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The organization of genes in yeast mitochondrial DNA

IV. Analysis of (dA·dT) clusters in yeast mitochondrial DNA by poly(U)-Sephadex chromatography


We have fractionated fragments of yeast mtDNA, obtained with restriction endonucleases, on poly(U)-Sephadex columns using the procedure of Flavell and Van den Berg (FEBS Letters (1975) 58, 90–93). The poly(U) forms a triple helix with (dA·dT) clusters in duplex DNA and fractionates DNA fragments on the basis of the length and number of clusters contained in them.

mtDNA fragments obtained with endonucleases PstI, BamHI, HindII, HindII+III, EcoRI, HapII and HhaI were separated by poly(U)-Sephadex in three groups: fragments not retained by the column in 2M LiCl, fragments partially retained and fragments (nearly) completely bound in 2 M LiCl and only eluted by 0.1 M LiCl. The separation obtained is adequate for analytical fractionation of fragments and it can be used for the preparative isolation of firmly-bound fragments.

In mtDNA digests made with endonuclease HapII, which gives about 70 separable fragments under our conditions, only about 10% of the fragments were firmly bound to poly(U)-Sephadex. This shows that the number of (dA·dT) clusters long enough to result in binding is limited in yeast mtDNA and its suggests that large fragments are bound by only one or a few clusters.

Corresponding segments of the physical map of the mtDNAs from Saccharomyces carlsbergensis and Saccharomyces cerevisiae strains JS1-3D and KL14-4A were bound to the column, showing that the (dA·dT) clusters responsible for binding are conserved in the evolution of mtDNA. However, one 3,000 bp insert, only present on KL14-4A mtDNA, causes the loss of a binding site, another long insert introduces a new binding site.

Fragments firmly bound to the columns are clustered in one quadrant of the physical map of these three mtDNAs. This quadrant also contains the large insertions present in KL14-4A mtDNA and absent from S. carlsbergensis mtDNA. The possible relation between (dA·dT) clusters and insertions is discussed.

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  1. Bernardi, G., Prunell, A., Fonty, G., Kopecka, H., Strauss, F.: The mitochondrial genome of yeast: Organization, evolution and peptite mutation. In:The genetic function of mitochondrial DNA (Saccone, C. and Kroon, A.M., eds.), pp. 185–198. Amsterdam: North-Holland 1976

  2. Coffin, J.M., Parsons, J.T., Rymo, L., Haroz, R.K., Weissmann, C.: A new approach to the isolation of RNA-DNA hybrids and its application to the quantitative determination of labelled tumor virus RNA. J. molec. Biol. 86, 373–396 (1974)

  3. Ehrlich, S.D., Thiery, J.P., Bernardi, G.: The mitochondrial genome of wild-type yeast cells. III. The pyrimidine tracts of mitochondrial DNA. J. molec. Biol.65, 207–212 (1972)

  4. Flavell, R.A., Van den Berg, F.M.: The isolation of duplex DNA containing (dA·dT) clusters by affinity chromatography on poly(U)-Sephadex. FEBS Letters 58, 90–93 (1975)

  5. Flavell, R.A., Van den Berg, F.M., Grosveld, G.C.: Isolation and characterization of the oligo (dA·dT) clusters and their flanking DNA segments in the rabbit genome. J. molec. Biol., 115, in press (1977)

  6. Hardies, S.C., Wells, R.D.: Preparative fractionation of DNA restriction fragments by reversed phase column chromatography. Proc. nat. Acad. Sci. (Wash.) 73, 3117–3121 (1976)

  7. Sanders, J.P.M., Borst, P., Weijers, P.J.: The organization of genes in yeast mitochondrial DNA. II. The physical map of EcoRI and HindII+III fragments. Molec. gen. Genet. 143, 53–64 (1975b)

  8. Sanders, J.P.M., Heyting, C., Borst, P.: The organization of genes in yeast mitochondrial DNA. I. The genes for large and small ribosomal RNA are far apart. Biochem. biophys. Res. Commun. 65, 699–707 (1975a)

  9. Sanders, J.P.M., Heyting, C., Borst, P.: The variability of the mitochondrial geneme of Saccharomyces strains. In: Genetics and biogenesis of chloroplasts and mitochondria (Bücher, Th., Neupert, W., Sebald, W. and Werner, S., eds.), pp. 511–517. Amsterdam: North-Holland 1976

  10. Sanders, J.P.M., Hevting, C., Verbeet, M.Ph., Meijlink, F.C.P.W., Borst, P.: The organization of genes in yeast mitochondrial DNA. III. Comparison of the physical maps of the mitochondrial DNAs from three wild-type Saccharomyces strains. Molec. gen. Genet. 157, 239–261 (1977)

  11. Stafford, D.W., Bieber, D.: Concentration of DNA solutions by extraction with 2-butanol. Biochim. biophys. Acta (Amst.) 378, 18–21 (1975)

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Correspondence to Piet Borst.

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Communicated by F. Kaudewitz

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Sanders, J.P.M., Borst, P. The organization of genes in yeast mitochondrial DNA. Molec. Gen. Genet. 157, 263–269 (1977).

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  • Fractionation
  • Saccharomyces Cerevisiae
  • Saccharomyces
  • LiCl
  • Analytical Fractionation