Recent advances in capillary electrophoresis of DNA fragments and PCR products.
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Bacillus anthracis↗
Biomedical subjects
C Gelfi
Publications and source records attributed to C Gelfi.
Double-gradient DGGE for optimized detection of DNA point mutations.
A novel technique is reported for screening point mutations is genomic DNA: double gradient, denaturing gradient gel electrophoresis (DG-DGGE). Unlike conventional DGGE, which exploits a single gradient of denaturing chemicals (typically urea and formamide) along the migration path to force the two hetero- and two homo-duplexes to partially unwind and separate, DG-DGGE superimposes a second (porous) gradient over the denaturing one. With the help of the sieving gradient, molecules such as the hetero-duplexes, which often produce curtains and smears instead of sharp zones, due to lack of a sharp melting transition, are re-compacted into remarkably narrow bands. Even homo-duplexes with minute melting temperature differences, giving a single band in DGGE, are resolved into two zones in DG-DGGE. The technique has been applied to the analysis of a number of point mutations in several exons of the cystic fibrosis transmembrane conductance regulator gene.
Cystic Fibrosis↗
Rapid detection of 21-hydroxylase deficiency mutations by allele-specific in vitro amplification and capillary zone electrophoresis.
A quick diagnosis of the classic form of 21-hydroxylase deficiency (simple virilizing and salt wasting) is of great importance, especially for prenatal diagnosis and treatment in pregnancies at risk. A method for simultaneous detection of common point mutations in the P450c21 B gene is here proposed by combining a nested PCR amplification refractory mutation system (ARMS) with capillary zone electrophoresis (CZE) in sieving liquid polymers. In the first PCR, B genes are selectively amplified. In the nested reaction, ARMS-detected wild-type and mutated alleles are separately pooled and resolved by CZE. CZE is performed in coated capillaries in the presence of 30 g/L hydroxyethyl cellulose in the background electrolyte for size separation of the DNA analytes. For high-sensitivity detection the electrophoresis buffer contains the fluorescent dye SYBR Green I. Laser-induced fluorescence detection is obtained by excitation at 488 nm and signal collection at 520 nm. Specificity and reproducibility of the protocols were established by using samples from 75 Italian families with 21-hydroxylase deficiency already genotyped by allele-specific oligonucleotide hybridization or direct sequencing. Whereas dot-blot is time consuming because of the high number of hybridizations with radioactive probes, this present protocol is more rapid, giving sufficient separation on CZE after PCR reactions without preconcentration or desalting of samples.
Adrenal Hyperplasia, Congenital↗
Novel acrylamido monomers with higher hydrophilicity and improved hydrolytic stability: I. Synthetic route and product characterization.
The novel acrylamido monomer reported by our group (N-acryloylaminoethoxyethanol, AAEE; Chiari et al., Electrophoresis 1994, 15, 177-186), found to combine high hydrophilicity with extraordinary resistance to alkaline hydrolysis, has come under closer scrutiny due to unexpected and random autopolymerization while stored as a 1/1 v/v water solution at 4 degrees C (possibly due to a greater oxidability of the ether group). We have additionally found a unique degradation pathway of the monomer, called "1-6 H-transfer", by which the C1 (on the double bond site), by constantly ramming against the C6, next to the ether oxygen (O7, which in fact favors the transfer of the hydrogen atom by C1), produces radicals which more efficiently add to the monomer favoring autopolymerization and cross-linking. A number of novel monomers is proposed while maintaining the other unique characteristics of AAEE. One of them, N-acryloylaminopropanol, offers all the unique, special qualities of AAEE, without the noxious aspects of autopolymerization. Additionally, a synthetic route was optimized, yielding an essentially pure product in a single reaction step, with a yield > 99% and an equivalent purity (> 99%). The synthesis consists in reacting acryloyl chloride at -40 degrees C in presence of a twofold molar excess of aminopropanol and in ethanol (instead of methanol) as solvent. Other solvents, as well as the use of triethylamine for neutralizing the HCl produced, were found to give a variety of undesired byproducts.
Acetone↗
Novel acrylamido monomers with higher hydrophilicity and improved hydrolytic stability: II. Properties of N-acryloylaminopropanol.
