and decreased levels of numerous chromosomal maintenance transcripts (SMC3) in the HEPES buffer cohort. The HEPES buffer cohort also revealed higher levels of transcripts suggesting increased oxidative (GPX1) and lysosomal stress (LAMP1).

CONCLUSION

The influence of zwitterionic buffer on intrinsic cellular mechanisms provides numerous concerns for their use in IVF clinical applications. The primary concern is the ICSI procedure, in which the surrounding buffer is allowed influx into the oocytes after membrane piercing. Selecting a physiological bicarbonate buffer may reduce imposed stress on oocytes, resulting in improved embryo development and clinical results because intracellular MOPS, and especially HEPES, may negatively impact intrinsic biological mechanisms, as revealed by transcriptome changes. These findings further support the utilization of bicarbonate buffer as the oocyte-holding medium during ICSI.

Use of In silico tools for screening buffers to overcome physical instability of Abatacept

Rheumatoid arthritis is an autoimmune disorder. Abatacept (CTLA4-Ig) is used for the treatment of Rheumatoid arthritis. Abatacept is a monoclonal antibody. Monoclonal antibodies undergo chemical (e.g. oxidation, deamidation, hydrolysis) and physical (e.g. aggregation, unfolding) instabilities while handling and storage. Abatacept is also prone to aggregation. Stabilizing agents such as buffers are used to stabilize monoclonal antibodies. But, the selection of the appropriate buffer is a time-consuming process because after testing many buffers based on the analysis of the results the appropriate buffer is identified. To overcome this issue in the current study computational tools were utilized to virtually screen different buffers to select the appropriate buffer. Ligand binding is the principal mechanism of conformational stability of proteins. For the buffers as well ligand binding is the most common mechanism for enhancing the thermodynamic stability of proteins. Generally it is observed that by enhancing the thermodynamic stability there is reduction in the rate of aggregation of proteins. Buffer (ligand) binds to the native state of the protein preferentially; it results in stabilization of the protein, while in the case of denatured protein it has no impact. There are many studies conducted involving the proteins in buffer solutions but very limited information is available about the mechanism of protein-buffer interactions. In the current study ligand binding mechanism of protein - buffer interaction was studied using molecular docking. After the docking buffers were ranked according to their energy value. The lower energy scores represent better protein-buffer (ligand) binding affinity compared to high energy values. It was observed that Phosphate with a binding affinity of -107.9 kcal/mol was the buffer with the least binding energy followed by Citrate (-70.6 kcal/mol), Melglumine (-66.6 kcal/mol), Arginine (-64.5 kcal/mol), Glucono delta lactone (-62.6 kcal/mol), Sodium citrate (-56.5 kcal/mol), Tromethamine (-52.3 kcal/mol), Glycine HCl (-37.2 kcal/mol), Sulfuric acid (-37.7 kcal/mol), Ammonium acetate (-31.1 kcal/mol), Acetic acid (-30.7 kcal/mol). With lower binding energy higher is the affinity between the ligand and protein. So phosphate was identified as a buffer with the highest affinity with Abatacept.

Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

This review describes the results obtained by using free-solution capillary electrophoresis to probe the electrostatic and hydrodynamic properties of DNA in solutions containing various monovalent cations. In brief, we found that the mobilities of double-stranded DNAs (dsDNAs) increase with increasing molecular weight before leveling off and becoming constant at molecular weights ≥400 bp. The mobilities of single-stranded DNAs (ssDNAs) go through a maximum at ∼10-20 nucleotides before decreasing and becoming constant for oligomers larger than ∼30-50 bases. The mobilities of both ss- and dsDNAs increase linearly with the logarithm of increasing charge per unit length and decrease linearly with the logarithm of increasing ionic strength. Surprisingly, ss- and dsDNA mobilities level off and become nearly constant at ionic strengths ≥0.6 M. The thermal stabilities of dsDNAs decrease linearly with increasing solution viscosity. The diffusion coefficients of dsDNA are modulated by the diffusion coefficients of their counterions because of electrostatic DNA-cation coupling interactions. Finally, the anomalously slow mobilities observed for A-tract-containing DNAs can be attributed both to differences in shape and to the preferential localization of small cations in the A-tract minor groove. Since many of these results are mirrored in other polyion-counterion systems, free-solution electrophoresis can be viewed as a reporter of the electrostatics and hydrodynamics of highly charged polyions. New results describing the mobilities of dsDNA analogues of a microRNA-messenger RNA complex are also presented.

