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C Gelfi

Publications and source records attributed to C Gelfi.

At least 55 records · Page 3Linked to original sources

Surface modification based on Si-O and Si-C sublayers and a series of N-substituted acrylamide top-layers for capillary electrophoresis.

Two approaches were used to prepare a series of surface-modified capillaries. In the first, a sublayer was formed by coupling gamma-methacryloxypropyltrimethoxysilane to the surface silanol groups forming an SI-O bond; a top layer was then formed by polymerizing acrylamide in the capillary, which reacted with the sublayer. In the second approach, a sublayer was formed by silanol chlorination, followed by Grignard coupling of vinylmagnesium bromide to form an Si-C bond at the surface; a top layer was formed by polymerizing either acrylamide (AA), dimethylacrylamide (DMA), N-acryloylaminoethoxyethanol (AAEE), or N-acryloylaminopropanol (AAP) onto the sublayer. The Si-Cpoly(AA) capillaries were more stable and produced an approximately 10-fold lower electroosmotic flow compared to the Si-O-poly(AA) capillaries. The Si-C sublayer was used to compare the performance of all four top layers. Electroosmotic flow decreased in the order: Si-O-poly(AA), Si-C-poly(AA), Si-Cpoly(AAEE), Si-C-poly(DMA), and Si-C-poly(AAP). Si-C-poly(AA) showed evidence of irreversible degradation at pH 9 already after 40-50 runs. Si-C-polyAAP-coated capillaries demonstrated superior efficiency and migration time reproducibility for a number of alkaline proteins and for fluorescently labeled ovalbumin. Excellent performance was maintained, in the case of poly(AAP), for a least 300 runs (of 30 min duration) at pH 9.0.

Acrylamide↗

Capillary zone electrophoresis of ds-DNA in isoelectric buffers: effect of adding of competing, nonamphoteric ions.

When separating ds-DNA in isoelectric His buffer (pH=pI=7.6), in the 50-250 mM concentration range, some unique phenomena were observed: improved resolution for smaller DNA fragments, up to ca. 150 bp, and a rapid deterioration of resolution above this critical length (which corresponds to the persistence length). Such phenomenon depended also on voltage and concentration of sieving liquid polymer. Direct binding of His to the DNA helix was hypothesized, with resultant stiffening and an increment of diameter of the DNA fragments, thus inducing an early onset of reptation at the applied voltage in the 100-300 V/cm range. In order to prove this hypothesis, "competing ions" (notably NaCl and KBr) were added to the His background electrolyte: a partial reversal of the His effect was already apparent at low concentrations of such ions (10 mM) and was complete at higher concentrations (30 and 50 mM). By molecular modeling, it was found that His could be docking on the negatively charged oxygen (bound to the phosphate) by offering both charged (primary and tertiary amino) groups to simultaneous binding, thus forming a salt and neutralizing the negative charge borne by the oxygen. The following characteristic bond distances were found: 0.34 nm between the N (imidazolic) and O; 0.32 nm between the primary N and O; 0.36 nm between the two nitrogens engaged in salt formation with the oxygen. In addition, for complexation to occur, the distance between the noncharged nitrogen in the imidazole ring and the nearest phosphate oxygen (engaged in the phosphodiester bridge) should be 0.44 nm. Under these conditions, the two rings present (a six-membered, ideal one, salt-linked with the oxygen and rather highly elongated, and the imidazole) will not be precisely coplanar, since the primary and tertiary nitrogens will be one slightly above and one slightly below the plane of the drawing. Upon extensive binding, occupying every available phosphate site, pi-pi interactions could occur among the stacks of bound His residues, thus further stabilizing the complex.

Buffers↗

Human globin chain separation by capillary electrophoresis in acidic isoelectric buffers.

A simple and reliable method, utilizing capillary electrophoresis in uncoated capillaries in acidic isoelectric buffers, is reported for screening for thalassemia and other defects on the synthesis of human globin chains. A solution of 50 mM iminodiacetic acid (pI 2.23), containing 7 M urea and 0.5% hydroxyethylcellulose (apparent pH 3.2) is used as background electrolyte for fast separation of heme-free, denatured globin (alpha, beta and gamma) chains. Due to the low conductivity of such a buffer, high voltage gradients (600 V/cm) can be applied, thus reducing the separation time to only a few minutes. It is additionally shown that inclusion of 2% surfactant (Tween 20) in the background electrolyte induces the splitting of the gamma chains into two zones, called Agamma and Ggamma, which represent the products of two genes coding for Ala or Gly as residue 136 of the chain.