The physico-chemical properties and the electrophoretic behavior of the novel set of monomers reported by (Simò-Alfonso et al., Electrophoresis 1996, 17, 723-731) have been evaluated. Of utmost importance was the combination of high hydrophilicity and extreme hydrolytic stability, most desired properties for, any electrophoretic matrix, especially for protein fractionation. One of these monomers (N-acryloylaminopropanol, AAP) was found indeed to be extremely hydrophilic (with a partition coefficient P of only 0.10, vs. P = 0.13 for N-acryloylaminoethoxyethanol and P = 0.20 for acrylamide) and to possess excellent stability to alkaline hydrolysis. Its hydrolysis constant (0.008 L mol-1 min-1), as a free monomer, in an alkaline milieu, was found to be about one order of magnitude lower than conventional acrylamide (0.05 L mol-1 min-1). In the polymer state, the resistance to hydrolysis of poly(AAP) was assessed as 500 times greater than a conventional poly(acrylamide) matrix.
Acrylamides↗
Novel acrylamido monomers with higher hydrophilicity and improved hydrolytic stability: III. DNA separations by capillary electrophoresis in poly (N-acryloylaminopropanol).
Separation of DNA fragments in a novel polymer network, consisting of N-acryloylaminopropanol (AAP) is reported. The performance of this novel monomer, as a sieving liquid polymer in capillary zone electrophoresis, was evaluated. In 50 microns ID capillaries, an 8% solution of poly (AAP) can afford apex-resolution of the 123/124 bp adjacent pair of DNA fragments in marker V, typically unresolved in any poly (acrylamide) formulation. It is proposed that the distal-OH group in the AAP molecule can form transient H-bonds with the DNA double helix. Molecular modeling shows a meandering structure for poly (AAP), lacing the walls of half a cylinder, with kinks protruding at regular intervals, potentially able to fit into the major groove of DNA. Contrary to previously held beliefs, there seems to be a minimum length of the polymer for proper sieving of DNAs. For poly (acrylamides), a weight average molecular mass Mw 30 000 polymer offers no resolution, whereas a polymer of 250 000 to 400 000 Da exhibits optimum resolving power. For poly (AAP), the optimal length is in excess of 450 000 Da in Mw. Thus, it is shown that both the chemical composition of the monomer and the length of the polymer play a subtle, cooperative role in DNA separation.
Acrylic Resins↗
Comparison of behavior of N-substituted acrylamides and celluloses on double-stranded DNA separations by capillary electrophoresis at 25 degrees and 60 degrees C.
The behavior of N-substituted poly(acrylamides) and of cellulose in the separation of double-stranded DNA by capillary zone electrophoresis (CZE) is evaluated. Contrary to previously held belief, which attributed best separations in poly(acrylamides) to small DNA fragments (typically in the 50-1000 bp size range) and in celluloses to large DNA fragments, we show that also celluloses can achieve fine sieving of short DNA sizes provided they are used at much higher concentrations than previously reported. For example, in the case of hydroxyethylcellulose (HEC), typically used at 0.2-0.8% concentrations, levels of 3% produce excellent patterns, at 25 degrees C, in the 50-600 bp size range. If separations are conducted at 60 degrees C, sieving is lost in most liquid polymers. However, if the concentration of HEC is raised to 6% and that of hydroxypropylmethylcellulose (HPMC) above 1%, sieving is fully restored. Also, N-substituted acrylamido derivatives, notably N-acryloylaminoethoxyethanol (AAEE) and N-acryloylaminopropanol (AAP) offer excellent performance at both 25 degrees and 60 degrees C, whereas plain poly(acrylamide) irreversibly collapses at high temperatures, possibly due to intrinsic instability of the amido bond under such harsh conditions. Among all the polymers investigated, an 8% solution of poly(AAP) offers the best performance and highest theoretical plates in the 25 degree-60 degree C interval. Separations at high temperatures are necessary when dealing with detection of point mutations in temperature-programmed CZE and are preferred in DNA sequencing. Two additional advantages are evident when running DNA separations at 60 degrees C: a marked reduction of analysis times and a linearization of the transit times of the larger (434-587 bp) DNA fragments, in all polymers tested.