Processing of the spectrofluorimetric data using the graphical methods and the maximum likelihood approach

The present work describes the calculation of the binding constants from spectrofluorimetric data using simple graphical methods and specialized software implementing the maximum likelihood approach. The following popular cases are analyzed: 1) protein-small molecule; 2) protein-metal complex; 3) DNA-small molecule; 4) DNA-metal complex interactions. The inability of graphical plots to return the correct results except for the simplest situation (single reaction with a non-fluorescent product) is demonstrated. The possibility of determining the most probable stoichiometric model using the maximum likelihood estimation (LSQ as its special case) is discussed as well as the limitations.

Tuning the Polymorphism of the Anti-VEGF G-rich V7t1 Aptamer by Covalent Dimeric Constructs

In the optimization process of nucleic acid aptamers, increased affinity and/or activity are generally searched by exploring structural analogues of the lead compound. In many cases, promising results have been obtained by dimerization of the starting aptamer. Here we studied a focused set of covalent dimers of the G-quadruplex (G4) forming anti-Vascular Endothelial Growth Factor (VEGF) V7t1 aptamer with the aim of identifying derivatives with improved properties. In the design of these covalent dimers, connecting linkers of different chemical nature, maintaining the same polarity along the strand or inverting it, have been introduced. These dimeric aptamers have been investigated using several biophysical techniques to disclose the conformational behavior, molecularity and thermal stability of the structures formed in different buffers. This in-depth biophysical characterization revealed the formation of stable G4 structures, however in some cases accompanied by alternative tridimensional arrangements. When tested for their VEGF₁₆₅ binding and antiproliferative activity in comparison with V7t1, these covalent dimers showed slightly lower binding ability to the target protein but similar if not slightly higher antiproliferative activity on human breast adenocarcinoma MCF-7 cells. These results provide useful information for the design of improved dimeric aptamers based on further optimization of the linker joining the two consecutive V7t1 sequences.

DNA translocation to giant unilamellar vesicles during electroporation is independent of DNA size

Delivery of naked DNA molecules into living cells via physical disruption of the membrane under electric pulses has potential biomedical applications ranging from gene electro-transfer, electro-chemotherapy, to gene therapy, yet the mechanisms involved in DNA transport remain vague. To investigate the mechanism of DNA translocation across the cell membrane, giant unilamellar vesicles (GUVs) were electroporated in the presence of DNA molecules keeping the size of the DNA molecules as a variable parameter. We experimentally determined the translocation efficiency for each size of the DNA molecule, to compare the results with the existing and conflicting theories of the translocation mechanism i.e. stochastic threading and bulk electrophoresis. We observed that the translocation efficiency is independent of DNA size (ranging from 25-20 000 bp, bp = base pairs), implying that DNA molecules translocate freely across the electro-pores in the lipid membrane in their native polymer conformation, as opposed to unravelling and threading through the electro-pore. Bulk electrophoretic mobility determines the relationship between translocation efficiency and the size of the DNA molecule. This research provides experimental evidence of the mechanistic understanding of DNA translocation across lipid membranes which is essential for devising efficient and predictable protocols for electric field mediated naked DNA delivery.

A quick and effective in-house method of DNA purification from agarose gel, suitable for sequencing

Sequencing of DNA fragments (e.g., ITS, 16S, 18S, particular genes, and molecular markers) is increasingly required in studies on microbial diversity, microbial genetic population and phylogeny, sequencing of alleles, and searching for SNPs, among others. The cost of obtaining these DNAs, in quantity and quality for sequencing, is high as it involves special kits to recover DNA from gel after PCR, or the cloning and purification of plasmids with commercial kits. Genetic population and other studies require the analyses of many samples, and therefore, the high cost represents an obstacle for carrying out such projects in countries where there is great biodiversity, such as the tropical and subtropical developing countries, where funds are limited. Modifying an already known method for DNA recovery from gel, the first in-house protocol of DNA recovery suitable for direct use in sequencing is presented herein. This protocol is broadly applicable on DNAs from all different living beings, e.g., bacteria, fungi, and plants. Its simplicity, speed, and low cost make this procedure amenable for high-throughput DNA sequencings as required in microbial population studies, development of molecular markers, molecular identification of strains in microbial collections, and others. Recovery of DNA fragments from agarose gel is one of the most common tasks in molecular biology laboratories. Therefore, its potential of applicability of the protocol presented here is enormous.

