Analysis and purification of DNA restriction fragments by high-performance liquid chromatography

Novel method for DNA methylation analysis using high-performance liquid chromatography and its clinical application

The aim of this study was to develop a new methodology that is suitable for DNA methylation diagnostics and to demonstrate its clinical applicability. We developed a new anion-exchange column for high-performance liquid chromatography (HPLC) with electrostatic and hydrophobic properties. Both cytosine and thymine, corresponding to methylated and unmethylated cytosine after bisulfite modification, respectively, are captured by electrostatic interaction and then discriminated from each other by their hydrophobic interactions. The DNA methylation levels of synthetic DNA were quantified accurately and reproducibly within 10 minutes without time-consuming pretreatment of PCR products, and the measured values were unaffected by the distribution of methylated CpG within the synthetic DNA fragments. When the DNA methylation status of the FAM150A gene, a marker of the CpG island methylator phenotype specific to clear cell renal cell carcinoma (ccRCC), was examined in 98 patients with ccRCC, bulk specimens of tumorous tissue including cancer cells showing DNA methylation of the FAM150A gene were easily identifiable by simply viewing the differentiated chromatograms, even when the cancer cell content was low. Sixteen ccRCC showing DNA methylation more frequently exhibited clinicopathological parameters reflecting tumor aggressiveness (ie, a larger diameter, higher histological grade, vascular involvement, renal vein tumor thrombi, infiltrating growth, tumor necrosis, renal pelvis invasion and higher pathological TNM stage), and had significantly lower recurrence-free and overall survival rates. These data indicate that HPLC analysis using this newly developed anion-exchange column could be a powerful tool for DNA methylation diagnostics, including prognostication of patients with cancers, in a clinical setting.

Micropellicular stationary phases for high-performance liquid chromatography of double-stranded DNA

The central role of nucleic acids in biosciences has effectuated the rapid development of numerous techniques for their isolation, separation, characterization and quantitation. Advances in high-performance liquid chromatography, particularly the introduction of novel microparticulate sorbents, have greatly promoted the separation and quantitation of nucleic acids. Because of their favorable mass transfer properties, micropellicular packing materials are advantageous for fast and high-resolution separations of double-stranded (ds) DNA molecules. With micropellicular packings, anion-exchange and ion-pair reversed-phase chromatography are the most popular chromatographic separation modes for dsDNA. The effective separation mechanisms in both chromatographic techniques are preferably described by nonstoichiometric models, that are founded on a better physicochemical background than traditional stoichiometric models. Column efficiency, retention characteristics, and size or sequence dependency of retention of dsDNA are greatly influenced by the chosen operational variables in both chromatographic modes. The applicability of HPLC with micropellicular stationary phases nucleic acids research includes preparative DNA fractionation, DNA restriction mapping, analysis of polymerase chain reaction products and purification of plasmid DNA.

Improved procedure for the preparation of DNA restriction fragments suitable for sequencing

A rapid and integrated procedure was developed for the preparation of small DNA restriction fragments (< or = 1000 bp) starting from a large cosmid (35,000 bp) containing exogenous DNA. The process is based on restriction enzymatic digestion followed by HPLC separation and fractions collection. All DNA fragments are separated in a single run, detected "on-line" by UV absorption, and straightforward collected with very high recovery. Small fragments can be directly subjected to the sequence procedure, whereas those larger than 1000 bp are redigested with a second enzyme, the fractionated subfragments are separated, ligated to plasmid vector, and sequenced. A human genomic cosmid of 35,000 bp (26H7) has been chosen as a model.

Size-dependent chromatographic separation of nucleic acids

Chromatographic procedures currently used for the size-dependent fractionation of nucleic acids are reviewed. First, an attempt is made to clarify the concept of "size" of nucleic acids and then various aspects of the chromatography of nucleic acids are considered. It is emphasized that consideration of the dynamic three-dimensional structure of large polynucleotides in a rapidly flowing eluent is essential for both the better understanding of mechanism and the development of sophisticated procedures. Of the practical chromatographic techniques that are not based on true size fractionation, ion-exchange chromatography on non-porous column packings appears to be the most efficient. Other methods, such as hydrophobic interaction, are unlikely to become popular. As for truly size-dependent modes, there are gel permeation and slalom chromatography. Although media with extremely large pores become available, the efficiency of gel permeation is still low as a practical separation procedure for large nucleic acid molecules. Its best use seems to be in the field of physicochemical research into nucleic acids in solution. The newly discovered slalom chromatography is based on a principle completely different from all other chromatographic modes. It enables the efficient separation of large double-stranded DNA fragments of 5-50 kilo base pairs by discriminating their length. It has proved not only to be useful as a tool for nucleic acid research but also to have great significance in other fields, e.g. the hydrodynamics of polymer solutions, the search for new chromatographic modes, etc.

Efficient large-scale purification of restriction fragments by solute-displacement ion-exchange HPLC

Extreme overloading of HPLC columns with sample can create a condition of binding site saturation causing competition and displacement among solutes during column elution. This has been termed solute-displacement chromatography (SD-HPLC). We present an example of this phenomenon for the preparative fractionation and purification of restriction fragments of almost identical size (1337 and 1388 bp) which cannot be resolved by agarose gel electrophoresis. Standard analytical ion-exchange HPLC chromatography failed to separate these fragments from each other and from an unexpectedly early eluting pUC-derived vector fragment of 2.7 kbp. We demonstrate that by intentional overloading of the small (4.6 x 35 mm) non-porous TSK-DEAE HPLC column, hundreds of micrograms of DNA restriction fragments could be resolved and purified in a single HPLC run of less than 30 minutes.

Identification and purification of overlapping cosmid clones of the region Xq24-qter of human X chromosome using HPLC

The assembly of a large physical map of genomes requires simultaneous analysis of many cosmid clones for overlapping regions. The search for overlapping regions may be achieved by various means. High-performance liquid chromatography (HPLC) provides an alternative to gel electrophoresis since microgram amounts of each DNA fragment may be collected into individual test tubes for further analysis. HPLC has been used to identify overlapping cosmid clones from a pool of cosmid DNA containing the terminal portion of the long arm of the human X chromosome (Xq24-qter). Among 400 cosmids analyzed, 3 were shown to overlap.