Acrylamides↗
Capillary electrophoresis of oligonucleotides in sieving liquid polymers in isoelectric buffers.
Analysis of oligonucleotides (especially in regard to assessing the purity of antisense compounds) is typically performed in 18% T sieving liquid polyacrylamide, in 30% formamide and 7 M urea. Up to 600 V/cm have been reported, with transit times, for 20 to 25 oligomers, of 15-20 min. We show that the same analysis can be performed in isoelectric buffers, typically histidine (His), and in more dilute linear polyacrylamides, e.g. 10% T (at 0% C), with much reduced analysis times. A series of His concentrations has been explored, ranging from 25 to 150 mM. Best performance is obtained in 100 mM His (at pH = pI, i.e., 7.47 at 25 degrees C), dissolved in 7 M urea, in presence of 10% sieving liquid linear polyacrylamide. Such a buffer allows delivering 800 V/cm without any loss of resolution due to Joule heating, with retention of very high resolving power down to fragments as short as tetranucleotides. Under these conditions, the analysis time for an antisense oligonucleotide containing fragments from a 10-mer to 18-mer is in a time window of 4-5 min. It is shown that the smallest fragment (10-mer) migrates in the capillary at the remarkable speed of 5 cm/min.
Buffers↗
Quantitation of glycated hemoglobins in human adult blood by capillary isoelectric focusing.
A precise and reproducible method for assessment of glycated hemoglobin in human adult red blood cells is reported, based on capillary isoelectric focusing (IEF). In order to obtain baseline resolution between adult hemoglobin (Hb A) and its glycated form (Hb A1c), two species which differ by minute delta pI values, < 0.03 pH units, the following procedure was adopted: the focusing mixture consisted of 5% Ampholine, pH 6-8, 0.5% Pharmalyte, pH 3-10, 3% short-chain liquid polyacrylamide and an equimolar mixture of two "separators", 0.33 M beta-alanine and 0.33 M 6-aminocaproic acid. The last two compounds flatten the pH gradient in the pI region of the two Hbs, thus allowing full separation. Additionally, the Hb samples, instead of being pulse-loaded, are uniformly distributed in the background electrolyte. A longer capillary life-time is obtained if all nonbuffering ions are eliminated; thus, as catholyte, 50 mM Lys (pH 9.7) is utilized and as anolyte 50 mM acetic acid (pH 3.5) is adopted. The percentages of Hb A1c, as obtained by capillary IEF, are in good agreement (+/- 6%) with data obtained by one of the standard zone electrophoretic methods in clinical chemistry, i.e., the Helena REP Glyco gel system.
Acrylic Resins↗
Rh D/d genotyping by quantitative polymerase chain reaction and capillary zone electrophoresis.
A safe and reliable method for determining RhD type (positive or negative) and zygosity (D/D or D/d) could have applications, for instance, in the prediction of the D genotype of a father in couples where there is an RhD-negative woman at risk of fetal alloimmunization. Capillary zone electrophoresis (CZE) is proposed as a novel, reliable and powerful method for quantitative evaluation of polymerase chain reaction (PCR) products. RhD is determined by amplifying a 136 bp region common to the RhCcEe and RhD genes and a 186 bp region specific of the RhD gene. RhD positive and negative samples are identified by polyacrylamide gel slab electrophoresis, followed by silver staining of the DNA bands, and by CZE in sieving liquid polymers, with direct on-line peak densitometric evaluation by exploiting the intrinsic UV absorbance of the DNA fragments at 254 nm. The CZE method allows not only a reliable assessment of the RhD type (the presence of both 136 bp and 186 bp fragments indicating an RhD-positive type, the presence of only the 136 bp fragment indicating an RhD-negative type), but also a rapid determination of the zygosity based on the quantitative expression ratio of the 136 bp/186 bp pair. Thus, a 2:1 peak ratio clearly indicates a D/D homozygous individual, whereas a 3:1 peak ratio gives evidence of a D/d heterozygous individual.
DNA↗
Isoelectric focusing in immobilized pH gradients.
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Acrylamides↗
Analysis of antisense oligonucleotides by capillary electrophoresis, gel-slab electrophoresis, and HPLC: a comparison.
