Separation of small DNA and RNA oligonucleotides by high-performance anion-exchange liquid chromatography

Anion exchange chromatography of oligonucleotides under denaturing conditions

Denaturing anion exchange HPLC simplifies the chromatographic profiles of self-complementary sequences such as d(CG)₆, d(CG)₆ with locked nucleic acid modifications, d(AT)₁₅, and polymerase chain reaction mixtures. These chromatographic conditions use eluents containing up to 4 M urea at pH 12.4, and lead to the abolishment of secondary structures and meaningful chromatographic patterns of self-complementary sequences. Similarly, PCR template, FAM-labelled primer and FAM-labelled PCR products were resolved, making interpretation of PCR reaction products possible.

A review on native and denaturing purification methods for non-coding RNA (ncRNA)

Recently, non-coding RNA (ncRNA) became the centerpiece of human genome research. Modern ncRNA-based research has revolutionized disease diagnosis and therapeutics. However, decoding structural/functional information of ncRNA requires large amount of pure RNA, and hence effective RNA preparation and purification protocols. This review focuses on purification schemes of synthetic oligonucleotides, particularly liquid chromatographic (LC) techniques as improved alternatives to urea-polyacrylamide gel electrophoresis (urea-PAGE) purification. Moreover, the review summarizes the shortcomings of urea-PAGE purification method and details the chromatographic purification such as affinity, ion-exchange (IE) or size-exclusion (SE) chromatography. Specifically, we discuss denaturing and native RNA purification schemes with newest developments. In short, the review evaluates nucleic acid purification schemes required for various structural analyses.

Discovered triethylamine as impurity in synthetic DNAs for and by electrochemiluminescence techniques

The purity of the synthetic oligonucleotides is very important because it is crucial for the accuracy of the established biological assays. Herein, it was discovered that one impurity in synthetic DNAs might affect the experiment results of electrochemiluminescence (ECL) detection techniques, which was never reported before. According to a series of experiments using ECL detection methods combined with capillary electrophoresis (CE) (CE-ECL), the impurity was identified as triethylamine (TEA), which came from incomplete removal after HPLC purification of synthetic DNAs. Moreover, CE-ECL technique was for the first time to be proposed for discovering, identifying and sensitive determining the possible impurity such as TEA in various DNA samples, which was usually neglected by other detection techniques for purification quality control of synthetic oligonucleotides. A detection range from 5.00×10(-10) to 2.00×10(-5) M with a detection limit as low as 50 nM (S/N=3) was reached for TEA. Through further designed ECL methods and data analysis, situations which would be really affected by the impurity of TEA were studied. To avoid or eliminate the impact of the TEA impurity on ECL applications, judgment basis for choosing purification ways was discussed according to individual requirements.

Studies on the nucleotide arrangement in DNA. Estimation of sequence isomers in pyrimidine deoxyribo-oligonucleotides

The population of pyrimidine deoxyribo-oligonucleotides obtained from DNA may be separated, first, into fractions comprising identical lengths (isotichs) and, subsequently, into the individual components of an isostich fraction varying in the cytidylic and thymidylic acid composition. At a third level of analysis the proportion of components exhibiting the same composition but different sequence may be determined. Selective removal of cytosine and the subsequent analysis for characteristic thymidine derivatives released during an acid-catalyzed beta-elimination reaction allowed estimation of the relative proportion of sequence isomers for pyrimidine isostichs of length two to five.

[Preparative isolation of hexa-, hepta-, octa-, nona- and decapyrimidine oligonucleotides from hydrolysates of depurinated herring sperm DNA]

The pyrimidine oligonucleotides (dT)5; (dT)6 and the mixtures of sequence isomers (dC, dT5); (dC2, dT5); (dC3, dT4); (dC4, dT3); (dC4, dT4); (dC3, dT5); (dC2, dT6); (dC4, dT5); (dC3, dT6); (dC2, dT7); (dC5, dT5); (dC4, dT6) and (dC3, dT7) with or without terminal phosphate groups have been isolated on a preparative scale from hydrolysates of depurinated herring sperm DNA by the following procedure. Herring sperm DNA (1 kg) is chemically depurinated and partially hydrolysed to a mixture of pyrimidine nucleotides. The partial hydrolysate is first separated into a low- and a high-molecular-weight pyrimidine nucleotide mixture by column chromatography on DEAE-cellulose. The mixture of high-molecular-weight pyrimidine nucleotides is subsequently fractionated on QAE-Sephadex. Impurities which are not fully removed by column chromatography are separated by paper chromatography. The compositions of the mixtures of sequence isomers are determined from the data of column, paper and homochromatography; from absorption characteristics and by enzymatic degradation.

Separation and sequencing of the sequence isomers of pyrimidine deoxypentanucleoside tetraphosphates by high-performance liquid chromatography

Chemical synthesis of DNA fragments with a defined sequence is extremely long and complex. A simpler alternative is isolation of fragments from partially hydrolysed DNA. Mixtures of sequence isomers of pyrimidine oligonucleotides were recently isolated on a preparative scale from hydrolysates of depurinated herring sperm DNA. These, however, could not be further separated by conventional techniques. Using high-performance liquid chromatography (HPLC), sequence isomers of pyrimidine di-, tri- and tetranucleotides were successfully separated and sequenced. In the present work, separation and sequencing of sequence isomers of pyrimidine pentanucleotides by HPLC was achieved, demonstrating the applicability of this particular approach in preparation of desired DNA fragments.