Acids↗

Optimized detection of DNA point mutations by double gradient denaturing gradient gel electrophoresis.

Denaturing gradient gel electrophoresis displays the highest detection rate among mutation scanning methods. In classical denaturing gradient gel electrophoresis the denaturant gradient range and migration times vary for every amplicon to be scanned, greatly affecting the routine application of the method. As an alternative, we developed double gradient denaturing gradient gel electrophoresis where a gradient of pore size is superimposed over the denaturing one, allowing maintenance of the zone-sharpening effect even over prolonged time runs, and adoption of identical run time conditions for all fragments analyzed. Here double gradient denaturing gradient gel electrophoresis has been applied to the analysis of a number of point mutations and polymorphisms located in several exons of three different genes, the cystic fibrosis transmembrane conductance regulator, the beta-globin and the p53 genes.

Cystic Fibrosis Transmembrane Conductance Regulato↗

Rapid capillary zone electrophoresis in isoelectric histidine buffer: high resolution of the poly-T tract allelic variants in intron 8 of the CFTR gene.

The poly-T tract in intron 8 of the cystic fibrosis conductance transmembrane regulator (CFTR) gene exists in three variants, 5T, 7T, and 9T. The 7T and 9T variants generate a predominantly normal transcript, whereas the 5T variant engenders an anomalous product. The analysis of the poly-T tract is assuming increasing relevance, both to assess the implication of the CFTR gene in congenital bilateral absence of the vas deferens and to evaluate genotype-phenotype correlation in cystic fibrosis. Mapping of the poly-T tract has been performed by cumbersome and time-consuming methodologies. Capillary zone electrophoresis, combined with laser-induced fluorescence detection, was introduced for a rapid separation of the poly-T tract amplified products. As separation buffer, we adopted 200 mmol/L histidine (pH = pI = 7.6), and the capillary was filled with 10% polyacrylamide, allowing separations in less than 10 min. Capillary zone electrophoresis results were in perfect agreement with dot-blot analysis.

Alleles↗

Electrophoresis gel media: the state of the art.

Some unique events have occurred in the last few years which might revolutionize the field of polyacrylamide gel electrophoresis. While it was widely recognized that such matrices could normally be cast with a small pore size distribution, typically of the order of a few nanometers diameter (for protein sieving), recent developments suggest that "macroporous" gels could also be produced in the domain of polyacrylamides. If constraints to chain motion are imposed during gel polymerization, large-pore structures can be grown. Such constraints can originate either from low temperatures or from the presence of preformed polymers in the gelling solution; in both cases, the growing chains are forced to "laterally aggregate" via inter-chain hydrogen bond formation. Upon consumption of pendant double bonds, such bundles are frozen in the three-dimensional space by permanent cross-links. As an additional development, a novel photopolymerization system is described, comprising a cationic dye (methylene blue) and a redox couple (sodium toluene sulfinate, a reducer, and diphenyliodonium chloride, a mild oxidizer). Methylene blue catalysis is characterized by a unique efficiency, ensuring >96% conversion of monomers, even in hydro-organic solvents and in the presence of surfactants, which normally quench or completely inhibit the persulphate-driven reaction. In addition, methylene blue-sustained photopolymerization can be operated in the entire pH 3-10 interval, where most other systems fail. Perhaps the most striking novelty in the field is the appearance of a novel monomer (N-acryloylaminopropanol, AAP) coupling a high hydrophilicity with a unique resistance to alkaline hydrolysis. Given the fact that a poly(AAP) matrix is 500 times more stable than a poly(acrylamide) gel, while being twice as hydrophilic, it is anticipated that this novel chemistry will have no difficulties in replacing the old electrophoretic anticonvective media. The review ends with a glimpse at novel sieving media in capillary zone electrophoresis: polymer networks. Such media, by providing an almost infinite range of pore sizes, due to the absence of a rigid support, allow sieving mechanisms to be operative over a wide interval of particle sizes, even up to genomic DNA. Viscous solutions of polymer networks, made with the novel poly(AAP) chemistry, allow repeated use of the same separation column, well above 50 injections. Silica-bound poly(AAP) chains provide effective quenching of electroosmosis and >200 analyses by isoelectric focusing.