Three techniques are evaluated for assessing the purity of synthetic oligodeoxyribonucleotides: reversed phase high-performance liquid chromatography (RP-HPLC), polyacrylamide gel-slab electrophoresis (PAGE), and capillary zone electrophoresis highly concentrated (18% T) entangled polymer networks (CZE). RP-HPLC does not seem to be able to discriminate and resolve the spectrum of failed sequences expected to accompany an oligonucleotide of a given length. The purity data, as given by the manufacturer, are most often close to 100%. PAGE in 20% T matrices, followed by ethidium bromide staining, gives a good resolution of failure sequences and purity assessments decidedly more realistic. CZE in 18% liquid polyacrylamide is able to resolve to baseline all shorter fragments and to give a precise evaluation of the amount of impurities, based on the intrinsic DNA absorbance at 254 nm. Most of the 18 mer oligonucleotides (and of their phosphorothioate derivatives) analyzed by us, as supplied by three different manufacturers, were found to be contaminated by a spectrum of failed and truncated sequences, ranging in size from 7 mer to 17 mer. The purity data rarely exceeded 80% and most often were of the order of 60%-70%. Conditions for a good routine performance of the CZE technique are described.
Base Sequence↗
Temperature-programmed capillary electrophoresis for detection of DNA point mutations.
A method for unambiguous determination of point mutations in genomic DNA, based on electrophoresis in thin capillaries, is reported here. The method is based on the principle of temperature gradient gel electrophoresis (TGGE), a variant of denaturing gradient gel electrophoresis (DGGE), and exploits the differential melting of mutant and wild-type PCR-amplified DNA fragments during electrophoresis through a temperature gradient. 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 melting points (Tms) 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 temperature increment applied is typically minute (1 degree -1.5 degrees C) and the sweep speed is rather shallow (e.g., 0.05 degree C/min). Additionally, the denaturing thermal gradient is not controlled externally, but generated internally by Joule heat produced by voltage ramps. Point mutants are fully resolved into a spectrum of four bands, with a dynamic range extending from 45 degrees C (low melters) up to 70 degrees C for high melters. The present method can thus be universally applied to any type of point mutation.
DNA↗
Gene dosage in capillary electrophoresis: pre-natal diagnosis of Down's syndrome.
Modern proposals for pre-natal genetic analysis of Down's syndrome consist in isolating DNA from amniotic cells and amplifying a highly polymorphic small tandem repeat region of the chromosome 21-specific D21S11 marker. The polymerase-chain-reaction-amplified fragments are typically 5'-end labelled with a green or blue fluorescent reporter and data acquisition occurs on-lane in DNA sequencing gel-slabs and equipment. The following patterns are expected: for normal individuals, 1 peak or two peaks in a 1:1 ratio. In the case of trisomy 21, the following patterns are found: either three peaks in a 1:1:1 ratio or a two-peak profile with a 2:1 gene ratio. We have developed a capillary electrophoretic system, offering precise diagnostic value by exploiting the intrinsic DNA absorbance at 254 nm. The separation occurs in capillaries coated with an extremely stable and hydrophilic layer of poly(N-acroyloyl amino ethoxy ethanol) and filled with a background electrolyte consisting of 89 mM Tris-borate, 2 mM EDTA, 2.5 microM ethidium bromide and 8% short-chain, low-viscosity, replaceable, liquid, linear, sieving polyacrylamide. The technique offers high reproducibility and precise on-line, automated peak acquisition and quantitation.
DNA Primers↗
CAG triplet analysis in families with androgen insensitivity syndrome by capillary electrophoresis in polymer networks.
The potential use of capillary zone electrophoresis in polymer networks (linear polymers above the entanglement threshold, added to the background electrolyte for sieving purposes) for analysis of DNA fragments amplified by a polymerase chain reaction, is shown. In typical runs, the capillary is filled with Tris-borate-EDTA buffer, at pH 8.3, containing 6% linear polyacrylamide as a dynamic sieving matrix. Such formulations allow replenishing the capillary with fresh sieving solution when resolution decays after prolonged use (typically > 30 injections per capillary are obtained). The DNA fragments are detected by their intrinsic absorbance at 254 nm. This system has been applied to the analysis of CAG triplet polymorphism in families carrying the androgen insensitivity syndrome. While easy separation is obtained for fragments 139 base pairs (bp) and 160 bp (in families carrying a difference of 7 CAG repeats) even more difficult cases (such as those of families exhibiting fragments of 136 and 139 bp, thus differing by only one CAG repeat) are resolved with precision and diagnostic value.