DNA strand break dependence on Tris and arginine scavenger concentrations under ultra-soft X-ray irradiation: the contribution of secondary arginine radicals

In this study, we used a bench-top cold-cathode ultra-soft X-ray (USX) generator to expose aqueous DNA plasmid solutions to low-LET radiation under various scavenging conditions. Single- and double-strand breaks were assessed using classic gel electrophoresis quantification of linear, circular and supercoiled plasmid DNA topologies. With their very low penetration range in water, USX can only interact with matter up to short distances, of the order of 50 μm. We validated a stirring procedure which makes it possible to expose 100 µL of aqueous samples (2 mm thick). The scavenging of OH radicals by Tris buffer was studied at ambient temperature under aerobic conditions and compared to data gathered in the literature. A very good agreement was found with the rare data dealing with DNA plasmid exposed to Al Kα photons at low temperature (T ≤ 277 K), which therefore validated the experimental procedure. The yields for DNA single-strand breaks determined during this study enabled the ratio of indirect to direct effects to be determined at 96.2%, in good agreement with the value of 97.7% stemming from a study based on γ-ray irradiation of frozen solutions of plasmid DNA. Then, arginine was used both to create a "biological-like" chemical environment around the DNA plasmids and as an OH radical scavenger, in vitro. Although arginine has a greater scavenging (protecting) power than Tris, surprisingly, it led to higher rates of strand breakage. Based on the specific binding modes of arginine to DNA, we suggest that the side effects observed are due to the presence of arginine near to, but also inside, the DNA double helix.

Are specific buffer effects the new frontier of Hofmeister phenomena? Insights from lysozyme adsorption on ordered mesoporous silica

Different 10 mM buffers at the same nominal pH affect specifically the adsorption of lysozyme on ordered mesoporous silica. It emerges that specific buffer effects should be considered within ‘Hofmeister phenomena’.

Extraction of an active enzyme by self-buffering ionic liquids: a green medium for enzymatic research

The extraction of a model enzyme α-chymotrypsin in its active conformation from an aqueous solution by using new biocompatible and self-buffering Good's buffer ionic liquids-based aqueous biphasic systemsis demonstrated.

Buffers more than buffering agent: introducing a new class of stabilizers for the protein BSA

In this study, we have analyzed the influence of four biological buffers on the thermal stability of bovine serum albumin (BSA) using dynamic light scattering (DLS).

Self-buffering and biocompatible ionic liquid based biological media for enzymatic research

New self-buffering Good's buffer ionic liquids (GBILs) were synthesized for biological research.

(Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review

The present work reviews, discusses and update the metal complexation characteristics of thirty one buffers commercially available. Additionally, their impact on the biological systems is also presented and discussed.

The free solution mobility of DNA and other analytes varies as the logarithm of the fractional negative charge

The free solution mobilities of ssDNA and dsDNA molecules with variable charge densities have been measured by CE. DNA charge density was modified either by appending positively or negatively charged groups to the thymine residues in a 98 bp DNA molecule, or by replacing some of the negatively charged phosphate internucleoside linkers in small ssDNA or dsDNA oligomers with positively charged phosphoramidate linkers. Mobility ratios were calculated for each dataset by dividing the mobility of a charge variant by the mobility of its unmodified parent DNA. Mobility ratios essentially eliminate the effect of the BGE on the observed mobility, making it possible to compare analytes measured under different experimental conditions. Neutral moieties attached to the thymine residues in the 98-bp DNA molecule had little or no effect on the mobility ratios, indicating that bulky substituents in the DNA major groove do not affect the mobility significantly. The mobility ratios observed for the thymine-modified and linker-modified DNA charge variants increased approximately linearly with the logarithm of the fractional negative charge of the DNA. Mobility ratios calculated from previous studies of linker-modified DNA charge variants and small multicharged organic molecules also increased approximately linearly with the logarithm of the fractional negative charge of the analyte. The results do not agree with the Debye-Hückel-Onsager theory of electrophoresis, which predicts that the mobility of an analyte should depend linearly on analyte charge, not the logarithm of the charge, when the frictional coefficient is held constant.

