Abstract
We isolated and cloned DNA fragments that exist as inverted-repeat structures in the genome of Pharbitis nil. The method used exploited the fact that if inverted repeat DNA is present in the DNA fragment, intramolecular double-stranded structures can be partly formed within single-stranded DNA molecules after denaturation and rapid renaturation of the fragment. The rapidly renaturing DNA fragments (termed snap-back DNA) were isolated by hybroxylapatite column chromatography and treatment with mungbean nuclease and were cloned into the pUC9 vector. Four snap-back DNA members out of thousands of independent clones obtained were characterized with respect to the reiteration frequency and the nucleotide sequences. When used as probes in Southern hybridization experiments, some of the members identified restriction fragment length polymorphism among the cultivars, suggesting that these sequences might be fluid in the genome. One of the four clones has regions of nucleotide sequence homology to those of inverted-repeat regions in the transposon Taml of Antirrhinum majus.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Explore related subjects
Discover the latest articles and news from researchers in related subjects, suggested using machine learning.References
Adams JW, Kaufman RE, Kretschmer PJ, Harrison M, Nienhuis AW: A family of long reiterated DNA sequences, one copy of which is next to the human beta globin. Nucleic Acids Res 8: 6113–6128 (1980).
Baker RF, Thomas Jr CA: The origin and complexity of inverted repeat DNA sequences in Drosophila. In: Bukhari AI, Shapiro JA, Adhya SL (eds) DNA Insertion Elements, Plasmids and Episomes, pp 463–469. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1977).
Barker RF, Thompson DV, Talbot DR, Swanson J, Bennetzen JL: Nucleotide sequence of the maize transposable element Mul. Nucleic Acids Res 12: 5955–5967 (1984).
Bonas U, Sommer H, Saedler H: The 17-kb Taml element of Antirrhinum majus induces a 3-bp duplication upon integration into the chalcone synthase gene. EMBO J 3: 1015–1019 (1984).
Chandler V, Rivin C, Walbot V: Stable non-mutator stocks of maize have sequences homologous to the Mul transposable element. Genetics 114: 1007–1021 (1986).
Fedoroff N, Wessler S, Shure M: Isolation of the transposable maize controlling elements Ac and Ds. Cell 35: 235–242 (1983).
Ford M, Fried M: Large inverted duplications are associated with gene amplification. Cell 45: 425–430 (1986).
Freeling M: Plant transposable elements and insertion sequences. Ann Rev Plant Physiol 35: 277–298 (1984).
Hattori M, Hidaka S, Sakaki Y: Sequence analysis of a Kpn I family member near the 3′ end of human β-globulin gene. Nucleic Acids Res 13: 7813–7827 (1985).
Houck CM, Rinehart FP, Schmid CW: A ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol 132: 289–306 (1979).
Hyrien O, Debatisse M, Buttin G, Robert de Saint Vincent B: The multicopy appearance of a large inverted duplication and the sequence at the inversion joint suggests a new model for gene amplification. EMBO J 7: 407–417 (1988).
Imai Y: Analysis of flower colour in Pharbitis nil. J Genet 24: 203–224 (1931).
Kuroiwa T, Miyamura S, Kawano S, Hizume M, Tho-e A, Miyakawa I, Sando N: Cytological characterization of NOR in the bivalent of Saccharomyces cerevisiae. Exp Cell Res 165: 199–206 (1986).
Leutwiler LS, Hough-Evans BR, Meyerowitz EM: The DNA of Arabidopsis thaliana. Mol Gen Genet 194: 15–23 (1984).
Maniatis T, Fritsch EF, Sambrook J: Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1982).
McClintock B: The significance of responses of the genome to challenge. Science 226: 792–801 (1984).
Muller-Neumann M, Yoder JI, Starlinger P: The DNA sequence of the transposable element Ac of Zea mays L. Mol Gen Genet 198: 19–24 (1984).
Murray MG, Thompson WF: Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8: 4321–4325 (1980).
Nevers P, Shepherd NS, Saedler H: Plant transposable elements. Adv Bot Res 12: 103–203 (1986).
Ohtsubo H, Nyman K, Doroszkiewicz W, Ohtsubo E: Multiple copies of iso-insertion sequences of IS1 in Shigella dysenteriae chromosome. Nature (London) 292: 640–643 (1981).
Passananti C, Davies B, Ford M, Fried M: Structure of an inverted duplication formed as a first step in a gene amplification event: implications for a model of gene amplification. EMBO J 6: 1697–1703 (1987).
Pereira A, Cuypers H, Gierl A, Schwarz-Sommer Z, Saedler H: Molecular analysis of the En/Spm transposable element system of Zea mays. EMBO J 5: 835–841 (1986).
Potter S, Truett M, Phillips M, Maher A: Eukaryotic transposable genetic elements with inverted terminal repeats. Cell 20: 639–647 (1980).
Sakano H, Hüppi K, Heinrich G, Tonegawa S: Sequences at the somatic recombination sites of immunoglobulin lightchain genes. Nature (London) 280: 288–294 (1979).
Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463–5467 (1977).
Shapiro JA: Mobile Genetic Elements. Academic Press, New York (1983).
Upadhyaya KC, Sommer H, Krebbers E, Saedler H: The paramutagenic line niv-44 has a 5 kb insert, Tam 2, in the chalcone synthase gene of Antirrhinum majus. Mol Gen Genet 199: 201–207 (1985).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Hirano, H., Komeda, Y. & Iino, T. Cloning and structural analysis of the snap-back DNA of Pharbitis nil . Plant Mol Biol 12, 235–244 (1989). https://doi.org/10.1007/BF00020508
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00020508