Characterization of the 'unusual' Mobility of Large Circular DNAs in Pulsed Field-gradient Electrophoresis

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1988 Feb 11

PMID 3344223

Citations 64

Authors

S M Beverley

Affiliations

Soon will be listed here.

Abstract

Large circular amplified DNAs (30 and 85 kb) present in methotrexate-resistant Leishmania major appear to migrate anomalously in pulsed field-gradient electrophoresis (PFGE), exhibiting pulse time-dependent mobility and migrating along a different apparent path relative to the large linear chromosomal DNAs. Quantitative studies indicate that the relative pulse-time dependence is actually conferred by the mobility properties of the large linear DNAs. One contributing factor to the difference in migration path is variability in the intrinsic voltage-dependence of mobility of supercoiled and linear DNAs, in combination with the asymmetrical/inhomogeneous voltage gradients. Certain linear chromosomes exhibit a previously undescribed pulse-time dependence in the voltage-dependence of mobility. When enzymatically relaxed or physically nicked the large circular DNAs fail to leave the well using any pulse time, a property also observed in conventional electrophoresis. These findings are relevant to PFGE theory, and its application to the study of circular DNA amplification in Leishmania and other species.

Citing Articles

Characterization of Temperate LPS-Binding Bordetella avium Phages That Lack Superinfection Immunity.

Serian D, Churin Y, Hammerl J, Rohde M, Jung A, Muller A Microbiol Spectr. 2023; 11(3):e0370222.

PMID: 37125905 PMC: 10269795. DOI: 10.1128/spectrum.03702-22.

Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA.

Mouakkad-Montoya L, Murata M, Sulovari A, Suzuki R, Osia B, Malkova A Proc Natl Acad Sci U S A. 2021; 118(47).

PMID: 34789574 PMC: 8617514. DOI: 10.1073/pnas.2102842118.

Extrachromosomal DNA amplicons in antimalarial-resistant Plasmodium falciparum.

McDaniels J, Huckaby A, Carter S, Lingeman S, Francis A, Congdon M Mol Microbiol. 2020; 115(4):574-590.

PMID: 33053232 PMC: 8246734. DOI: 10.1111/mmi.14624.

Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.

Klein H, Bacinskaja G, Che J, Cheblal A, Elango R, Epshtein A Microb Cell. 2019; 6(1):1-64.

PMID: 30652105 PMC: 6334234. DOI: 10.15698/mic2019.01.664.

Degradation of RNA during lysis of Escherichia coli cells in agarose plugs breaks the chromosome.

Khan S, Kuzminov A PLoS One. 2017; 12(12):e0190177.

PMID: 29267353 PMC: 5739488. DOI: 10.1371/journal.pone.0190177.

References

Fisher M, DINGMAN C . Role of molecular conformation in determining the electrophoretic properties of polynucleotides in agarose-acrylamide composite gels. Biochemistry. 1971; 10(10):1895-9. DOI: 10.1021/bi00786a026. View

Hightower R, Metge D, Santi D . Plasmid migration using orthogonal-field-alternation gel electrophoresis. Nucleic Acids Res. 1987; 15(20):8387-98. PMC: 306366. DOI: 10.1093/nar/15.20.8387. View

Johnson P, Grossman L . Electrophoresis of DNA in agarose gels. Optimizing separations of conformational isomers of double- and single-stranded DNAs. Biochemistry. 1977; 16(19):4217-25. DOI: 10.1021/bi00638a014. View

Gellert M . DNA topoisomerases. Annu Rev Biochem. 1981; 50:879-910. DOI: 10.1146/annurev.bi.50.070181.004311. View

Schindler C, Krolewski J, Rush M . Selective trapping of circular double-stranded DNA molecules in solidifying agarose. Plasmid. 1982; 7(3):263-70. DOI: 10.1016/0147-619x(82)90007-5. View

Coderre J, Beverley S, Schimke R, Santi D . Overproduction of a bifunctional thymidylate synthetase-dihydrofolate reductase and DNA amplification in methotrexate-resistant Leishmania tropica. Proc Natl Acad Sci U S A. 1983; 80(8):2132-6. PMC: 393771. DOI: 10.1073/pnas.80.8.2132. View

Ebrahimzadeh A, Jones T . A comparative study of different Leishmania tropica isolates from Iran: correlation between infectivity and cytochemical properties. Am J Trop Med Hyg. 1983; 32(4):694-702. DOI: 10.4269/ajtmh.1983.32.694. View

Serwer P, Allen J . Conformation of double-stranded DNA during agarose gel electrophoresis: fractionation of linear and circular molecules with molecular weights between 3 X 10(6) and 26 X 10(6). Biochemistry. 1984; 23(5):922-7. DOI: 10.1021/bi00300a020. View

Schwartz D, Cantor C . Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984; 37(1):67-75. DOI: 10.1016/0092-8674(84)90301-5. View

10.

Van der Ploeg L, Schwartz D, Cantor C, Borst P . Antigenic variation in Trypanosoma brucei analyzed by electrophoretic separation of chromosome-sized DNA molecules. Cell. 1984; 37(1):77-84. DOI: 10.1016/0092-8674(84)90302-7. View

11.

Schimke R . Gene amplification in cultured animal cells. Cell. 1984; 37(3):705-13. DOI: 10.1016/0092-8674(84)90406-9. View

12.

Carle G, Olson M . Separation of chromosomal DNA molecules from yeast by orthogonal-field-alternation gel electrophoresis. Nucleic Acids Res. 1984; 12(14):5647-64. PMC: 320021. DOI: 10.1093/nar/12.14.5647. View

13.

Beverley S, Coderre J, Santi D, Schimke R . Unstable DNA amplifications in methotrexate-resistant Leishmania consist of extrachromosomal circles which relocalize during stabilization. Cell. 1984; 38(2):431-9. DOI: 10.1016/0092-8674(84)90498-7. View

14.

Stark G, Wahl G . Gene amplification. Annu Rev Biochem. 1984; 53:447-91. DOI: 10.1146/annurev.bi.53.070184.002311. View

15.

Carle G, Olson M . An electrophoretic karyotype for yeast. Proc Natl Acad Sci U S A. 1985; 82(11):3756-60. PMC: 397866. DOI: 10.1073/pnas.82.11.3756. View

16.

Spithill T, Samaras N . The molecular karyotype of Leishmania major and mapping of alpha and beta tubulin gene families to multiple unlinked chromosomal loci. Nucleic Acids Res. 1985; 13(11):4155-69. PMC: 341303. DOI: 10.1093/nar/13.11.4155. View

17.

Garvey E, Coderre J, Santi D . Selection and properties of Leishmania tropica resistant to 10-propargyl-5,8-dideazafolate, an inhibitor of thymidylate synthetase. Mol Biochem Parasitol. 1985; 17(1):79-91. DOI: 10.1016/0166-6851(85)90129-x. View

18.

Rush M, Misra R . Extrachromosomal DNA in eucaryotes. Plasmid. 1985; 14(3):177-91. DOI: 10.1016/0147-619x(85)90001-0. View

19.

Carle G, Frank M, Olson M . Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science. 1986; 232(4746):65-8. DOI: 10.1126/science.3952500. View

20.

Giannini S, Schittini M, Keithly J, Warburton P, Cantor C, Van der Ploeg L . Karyotype analysis of Leishmania species and its use in classification and clinical diagnosis. Science. 1986; 232(4751):762-5. DOI: 10.1126/science.3961502. View