Characterization of metal ion-nucleic acid interactions in solution

Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

Embryo culture media for human IVF: which possibilities exist?

The last three decades have seen considerable progress in the development of culture media for ART and infertility treatment. Basic research on the metabolism of mammalian preimplantation embryos demonstrated the specific needs in the evolving stage of the embryo growing in vitro. Two different philosophies led to two different culture strategies for human preimplantation embryos: the 'back-to-nature' or sequential culture principle, and 'let-the-embryo-choose' or one-step culture principle. Both systems are commercially available and the discussion between the different groups of scientists is ongoing. As a matter of fact, all ART culture media currently used are not optimal for the growing human preimplantation embryo. However, further research is needed to reduce stress to the human preimplantation embryo and determine how many embryos from a treatment cycle are capable of producing a live birth.

Biological pH buffers in IVF: help or hindrance to success

PURPOSE

Minimizing environmental stress helps maintain cellular homeostasis and is a crucial component in optimizing embryo development in vitro and resulting ART success. One stressor of particular interest is pH. Biologic buffers, such as HEPES and MOPS, are valuable tools for stabilizing pH. The objective of this manuscript is to summarize efficacy and impact of various pH buffers used during IVF lab procedures

METHODS

Keyword searches were performed using Pubmed and Medline and relevant literature reviewed.

RESULTS

Various pH buffers have been used with varying degrees of success for gamete and embryo processing in a variety of animal species, as well as in human.

CONCLUSION

Though biologic buffers off a means to improve pH stability, not all buffers may be appropriate for use with gametes and embryos. Specific buffers may have undesired effects, and these may be buffer, species, cell type or concentration dependent. Continued research is needed to further refine and improve the use of biologic buffers for use in human ART.

Improved DNA electrophoresis in conditions favoring polyborates and lewis acid complexation

Spatial compression among the longer DNA fragments occurs during DNA electrophoresis in agarose and non-agarose gels when using certain ions in the conductive buffer, impairing the range of fragment sizes resolved well in a single gel. Substitutions using various polyhydroxyl anions supported the underlying phenomenon as the complexation of Lewis acids to DNA. We saw significant improvements using conditions (lithium borate 10 mM cations, pH 6.5) favoring the formation of borate polyanions and having lower conductance and Joule heating, delayed electrolyte exhaustion, faster electrophoretic run-speed, and sharper separation of DNA bands from 100 bp to 12 kb in a single run.

Interaction study of a lysozyme-binding aptamer with mono- and divalent cations by ACE

Binding between an aptamer and its target is highly dependent on the conformation of the aptamer molecule, this latter seeming to be affected by a variety of cations. As only a few studies have reported on the interactions of monovalent or divalent cations with aptamers, we describe herein the use of ACE in its mobility shift format for investigating interactions between various monovalent (Na+, K+, Cs+ or divalent (Mg2+, Ca2+, Ba2+) cations and a 30-mer lysozyme-binding aptamer. This study was performed in BGEs of different natures (phosphate and MOPS buffers) and ionic strengths. First, the effective charges of the aptamer in 30 mM ionic strength phosphate and MOPS (pH 7.0) were estimated to be 7.4 and 3.6, respectively. Then, corrections for ionic strength and counterion condensation effects were performed for all studies. The effective mobility shift was attributed not only to these effects, but also to a possible interaction with the buffer components (binary or ternary complexes) as well as possible conformational changes of the aptamer. Finally, apparent binding constants were calculated for divalent cations with mathematical linearization methods, and the influence of the nature of the BGE was evidenced.

Optimizing the culture environment in the IVF laboratory: impact of pH and buffer capacity on gamete and embryo quality

Supplying and maintaining appropriate culture conditions is critical to minimize stress imposed upon gametes and embryos and to optimize the in-vitro environment. One parameter that requires close scrutiny in this endeavour is pH. Though embryos have a limited ability to regulate their internal pH (pH(i)), oocytes lack robust mechanisms. Thus, careful attention to external pH (pH(e)) of culture media is imperative in IVF. Ability to withstand deviations in hydrogen ion concentration varies depending on culture conditions, as well as laboratory procedures. Cryopreserved--thaw--thawed embryos, as well as denuded oocytes, are especially susceptible to perturbations in pH(e). Therefore, proper setting, monitoring and stabilizing of pH(e) during IVF laboratory procedures is a crucial component of a rigorous quality control programme. Here, importance of both pH(i) and pH(e) in respect to gamete and embryo quality are discussed. Furthermore, factors influencing selection of pH(e), as well as emerging methods to stabilize pH(e) in the IVF laboratory are detailed.