Androgen-Insensitivity Syndrome↗
Separation and quantitation of reverse transcriptase polymerase chain reaction fragments of basic fibroblast growth factor by capillary electrophoresis in polymer networks.
In human ovarian carcinomas (epithelial and endometrial tumors) the presence of mRNA coding for the basic fibroblast growth factor (bFGF) was previously demonstrated by reverse transcription-polymerase chain reaction (PCR). For quantitation purposes, competitive PCR is adopted, using a competing fragment a sequence of a highly homologous bovine bFGF. However, separation and detection of the PCR products by slab gel electrophoresis and ethidium bromide staining gives poor quantitative data due to the nonstoichiometric binding of the dye. Thus, the only possible quantitation that can be obtained is via autoradiography with 32P-labeled primers. We report here a capillary electrophoresis protocol, in 6% linear, liquid polyacrylamide as a sieving system, able to fully resolve and quantify the undigested (354 bp) bovine and the digested (295 bp and 59 bp) human fragments, with peak ratios in good agreement with the autoradiographic data.
Adrenal Cortex↗
Screening of umbilical cord blood hemoglobins by isoelectric focusing in capillaries.
Separation and quantitation of the three main hemoglobin components of umbilical cord blood (fetal, acetylated fetal and adult hemoglobins; Hb F, Fac, A) by capillary isoelectric focusing (IEF) in a pH 6-8 gradient is reported. Even in coated capillaries (with covalently bound chains of linear acrylamido derivatives, notably N-acryloylaminoethoxyethanol), no base line separation is obtained between Hb F and A, although this is routinely achieved in gel slab IEF. However, when the carrier ampholyte buffers were added to 3% short-chain liquid linear polyacrylamide, base line resolution and stabilization of peak transit times were obtained. This suggests that even in the best coating procedures, patches of the inner capillary surface could still be naked, so that the static coating is complemented by a dynamic coating on the unoccupied sites. An additional improvement in separation occurs if the above mixture, comprising 5% carrier ampholytes in the pH 6-8 range and 3% soluble polyacrylamide, is made to contain 50 mM beta-alanine, a "separator" known to flatten the pH gradient around pH 7. In the normal newborns analyzed (n = 30), the following average values were obtained: Hb F, 70.1% (range 65-75%); Hb A, 20.2% (range 15-25%); and HbFac, 9.5% (range 7-11%).
Acetylation↗
Amplification of 18 dystrophin gene exons in DMD/BMD patients: simultaneous resolution by capillary electrophoresis in sieving liquid polymers.
Duchenne (DMD) and Becker (BMD) muscular dystrophies are the two most common myopathies described so far. In the late 80s, Chamberlain et al. and Beggs et al. proposed two PCR assays allowing detection of over 98% DMD/BMD deletions. Since each of them is based on specific co-amplification of 9 dystrophin gene exons, a method attempting simultaneous analysis of DMD/BMD should offer unambiguous resolution and identification of 18 DNA fragments ranging in size from approximately 100 to 500 bp. We have developed a novel capillary electrophoresis method that allows simultaneous analysis of the two PCR sets with full diagnostic value. It consists of (a) an ultrastable inner capillary coating based on a novel acrylamide monomer (N-acryloyl amino ethoxy ethanol); (b) a very low viscosity (barely 70 mPa) sieving polymer solution, formed by short-chain (average mol wt of 230,000, 55,000 Mn) polyacrylamides; (c) substitution of four fragments in the classical multiplex reaction (181 and 535 bp in the Beggs, 416 and 459 bp in the Chamberlain) with four new fragments of different lengths (170, 313, 154 and 88 bp, respectively). These new conditions allow resolution and unambiguous identification of all 18 PCR-amplified fragments in a single electrophoretic run. The set of 18 fragments comprises the following: 88, 113, 139, 154, 170, 196, 202, 238, 268, 271, 313, 331, 357, 360, 388, 410, 506 and 547 bp.
Acrylic Resins↗