Acrylamides↗

Current trends in capillary isoelectric focusing of proteins.

Isoelectric focusing (IEF) in thin capillaries is reviewed here. After an introduction on the genesis and chemistry of the carrier ampholyte buffers, different approaches to IEF are discussed and evaluated. The classical approach consists on IEF under conditions of suppressed electroosmotic (EOF) flow, usually obtained by covalently bonding hydrophilic polymers to the inner capillary wall. The other approach consists of IEF in dynamically (and partially) coated capillaries, so as to allow a reduced EOF flow to coexist with the IEF process, so that focusing and transport of the train of stacked bands occurs simultaneously. The various experimental parameters: focusing, elution and detection steps, pI measurements, as well as typical drawbacks, such as isoelectric precipitation are evaluated. The review ends with some examples of analytical separations, at the moment mostly limited to focusing of native hemoglobins (normal and point mutants). These separations are compared with those obtained by slab-gel IEF and in immobilized pH gradients.

Animals↗

Non-isocratic capillary electrophoresis for detection of DNA point mutations.

Capillary electrophoresis under non-isocratic conditions is reviewed here. In particular, these conditions are elicited by programming the temperature over the run, just as in temperature-programmed gas chromatography. There is at least one major instance in which this technique is particularly useful: detection of DNA point mutations in PCR-amplified DNA fragments. In this case, migration of DNA homo- and hetero-duplexes against a denaturing gradient (either thermal or chemical) is the only technique capable of developing a pattern of four zones, indicative of the presence of a point mutation in genomic DNA, and due to the formation of two homo- (Wt/Wt, M/M, where Wt = wild type and M = mutant) and two hetero- (Wt/M and Wt/M) duplexes, formed by fully denaturing and then re-annealing the Wt and M filaments in solution. It is demonstrated that it is possible to obtain such gradients (which do not exist in space, i.e., along the length of the capillary, but in time), simply by producing voltage ramps, which in turn generate temperature ramps from within the capillary lumen, rather than from without, by circulating liquids and thermostats. This technique can be applied to any possible type of mutation, from low- to intermediate to high-melters, i.e., from 40 degrees C up to 60-65 degrees C. Examples of separations of point mutations in the cystic fibrosis transmembrane regulator gene and in the beta-globin chain gene are shown.

DNA↗

Study of haptoglobin-hemoglobin complexes by titration curves, capillary electrophoresis and capillary isoelectric focusing.

A novel method is described for monitoring complex formation between macromolecules, based on combined isoelectric focusing-electrophoresis in capillaries. The example studied is the binding of serum haptoglobin (Hp) to hemoglobin (Hb). A known amount of Hb is focused in a capillary in a pH 6-8 range (pI of Hb = 7.0) and thus kept temporarily "immobilized" in the electrophoretic chamber. Subsequently, increasing amounts of ligand (Hp) are loaded cathodically and allowed to sweep past the focused Hb zone. As the complex formed has a pI value well-outside the bounds of such a pH gradient (the 1:1 molar Hb-Hp complex has a pI of 5.5, the 1 to 1/2 molar Hp-Hb complex has a pI of 5.0) it escapes immobilization and moves past the detector window, where it is monitored and quantified. Since the detector is set at 416 nm, where only Hb absorbs, and since the molar extinction coefficient of Hb is well known, it is quite easy to calculate the molar amount of Hb bound to the complex. As an additional check, the amount of unreacted Hb can now be mobilized by disrupting the pH gradient and allowing this residual free Hb to also reach the detector and be quantified. The method is easy, fast, simple and fully automated and thus could represent a valid alternative to existing methods in clinical chemistry for quantifying the amount of Hp in human sera in pathological conditions, such as hemolytic anemias and transfusion reactions.

Ampholyte Mixtures↗

Recent advances in capillary electrophoresis of DNA fragments and PCR products in poly(n-substituted acrylamides).