The effect of different zwitterionic buffers and PBS used for out-of-incubator procedures during standard in vitro embryo production on development, morphology and gene expression of bovine embryos

The effect of the zwitterionic buffers HEPES, TES and MOPS and of PBS used for out-of-incubator procedures during standard in vitro embryo production on bovine oocytes and embryo development, morphology and on the expression patterns of eight selected genes: Fgf-4, Lama1, Ube2a, Gsta4, Il6, Sod1, Prss11 and Hspb1, was evaluated. All buffers were prepared at a concentration of 10 mM in TALP medium, with the exception of PBS. The total time of oocyte/embryo exposure to each buffer was approximately 41 min. The cleavage rates and number of embryos that developed to > or =8 cells at day 4 were no different among the buffers tested, however, more blastocysts developed at day 7, 8 and 9 in HEPES and MOPS treatments than in PBS and TES (P<0.05). No difference between buffers in total and apoptotic cell number was found. Except for Hspb1 and Ube2a genes, the levels of expression of the six remaining transcripts were higher in in vivo than in in vitro embryos irrespective of buffer used (P<0.05). In addition, higher expression of Hspb1 and lower expression of Ube2a and Lama1 were observed in PBS and TES than in MOPS and HEPES treatments (P<0.05). Expression of Fgf-4 and Gsta4 in the in vitro embryos was lower in PBS than in the remaining three buffers (P<0.05) and the level of expression of the Il6 gene was not affected by any buffer tested but was lower in in vitro than in in vivo derived embryos. Expression of both Sod1 and Prss11 genes in MOPS were at the level of the in vivo embryos. These results showed that the choice of buffer and short exposure time of approximately 41 min, affects mRNA expression of in vitro produced bovine embryos.

High-sensitive determination of human alpha-thrombin by its 29-mer aptamer in affinity probe capillary electrophoresis

ACE technique provides an effective tool for the separation and identification of disease-related biomarkers in clinical analysis. In recent years, a couple of synthetic DNA or RNA oligonucleotides, known as aptamers, rival the specificity and affinity for targets to antibodies and are employed as one kind of powerful affinity probe in ACE. In this work, based on high affinity between antithrombin aptamer and thrombin (their dissociation constant is 0.5 nM), a carboxyfluorescein-labeled 29-nucleotide (nt) aptamer (F29-mer) was used and an aptamer-based affinity probe CE (aptamer-based APCE) method was successfully established for high-sensitive detection and quantitative analysis of thrombin. Experimental conditions including incubation temperature and time, buffer composition, and concentration of cations were investigated and optimized. Under the optimized condition, the linear range was from 0 to 400 nM and the LOD was 2 nM (74 ng/mL, S/N = 3), i.e., 40 amol, both in running buffer and in 5% v/v human serum. This LOD is the lowest one than those achieved by the previous APCE methods but based on a 15-mer aptamer. This approach offers a promising method for the rapid, selective, and sensitive detection of thrombin in practical utility. Further binding experiments using one carboxyfluorescein-labeled aptamer and the other nonlabeled aptamer or vice versa were carried out to deduce the formation of ternary complex when these two aptamers coexisted in the free solution with thrombin.

Do zwitterions contribute to the ionic strength of a solution?

Capillary electrophoresis has been used to determine whether zwitterions contribute to the ionic strength of a solution, by measuring the mobility of a double-stranded DNA oligomer in cacodylate-buffered solutions containing various concentrations of the ionic salt tetraethylammonium chloride (TEA(+)Cl(-)) or the zwitterion tricine(+/-). The mobility of the DNA decreased as the square root of ionic strength, as expected from the Debye-Hückel-Onsager theory of electrophoresis, when TEA(+)Cl(-) was added to the buffer. However, the mobility was independent of the concentration of added tricine(+/-). Hence, zwitterions do not contribute to the ionic strength of a solution.

