Fractionation of biologically active messenger RNAs by HPLC gel filtration

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.

Synthetic oligonucleotides with particular base sequences from the cDNA encoding proteins of Mycobacterium bovis BCG induce interferons and activate natural killer cells

Thirteen kinds of 45-mer single-stranded oligonucleotide, having sequence randomly selected from the known cDNA encoding BCG proteins, were tested for their capability to augment natural killer (NK) cell activity of mouse spleen cells in vitro. Six out of the 13 oligonucleotides showed the activity, while the others did not. In order to know the minimal and essential sequence(s) responsible for the biological activity, 2 kinds of 30-mer and 5 kinds of 15-mer oligonucleotide fragments of an active 45-mer nucleotide were tested for their activity. One of the 30-mer oligonucleotides, designated BCG-A4a, was active, but the other 30-mer was inactive. All of the 15-mer oligonucleotide fragments were inactive. The BCG-A4a also stimulated the spleen cells to produce interferon (IFN)-alpha and -gamma. An experiment using anti-IFN antisera showed that the NK cell activation by the oligonucleotide was ascribed to the IFN-alpha produced. It was noticed that all of the biologically active oligonucleotides possessed one or more palindrome sequence(s), and the inactive ones did not, with an exception of a 45-mer inactive oligonucleotide containing overlapping palindrome sequences (GGGCCCGGG). These findings strongly suggest that certain palindrome sequences, like GACGTC, GGCGCC and TGCGCA, are essential for 30-mer oligonucleotides, like BCG-A4a, to induce IFNs.

The soluble glycoprotein of vesicular stomatitis virus is formed during or shortly after the translation process

Gs protein is a shorter, soluble form of the viral G protein of vesicular stomatitis virus (VSV) lacking the membrane-anchoring domain. Production of Gs protein appears to be a general property of VSV because infection of BHK-21 cells by five different isolates of the VSV serotype Indiana led in all cases to the synthesis of Gs protein. Moreover, it is formed in a variety of eucaryotic cell lines after VSV infection. In pulse-chase experiments, we observed a time-dependent change in the ratio of G to Gs protein released into the growth medium, suggesting that Gs is formed intracellularly rather than on the cell surface. Further experiments revealed that Gs protein can be synthesized in vitro in the reticulocyte lysate system after addition of a viral mRNA fraction and in a coupled transcription-translation system with VSV core particles. In the presence of microsomal membranes both G and Gs protein were glycosylated in the reticulocyte lysate, confirming that the authentic Gs protein is synthesized in vitro. The addition of various protease inhibitors to the cell-free system and variation of the incubation conditions did not alter the ratio of G to Gs formation. Taken together, these experiments suggest strongly that Gs protein is not a product of a membrane-associated proteolytic activity but is formed during or shortly after the translation process. Our attempts to detect a specific, shorter mRNA coding for the Gs protein by molecular hybridization procedures did not reveal the existence of such a mRNA species.

The cytoplasmic 4S translation inhibitory RNA species of chick embryonic muscle: fractionation of biologically active subspecies by high performance liquid chromatography

A 4S RNA species (iRNA) isolated from chick embryonic muscle which is a potent inhibitor of mRNA translation in vitro shows heterogeneity in the 70-100 nucleotide size range (Sarkar, S., Mukherjee, A.K., and Guha, C. (1981) J. Biol. Chem., 256, 5077-5086). The iRNA was fractionated by HPLC on different size exclusion columns using a variety of elution conditions. Chromatography of iRNA on a TSK 4000 SW column and elution with a low ionic strength buffer gave three components, one of which contained a pure subspecies of about 90-100 nucleotides size, as shown by a single band on PAGE analysis in 99% formamide. The biological activity of this purified subspecies showed that this is a more potent inhibitor of globin mRNA translation than unfractionated iRNA (Sarkar, S., Mukherjee, A.K., and Guha, C., (1981) J. Biol. Chem. 256, 5077-5086). Partial resolution of three additional low molecular weight iRNA subspecies in the 70-80 nucleotide size range in biologically active form was obtained on chromatography of unfractionated iRNA on TSK 4000 SW column in the presence of 0.5 M NaCl or on TSK 3000 SW column in the presence of low salt. The fractionation of iRNA by HPLC appears to be primarily based on size. These results strongly suggest that HPLC may also be useful for the fractionation of a variety of low molecular weight eukaryotic nuclear and cytoplasmic RNAs with retention of biological activity.

Increase of cloning efficiencies by using high-performance liquid chromatography-purified vectors and linkers

High-performance liquid chromatography (HPLC) was applied to the purification of vector and linker DNAs used in molecular cloning experiments. The data clearly demonstrate that HPLC (Blue Column from LKB/TSK G 4000 SW) based on steric exclusion is a very rapid and convenient method for the size separation of DNA fragments that are virtually free of any contamination. Application of vector and linker DNAs, purified by this method, enabled us to clone nanogram amounts of avian myeloblastosis virus RNA, which was used for the evaluation of a recently described cloning procedure.

Fractionation of mammalian tissue mRNAs by high-performance gel filtration chromatography

Total RNA was prepared from the free polysomes of bovine adrenal cortex and fractionated by high-performance gel filtration chromatography using a TSK-GEL G4000SW or G5000PW column. The former column gave better separation of 28 and 18 S rRNA than did the latter column when a suitable elution condition was selected. The separation of mRNAs by gel filtration chromatography was examined by in vitro translation of the fractionated RNA samples, and the fractionation of mRNAs roughly according to their sizes was confirmed. Significant enrichment of the mRNA of cytochrome P-450(SCC), whose in vitro-synthesized peptide had a molecular weight of 55,000, was achieved.

Purification of poly(A)-messenger ribonucleic acid by reversed-phase high-performance liquid chromatography

Polyadenylated messenger ribonucleic acid [poly(A)-mRNA] was purified by reversed-phase high-performance liquid chromatography (RP-HPLC). Partially purified poly(A)-mRNA was prepared from rat liver polysomes by magnesium precipitation followed by affinity chromatography on an oligo(dT) cellulose column. Translatable poly(A)-mRNA, as assayed by in vitro translation in a rabbit reticulocyte system, was resolved from non-translatable RNA by RP-HPLC. The separation appears to be due to the presence of poly(A) residues on the 3' terminus of the mRNA.