In this article, capillary electrophoresis of DNA fragments and polymerase chain reaction products in sieving liquid polymers is reviewed. The first part of the review is dedicated to the development of N-substituted acrylamides, which in general guarantee a greater resistance to hydrolytic attack. Among the various monomers developed, an outstanding molecule appears to be N-acryloyl aminopropanol (AAP), which combines an extreme resistance to alkaline hydrolysis (500 times greater than plain acrylamide) with a substantially higher hydrophilicity. Poly(AAP) matrices exhibit a unique behavior in DNA separations, especially at high temperatures (60 degrees C), where most other matrices fail. In separation of antisense oligonucleotides, isoelectric buffers allow very high field strengths (up to 800 V/cm) due to their extremely low conductivity, thus permitting separations on the order of a few minutes. Among such buffers, histidine (pH = pI = 7.47) and lysine (pH = pI = 9.74) appear to be the best ones. Detection of DNA point mutations is accomplished with a peculiar nonisocratic capillary zone electrophoresis (CZE), consisting of creating temporal thermal gradients, analogous to temperature-programmed gas chromatography. A unique approach is described, consisting of creating temperature gradients not with external thermostats, but with internal Joule effects produced by voltage programming (which results in temperature ramps). The review ends with some unique applications of CZE: the possibility of precise gene dosage, relying on on-line detection and quantitation of the separated peaks. Examples of such gene dosages are given, such as assessment of Down's syndrome and determination of homozygous and heterozygous states of RhD blood groups.

Acrylamides↗

The free solution mobility of DNA.

The free solution mobility of DNA has been measured by capillary electrophoresis in the two buffers most commonly used for DNA gel electrophoresis, Tris-borate-EDTA (TBE) and Tris-acetate-EDTA (TAE). The capillaries were coated with polymers of either of two novel acrylamide monomers, N-acryloylaminoethoxyethanol or N-acryloylaminopropanol, both of which are stable at basic pH and effectively eliminate the electroendosmotic mobility due to the capillary walls. The free solution mobility of DNA in TAE buffer was found to be (3.75 +/- 0.04) x 10(-4) cm2 V-1 s-1 at 25 degrees C, independent of DNA concentration, sample size, electric field strength, and capillary coating, and in good agreement with other values in the literature. The free solution mobility was independent of DNA molecular weight from approximately 400 base pairs to 48.5 kilobase pairs, but decreased monotonically with decreasing molecular weight for smaller fragments. Surprisingly, the free solution mobility of DNA in TBE buffer was found to be (4.5 +/- 0.1) x 10(-4) cm2 V-1 s-1, about 20% larger than observed in TAE buffer, presumably because of the formation of nonspecific borate-deoxyribose complexes.

DNA↗

Capillary zone electrophoresis of oligonucleotides in isoelectric buffers and against a stationary pH gradient.

Capillary zone electrophoresis of oligonucleotides in a background electrolyte of two different types of stationary buffers is proposed: single, isoelectric amphoteres and focused carrier ampholytes. In the first case, two zwitterionic molecules are evaluated: lysine and histidine. Although the former has a five times higher buffering power (beta) at the pI (9.74) than the latter (pI 7.47), due to the favorable delta pK value (1.6 vs. 3) and thus should be the preferred species, a new parameter for evaluating the performance of isoelectric buffers is proposed: the beta/lambda ratio, i.e., the ratio between the buffering power and its conductivity. Ideal buffers are those with the highest beta/lambda ratio, since this allows delivering very high voltage gradients with minimal Joule effects. Since the pI of Lys is situated in a pH region (9.74) where bulk water begins to conduct, whereas His has a pI close to neutrality, the beta/lambda ratio is more favorable for His than for Lys. In the second case (zone electrophoresis of oligonucleotides against a preformed pH gradient), it is shown that migration against a pH 6.5-10 Pharmalyte carrier ampholyte pH gradient offers a unique analyte resolution. This is possibly due to two effects: (i) When injected at the alkaline extreme (ca. pH 10) of the pH gradient, the oligonucleotide zones undergo a stacking effect, with consequent zone sharpening, due to modulation of their free mobility via protonation of the -OH group (enolate ion) in the hetero aromatic rings of G and T, which undergo a lactam-lactim transition. (ii) As the zones migrate down the pH gradient, they transit through a pH 6.5-8.5 zone where, for Pharmalytes, the beta/lambda ratio reaches a maximum and is constant as well. This last condition allows high voltage gradients (typically 1000 V/cm, even in 75 microm capillaries) to be delivered, thus greatly reducing the analysis time and maintaining peak sharpness, due to limited diffusion.