Quantitative analysis of cation binding to the adenosine nucleotides using the variable ionic strength method: validation of the Debye-Hückel-Onsager theory of electrophoresis in the absence of counterion binding

The free solution mobilities of the adenosine nucleotides 5'-adenosine triphosphate (ATP), 5'-adenosine diphosphate (ADP), 5'-adenosine monophosphate (AMP), and 3'-5'-cyclic AMP (cAMP) have been measured in diethylmalonate buffers containing a wide variety of monovalent cations. The mobilities of all nucleotides increase gradually with the increase in intrinsic conductivity of the cation in the BGE. However, at a given conductivity, the mobilities observed for ATP, ADP, and AMP in BGEs containing alkali metal ions and other cations are lower than these observed in BGEs containing tetraalkylammonium ions. Since the mobility of cAMP is independent of the cation in the BGE, the results suggest that the relatively low mobilities observed for ATP, ADP, and AMP in BGEs containing cations other than a tetraalkylammonium ion are due to cation binding, reducing the effective net charge of the nucleotide and thereby reducing the observed mobility. To measure the binding quantitatively, the mobilities of the nucleotides were measured as a function of ionic strength. The mobilities of ATP, ADP, and AMP decrease nonlinearly with the square root of ionic strength (I(1/2)) in BGEs containing an alkali metal ion or Tris(+). By contrast, the mobilities decrease linearly with I(1/2) in BGEs containing a nonbinding quaternary ammonium ion, as expected from Debye-Hückel-Onsager (DHO) theory. The mobility of cAMP, a nonbinding analyte, decreases linearly with I(1/2), regardless of the cation in the BGE. Hence, a nonlinear decrease of the mobility of an analyte with I(1/2) appears to be a hallmark of counterion binding. The curved mobility profiles observed for ATP, ADP, and AMP in BGEs containing an alkali metal ion or Tris(+) were analyzed by nonlinear curve fitting, using difference mobility profiles to correct for the effect of the physical properties of BGE on the observed mobilities. The calculated apparent dissociation constants range from 22 to 344 mM, depending on the particular cation-nucleotide pair. Similar values have been obtained by other investigators, using different methods. Interestingly, Tris(+) and Li(+) bind to the adenosine nucleotides with approximately equal affinities, suggesting that positively charged Tris(+) buffer ions can compete with alkali metal ions in Tris-buffered solutions.

Quantification of single-stranded nucleic acid and oligonucleotide interactions with metal ions by affinity capillary electrophoresis: part I

The interactions between oligonucleotides and inorganic cations have been measured by capillary zone electrophoresis. With increasing concentrations of divalent cations (Ca(2+), Mg(2+), Mn(2+) and Ni(2+)) in the running buffer, the migration behavior was evaluated by calculation of the binding constants. Besides these fundamental studies of binding equilibria, different buffer components, tris(hydroxymethyl)aminomethane and 3-(N-morpholino)propanesulfonic acid, have been investigated and their effects on metal ion binding quantified.

Effect of buffer flow on DNA separation in a microfabricated electrophoresis system

An adequate buffer reservoir is one essential component of an electrophoresis system, providing current carrying ions and maintaining constant pH. In a microfabricated DNA separation system with on-chip electrodes, the amount of buffer used is limited by the design of the device; the buffer continuity can be easily disturbed by the production of bubbles. Continuously flowing 1 x Tris-borate-EDTA (TBE) buffer over the electrodes at the cathodic end solves both problems. This flow increases the resolution for ssDNA primer separations (21 and 25 bases) to a maximum value of 1.4 within a distance of 1.2 cm, about four times higher than that without flow. Similar improvement has been achieved for dsDNA separation (20 bp ladder; BioRad) at a distance of only 0.4 cm, giving baseline resolution for bands from 20 to 240 bp. We have also investigated the effect of buffer concentration on resolution, and no similar improvement can be obtained by merely increasing the buffer concentration without flow.

