Summary
Two-dimensional gel electrophoresis, at high and low temperatures, and gel mobilities of circularly permuted DNA segments showed a large bending locus about 50 bp downstream from the right border of the 245 by oriC box, a minimal essential region of autonomous replication on the Escherichia coli chromosome. Bending was strongly enhanced by Dam methylation. In DNA from a Dam− strain, the mobility anomaly arising from altered conformation was much reduced, but was raised to the original level by methylation in vivo or in vitro. Enhancement of the mobility anomaly was also observed by hybrid formation of the Dam− strand with the Dam+ strand. Near the bending center, GATC, the target of Dam methylase, occurs seven times arranged essentially on the same face of the helix with 10.5 by per turn. We concluded that small bends at each Dam site added up to the large bending detectable by gel electrophoresis.
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References
Anderson JN (1986) Detection, sequence patterns and function of unusual DNA structures. Nucleic Acids Res 14:8513–8533
Bossi L, Smith DM (1984) Conformational change in the DNA associated with an unusual promoter mutation in a tRNA operon of Salmonella. Cell 39:643–652
Bramhill D, Kornberg A (1988) A model for initiation at origins of DNA replication. Cell 54:915–918
Calladine CR, Drew HR (1986) Principles of sequence-dependent flexure of DNA. J Mol Biol 192:907–918
Cheng S-C, Herman G, Modrich P (1985) Extent of equilibrium perturbation of the DNA helix upon enzymatic methylation of adenine residues. J Biol Chem 260:191–194
Diekmann S (1987) DNA methylation can enhance or induce DNA curvature. EMBO J 6:4213–4217
Diekmann S, McLaughlin LW (1988) DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction. JMol Biol 202:828–834
Diekmann S, Wang JC (1985) On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities. J Mol Biol 186:1–11
Fuller RS, Funnell BE, Kornberg A (1984) The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell 38:889–900
Gourse RL, de Boer HA, Nomura M (1986) DNA determinants of rRNA synthesis in E. coli: Growth rate dependent regulation, feedback inhibition, upstream activation, antitermination. Cell 44:197–205
Hagerman PL (1984) Evidence for the existence of stable curvature of DNA in solution. Proc Natl Acad Sci USA 81:4632–4636
Hagerman PL (1988) Sequence-dependent curvature of DNA. In: Well RD, Harvey SC (eds) Unusual DNA structures. Springer, New York, pp 226–236
Hirano M, Shigesada K, Imai M (1987) Construction and characterization of plasmid and lambda phage vector systems for study of transcriptional control in Escherichia coli. Gene 57:89–99
Hsieh C-H, Griffith JD (1988) The terminus of SV40 DNA replication and transcription contains a sharp sequence-directed curve. Cell 52:535–544
Kimura T, Takeya T, Takanami M (1989) Reconstitution of nucleosomes in vitro with a plasmid carrying the long terminal repeat of Moloney murine leukemia virus. Biochim Biophys Acta 1007:318–324
Koo H-S, Wu H-M, Crothers DM (1986) DNA bending at adenine-thymine tracts. Nature 320:501–506
Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Marini JC, Levene SD, Crothers DM, Englund PT (1982) Bent helical structure in kenetoplast DNA. Proc Natl Acad Sci USA 79:7664–7668
Marinus MG, Morris NR (1974) Biological function for 6-methyladenine residues in the DNA of Escherichia coli K-12. J Mol Biol 85:309–322
Matsui M, Oka A, Takanami M, Yasuda S, Hirota Y (1985) Sites of dnaA protein-binding in the replication origin of the Escherichia coli K-12 chromosome. J Mol Biol 184:529–533
Messer W, Bellekes U, Lother H (1985) Effect of dam methylation on the activity of the E. coli replication origin, oriC. EMBO J 4:1327–1332
Mizuno T (1987a) Static bend of DNA helix at the activator recognition site of the ompF promoter in Escherichia coli. Gene 54:57–64
Mizuno T (1987b) Random cloning of bent DNA segments from Escherichia coli chromosome and primary characterization of their structures. Nucleic Acids Res 15:6827–6841
Ogden GB, Pratt ML, Schaechter M (1988) The replication origin of the E. coli chromosome binds to cell membranes only when hemimethylated. Cell 54:127–135
Oka A, Sugimoto K, Takanami M, Hirota Y (1980) Replication origin of the Escherichia coli K-12 chromosome: The size and structure of the minimum DNA segment carrying the information for autonomous replication. Mol Gen Genet 178:9–20
Oka A, Sasaki H, Sugimoto K, Takanami M (1984) Sequence organization of replication origin of the Escherichia coli K-12 chromosome. J Mol Biol 176:443–458
Russell DW, Zinder ND (1987) Hemimethylation prevents DNA replication in E. coli. Cell 50:1071–1079
Ryder K, Silver S, DeLucia AL, Fanning E, Tegtmeyer P (1986) An altered DNA conformation in origin region I is a determinant for the bending of SV40 large T antigen. Cell 44:719–725
Smith DW, Garland AM, Herman G, Enns RE, Baker TA, Zyskind JW (1985) Importance of state of methylation of oriC. GATC sites in initiation of DNA replication in Escherichia coli. EMBO J 4:1319–1326
Snyder M, Buchman AR, Davis RW (1986) Bent DNA at a yeast autonomously replicating sequence. Nature 324:87–89
Stenzel TT, Patel P, Bastia D (1987) The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101. Cell 49:709–717
Tabata S, Oka A, Sugimoto K, Takanami M, Yasuda S, Hirota Y (1983) The 245 base-pair oriC sequence of the E. coli chromosome directs bidirectional replication at an adjacent region. Nucleic Acids Res 11:2617–2626
Trifonov EN, Ulanovsky LE (1988) Inherently curved DNA and its structural elements. In: Wells RD, Harvey SC (eds) Unusual DNA structures. Springer, New York, pp 173–187
Ulanvosky LE, Trifonov EN (1987) Estimation of wedge components in curved DNA. Nature 326:720–722
Wu H-M, Crothers DM (1984) The locus of sequence-directed and protein-induced DNA bending. Nature 308:509–513
Yasuda S, Hirota Y (1977) Cloning and mapping of the replication origin of Escherichia coli. Proc Natl Acad Sci USA 74:5458–5462
Zahn K, Blattner FR (1985) Sequence-induced DNA curvature at the bacteriophage lambda origin of replication. Nature 317:451–453
Zinkel SS, Crothers DM (1987) DNA bend direction by phase sensitive detection. Nature 328:178–181
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Kimura, T., Asai, T., Imai, M. et al. Methylation strongly enhances DNA bending in the replication origin region of the Escherichia coli chromosome. Molec. Gen. Genet. 219, 69–74 (1989). https://doi.org/10.1007/BF00261159
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DOI: https://doi.org/10.1007/BF00261159