Buffers↗

Temperature-programmed capillary electrophoresis for the analysis of high-melting point mutants in thalassemias.

The behavior of different sieving polymers for unambiguous determination of point mutations in genomic DNA, based on electrophoresis in thin capillaries, is evaluated. High melters from thalassemia patients are separated by exploiting the principle of denaturing gradient gel electrophoresis, in fact, of its variant utilizing temperature gradients (TGGE), along the migration path, encompassing the melting points of both homo- and heteroduplex, polymerase chain reaction (PCR)-amplified DNA fragments. Unlike TGGE, where the temperature gradient exists along the separation space, the denaturing temperature gradient in the fused-silica capillaries is time-programmed, so as to reach the Tm's of all species under analysis prior to electrophoretic transport past the detector window. The DNA fragments are injected in a capillary maintained (by combined chemical and thermal means) just below the expected Tm values. The deltaT applied is rather minute (1-1.5 degrees C) and the temperature gradient quite shallow (e.g., 0.05 degrees C/min). The denaturing thermal gradient is generated internally, via Joule heat produced by voltage ramps. This method is applied to the analysis of the most common point mutations in thalassemias, characterized by being high melters (in the temperature range of 60-62 degrees C) in presence of 6 M urea. Point mutants are fully resolved into a spectrum of four bands only when poly(N-acryloylaminopropanol) and hydroxyethylcellulose are used. However, the former offers the best separation capability at such high temperatures.

DNA↗

Capillary electrophoresis of DNA for molecular diagnostics.

A number of applications of capillary zone electrophoresis (CZE) in sieving liquid polymers (notably linear polyacrylamides and cellulose) for the analysis of polymerase chain reaction (PCR) products of clinically relevant, diagnostic DNA, are reviewed. The fields covered are: human genetics, quantitative gene dosage, microbiology and virology, forensic medicine and therapeutic DNA (notably, antisense nucleotides). Some unique, novel developments are highlighted, such as: (i) nonisocratic CZE, i.e., temperature-programmed CZE for detection of DNA point mutations; (ii) the synthesis of novel N-substituted acrylamides, offering extreme resistance to alkaline hydrolysis coupled to high hydrophilicity. In the field of denaturing gradient gel electrophoresis (DGGE), as routinely performed in gel slabs, a novel methodology is described in CZE: double-gradient DGGE. In this technique, two gradients are simultaneously applied along the migration direction: a chemical (or thermal) denaturing gradient, for partially unwinding homo- and hetero-duplexes of DNA, and a porosity gradient, for recompacting diffuse bands melting over a broader range of denaturing conditions. It is thus demonstrated that chemical gradients, in addition to temperature gradients, can be easily implemented even in a capillary format.

Bacterial Infections↗

Capillary zone electrophoresis of oligonucleotides and peptides in isoelectric buffers: theory and methodology.

The use of isoelectric buffers in capillary zone electrophoresis is reviewed. Such buffers allow application of extremely high voltage gradients (up to 1000 V/cm in relatively high bore capillary, e.g. 75 to 100 microm internal diameter), permitting separations of the order of a few minutes and thus favoring high resolution due to minimal, diffusion-driven peak spreading. The fundamental properties of ampholytes are first discussed, such as buffering power (beta) as a function of delta pK, i.e. of the distance between the pI value and neighboring protolytic groups. The highest possible relative beta value (= 2) is obtained for amphoteres possessing a delta pK = 0.6, a condition not met by existing amphoteric species. A novel parameter for ampholyte evaluation is then proposed, namely the beta/lambda ratio, i.e. the ratio between the beta power and conductivity at the pI value. It is additionally shown that the pI is not a constant value, but depends on ampholyte concentration in solution. In addition, at constant concentration, the theoretical pI can change as a function of delta pK. Isoelectric His and, to a lesser extent, Lys have been found to offer unique separations of oligonucleotides in sieving liquid polymers. In the absense of sieving media, isoelectric Asp, in presence of 7 M urea (apparent pH 3.77), permits unique separations of oligonucleotides having the same length but different nucleotide composition. Isoelectric Asp (pI 2.77 at 50 mM concentration) provides a medium of high resolving power for generating peptide maps. In difficult cases, of coincident titration curves, the pH can be moved up to higher values (e.g. pH 3.0 for 30 mM Asp) thus eliciting separation of unresolved peptides at pH 2.77. This was illustrated by running peptide maps of tryptic digests of human beta-globin chains. Also imino diacetic acid (pI 2.33 at 50 mM concentration) allows generation of high resolution peptide maps.