History and principles of conductive media for standard DNA electrophoresis

DNA electrophoresis has been a dominant technique in molecular biology for 30 years. The foundation for this common technique is based on a few simple electrochemical principles. Electrophoretic DNA separation borrowed from existing protein and RNA techniques developed in the 1950s and 1960s. For 30 years, common DNA electrophoretic conductive media remained largely unchanged, with Tris as the primary cation. DNA electrophoresis relies simply upon the negative charge of the phosphate backbone and the ability to distribute a voltage gradient in a sieving matrix. Nevertheless, the conductive properties in DNA electrophoresis are complicated by choices involving voltage, electric current, conductivity, temperature, and the concentration and identity of the ionic species present. Differences among the extant chemical recipes for common conductive media affect central properties. Tris-based buffers, even in optimal form, create a runaway positive feedback loop between heat generation and retention, temperature, conductivity, and current. This is undesirable, leading to limitations on the permissible electric field and to impaired resolution. Recently, we developed low-molarity conductive media to mitigate this positive feedback loop. Such media allow for application of a higher electric field. Applications of DNA electrophoresis can now be reengineered for lower ionic strength, higher field strengths, and lower requirements for heat dissipation.

Novel elution strategy for monitoring DNA counter-migration in the presence of electroosmotic flow

The migration behavior of native (i.e., unlabelled) DNA in the presence of electroosmotic flow (EOF) was investigated in bare fused-silica capillaries. Employing a novel elution strategy, the influence of EOF on the net mobility of DNA was assessed by collecting the DNA that migrated anodically (i.e., against EOF) and out of the capillary inlet. Various conditions of pH and buffer-zone continuity were employed to characterize this phenomenon. Tris acid (TA, pH 5.14) and Tris base (TB, pH 9.36) were used as buffers in continuous systems, in which the capillary and the inlet reservoir contain the same buffer, and discontinuous systems, in which the capillary contains either TA or TB, and the inlet reservoir contains water. DNA that was ejected into the inlet vial was subsequently analyzed by capillary electrophoresis-laser-induced fluorescence. Both phiX174/HaeIII DNA and the beta-actin product of single-cell reverse transcriptase-polymerase chain reaction were used as DNA samples in this study. The mechanism of elution was found to depend on bulk flow, in the case of continuous solutions. However, with the discontinuous system, a localized decrease in EOF generated in the capillary tip appeared to impact elution. These findings serve to introduce an alternative approach for characterizing the mobility of highly charged species.

Portable capillary electrophoresis system with potential gradient detection for separation of DNA fragments

A portable capillary electrophoresis (CE) system with a novel potential gradient detection (PGD) was utilized to separate DNA fragments. For the first time it was demonstrated that separation of DNA fragments in polymer solution could be detected by a portable CE system integrated with PGD, with a limit of detection (LOD) comparable to that of the CE-ultraviolet (UV) method. Effects of buffer solution, sieving medium, and applied voltage were also investigated. The portable CE-PGD system shows several potential advantages, such as simplicity, cost effectiveness, and miniaturization.

Small molecular ion adsorption on proteins and DNAs revealed by separation techniques

Ion binding is a term that assumes that the ion is included in the solvation sphere characterising the biomolecule. The binding forces are not clearly stated except for electrostatic attraction; weak forces (hydrogen bonds and Van der Waals forces) are likely involved. Many publications have dealt with ion binding to proteins and the consequences over the past 10 years, but only a few studies were performed using high-performance liquid chromatography (HPLC: ion exchange, reversed phase without the well-identified immobilised metal affinity chromatography) and capillary zone electrophoresis (CZE). This review focuses on the binding of proteins and DNAs mainly to the oxyanions (phosphate, borate, citrate) and amines used as buffers for both the HPLC eluent and the background electrolyte of CZE. Such specific ion adsorption on biomolecules is evidenced by physico-chemical characteristics such as the mobility or retention volume, closely associated with the net charge, which differ from the expected or experimental data obtained under the conditions of an indifferent electrolyte. It is shown that ion binding to proteins is a key parameter in the electrostatic repulsion between the free protein and a fouled membrane in the ultrafiltration separation of a protein mixture.

Resolution of Multiple ssDNA Structures in Free Solution Electrophoresis

By using high concentrations of buffer, electroosmotic flow within uncoated channels of a microfluidic chip was minimized, allowing the free solution electrophoretic separation of DNA. More importantly, because of the ability to efficiently dissipate heat within these channels, field strengths as high as 600 V/cm could be applied with minimal Joule heating (<2 degrees C). As a result of the higher field strengths, separations within an 8-cm-long channel were achieved within a few minutes. However, when the electrophoretic separation of single-stranded DNA (ssDNA) less than 22 bases in length was performed, containing the fluorophore Texas Red as an end label, more than the expected single peak was observed at this high electric field. On the other hand, the free solution electrophoresis of a double-stranded DNA (dsDNA) consisting of a random sequence did exhibit the expected single peak. The appearance of these multiple peaks for ssDNA is shown to be dependent upon the base content and sequence of the ssDNA as well as on the chemical structure of the fluorophore used to tag the DNA for detection. Specifically, the peaks can be attributed to different secondary structures that result either from hydrophobic interactions between the DNA bases and an uncharged fluorescent dye or from G-quadruplexes within guanine-rich strands.

Simple coating of capillaries with anionic liposomes in capillary electrophoresis

A new and relatively simple method was developed for coating of capillaries in electrophoresis with liposomes. The liposomes, with a diameter of about 100 nm, are large unilamellar vesicles prepared by extrusion. The liposomes contained 1-palmitoyl-2-oleyl-sn-glycero-3-phosphatidylcholine (POPC) or POPC with different proportions of bovine brain phosphatidylserine (PS) and cholesterol. They formed a bilayer structure on the silica surface enabling the separation of neutral compounds. The effectiveness of the coating in separation was evaluated with use of uncharged steroids as model compounds. The coating was also studied by measuring the electroosmotic flow. The best results, taking into consideration both separation and stability, were achieved with anionic 80:20 mol% POPC/PS liposomes. In addition, the effect of coating conditions on the results was investigated. Among the buffers studied [N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES), phosphate, tris(hydroxymethyl)aminomethane (Tris) and N-tris(hydroxymethyl)methylglycine (Tricine)], HEPES seemed to have a significant effect on the success of the coating. Successful separation of steroids was achieved only when HEPES buffer was used in the coating procedure and in the background electrolyte solution for the separation. With all other buffers the peaks of the model compounds overlapped.

Comparison of the separation of large DNA fragments in the presence and absence of electroosmotic flow at high pH

This paper describes the analysis of large DNA fragments at pH > 10.0 by capillary electrophoresis (CE) in the presence of electroosmotic flow (EOF) using hydroxyethylcellulose (HEC) solution. HEC solution in the anodic reservoir enters the capillaries filled with high-pH buffer by EOF after sample injection. With respect to resolution, sensitivity, and speed, separation conducted under discontinuous conditions (different pH values of HEC solutions and buffer filling the capillary) is appropriate. Using HEC solution at concentrations higher than its entanglement threshold ensures a good separation of large DNA fragments in the presence of EOF at high pH. In addition to pH and HEC, the electrolyte species, dimethylamine, methylamine, and piperidine, play different roles in determining the resolution. The separation of DNA fragments ranging in size from 5 to 40 kilo base pairs was completed in 6 min using 1.5% HEC prepared in 20 mM methylamine-borate, pH 12.0, and the capillary filled with 40 mM dimethylamine-borate, pH 10.0. In comparison, this method allows faster separations of large DNA fragments compared with that conducted in the absence of EOF using dilute HEC solutions.

Potential binding of borate ions to mono- and oligonucleotides: a capillary electrophoresis investigation

The potential binding of borate to oligonucleotides and DNA fragments is here investigated. In case of free nucleotides, such as AMP, there appears to be a weak binding, although no free versus complexed species could ever be separated under any experimental condition. The binding was suggested by the strong peak asymmetry and by the fact that, at progressively lower borate molarities in the background electrolyte, the peak shape suddenly switched from fronting to tailing. This indicated, as also confirmed by theoretical simulations, that the AMP-borate complex was the slow, not the fast moving species. On the contrary, in the case of free adenosine, strong binding ensued, since in Tris-acetate buffer this compound was only eluted with the electroendoosmotic flux, being neutral, whereas in Tris-borate it had a much higher mobility, comparable to, although lower than, that of AMP. When running oligonucleotides, at standard borate molarities (ca. 45 mM), and under strict iso-ionic strength conditions, no binding to borate could be demonstrated, since the free mobility of a 24-mer DNA was identical in TA and TB buffers. However, at very high borate molarities (200 mM) and high pH values (pH 8.92), some binding to oligonucleotides could occur, since in these latter conditions the mobility of a 24-mer was seen to be ca. 20% lower than at pH 7.69, a pH value that should discourage any complex formation.