Buffers↗

Electrophoresis of DNA sequencing fragments at elevated temperature in capillaries filled with poly(N-acryloylaminopropanol) gels.

The performance of poly(N-acryloylaminopropanol) (poly AAP) gel columns, proved to be stable during electrophoresis at elevated temperature, was investigated. The column manufacturing procedure included the preparation of a coating of the inner wall of the fused silica capillary column with linear poly(AAP). Then, a mixture of the AAP monomer, the cross-linker dihydroxyethylenebisacrylamide (DHEBA) and linear poly(AAP) was introduced into the column and in situ polymerized (for preparation of linear gel columns, the addition of DHEBA was omitted). The poly(AAP) columns were first evaluated by electrophoresis of oligonucleotides at room temperature and at 50 degrees C, utilizing 260 nm UV-absorbance detection. In a further evaluation of column performance, samples of T-terminated DNA Sanger fragments from the bacteria Moraxella were separated at 200 V/cm electrical field strength, utilizing a 488 nm argon ion laser and a confocal optical setup for laser-induced fluorescence (LIF) detection. A temperature increase from 25 degrees C to 50 degrees C effectively released a compression of DNA bands. However, for cross-linked poly(AAP) gel columns, the elevated temperature resulted in a considerable reduction of the DNA sequence reading length. When a linear poly(AAP) column was utilized, no detrimental effect of elevated temperature on the separation could be observed.

Acrylic Resins↗

Separation of oligonucleotides of identical size, but different base composition, by free zone capillary electrophoresis in strongly acidic, isoelectric buffers.

A novel method for analyzing oligonucleotides of the same length, but bearing a single base substitution, is reported, based on free zone capillary electrophoresis (CZE) under rather acidic pH values. For this purpose, a set of four 18-mers of fairly random base composition has been synthesized, bearing, in nucleotide 9, the following bases: T, C, G or A. Theoretical predictions, based on titration curves of single free nucleotides, allowed us to predict that the simultaneous separation of a mixture of all four oligonucleotides could be possible in a pH 3-4 window. In fact, electrophoresis at pH 5.7 gave a single, asymmetric peak, whereas CZE at pH 4.8 could resolve three out of four species (the T9 and G9 oligonucleotides co-migrating into a single zone). A unique separation power could be obtained at pH 3.3 in a buffer comprising an amphoteric species (isoelectric iminodiacetic acid, IDA) and 7 M urea. Although IDA exhibited a pI of 2.23 (for a 100 mM solution), the addition of 7 M urea (necessary to denature the oligonucleotides) raised the apparent pH of the solution to 3.3.

Acids↗

Detection of p53 point mutations by double-gradient, denaturing gradient gel electrophoresis.

Genetic instability is a typical feature of tumor cells. This evidence has stimulated the development of rapid methods for detection of gene mutations. A new, improved protocol for denaturing gradient gel electrophoresis (DGGE), to screen for point mutations in genomic DNA, is reported: double gradient (DG) DGGE. In this technique, to the primary, denaturing gradient (typically 30-80% or 40-80% urea/formamide) a secondary gradient, colinear with the first, is superimposed: a porosity gradient (typically 6.5-12% polyacrylamide). The secondary gradient acts by recompacting smeared and diffuse bands of heteroduplexes, which are often indistinguishable from background fluorescence, and by augmenting the resolution between closely spaced homoduplex zones. This allows proper densitometric quantitation of the ratio of the two homoduplex bands. The reliability of this technique has been documented by detection of a number of mutations in exons 6 and 8 of the p53 gene which had escaped revelation by single-strand conformational polymorphism (SSCP) analysis. Additionally, the precise assessment of ratio of the doublet of homoduplex bands has allowed quantitation of the extent of p53 mutation in a mixed cell population extracted from a tumor specimen.

Electrophoresis, Polyacrylamide Gel↗