Base methylation and local DNA helix stability. Effect on the kinetics of cruciform extrusion.

We have studied the effect of base methylation on the rate of cruciform extrusion. A number of inverted repeats with central restriction sites were methylated at N6-adenine and C-5-cytosine, and rate constants for cruciform extrusion at 37 degrees C were measured. The effect of A-methylation at two bases was to enhance the rate for extrusion by nearly fourfold, while C-methylation lead to reduced extrusion rates, by factors of 1.7 and 2.7. The bkb inverted repeat, which has a central GGATCC sequence, was independently and simultaneously methylated at adenine and cytosine. It was found that the effects of the two kinds of modification could be treated effectively independently. The results reveal the local helical destabilization and stabilization due to A and C-methylation, respectively.

[1]  J. McGhee,et al.  Specific DNA methylation sites in the vicinity of the chicken β-globin genes , 1979, Nature.

[2]  G. Martin,et al.  Methylation of the Hprt gene on the inactive X occurs after chromosome inactivation , 1987, Cell.

[3]  S. Diekmann.  DNA methylation can enhance or induce DNA curvature. , 1987, The EMBO journal.

[4]  M. Surani,et al.  Genomic imprinting determines methylation of parental alleles in transgenic mice , 1987, Nature.

[5]  R. Burdon,et al.  The in vivo methylation of DNA in mouse fibroblasts. , 1969, Biochimica et biophysica acta.

[6]  Long range structural communication between sequences in supercoiled DNA. Sequence dependence of contextual influence on cruciform extrusion mechanism. , 1988, The Journal of biological chemistry.

[7]  M. Meselson,et al.  Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli. , 1983, Genetics.

[8]  P. Forterre,et al.  In vitro replication of a dam methylated and non-methylated ori-C plasmid. , 1984, Journal of molecular biology.

[9]  A. Riggs,et al.  DNA methylation and gene function. , 1980, Science.

[10]  T. Watanabe,et al.  EPISOME-MEDIATED TRANSFER OF DRUG RESISTANCE IN ENTEROBACTERIACEAE VII , 1964, Journal of bacteriology.

[11]  W. Arber,et al.  Promotion and limitation of genetic exchange. , 1979, Experientia.

[12]  P Chambon,et al.  DNA methylation: organ specific variations in the methylation pattern within and around ovalbumin and other chicken genes. , 1979, Nucleic acids research.

[13]  Yusaku Tagashira,et al.  Stabilities of nearest‐neighbor doublets in double‐helical DNA determined by fitting calculated melting profiles to observed profiles , 1981 .

[14]  T. Mohandas,et al.  Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation. , 1981, Science.

[15]  Peter B. Becker,et al.  Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors , 1987, Cell.

[16]  H. Boyer,et al.  A complementation analysis of the restriction and modification of DNA in Escherichia coli. , 1969, Journal of molecular biology.

[17]  D. Lilley,et al.  Influence of cation size and charge on the extrusion of a salt-dependent cruciform. , 1987, Journal of molecular biology.

[18]  B. Vanyushin,et al.  Rare Bases in Animal DNA , 1970, Nature.

[19]  G. A. van der Marel,et al.  Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy. 2. The hairpin form. , 1987, European journal of biochemistry.

[20]  J. Biernat,et al.  Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. , 1984, Nucleic acids research.

[21]  M. Marinus,et al.  Isolation of Deoxyribonucleic Acid Methylase Mutants of Escherichia coli K-12 , 1973, Journal of bacteriology.

[22]  R. Myers,et al.  Alterations in DNA helix stability due to base modifications can be evaluated using denaturing gradient gel electrophoresis. , 1987, Journal of molecular biology.

[23]  M. Dunn,et al.  The determination of glycine in protein hydrolysates with Leuconostoc mesenteroides P-60. , 1947, The Journal of biological chemistry.

[24]  A. Bird,et al.  Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. , 1978, Journal of molecular biology.

[25]  P. Young,et al.  Induction of alpha-fetoprotein synthesis in differentiating F9 teratocarcinoma cells is accompanied by a genome-wide loss of DNA methylation , 1984, Molecular and cellular biology.

[26]  P. V. von Hippel,et al.  Effects of methylation on the stability of nucleic acid conformations. Studies at the polymer level. , 1978, The Journal of biological chemistry.

[27]  V R Potter,et al.  Methylation of mammalian DNA: studies on Novikoff hepatoma cells in tissue culture. , 1969, Journal of molecular biology.

[28]  S. Glover,et al.  The isolation and properties of non-restricting mutants of two different host specificities associated with drug resistance factors. , 1970, Journal of general microbiology.

[29]  D. Lilley,et al.  Helix stability and the mechanism of cruciform extrusion in supercoiled DNA molecules. , 1988, Nucleic acids research.

[30]  D. Simon,et al.  Maternal inhibition of hepatitis B surface antigen gene expression in transgenic mice correlates with de novo methylation , 1987, Nature.

[31]  H. Blöcker,et al.  The mom gene of bacteriophage Mu: the mechanism of methylation‐dependent expression. , 1986, The EMBO journal.

[32]  A. Kornberg,et al.  Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome , 1988, Cell.

[33]  R. Flavell,et al.  DNA methylation in the human γδβ-globin locus in erythroid and nonerythroid tissues , 1980, Cell.

[34]  N. Kleckner,et al.  IS10 transposition is regulated by DNA adenine methylation , 1985, Cell.

[35]  C. Sapienza,et al.  Degree of methylation of transgenes is dependent on gamete of origin , 1987, Nature.

[36]  W. Doerfler,et al.  DNA methylation and gene activity. , 1983, Annual review of biochemistry.

[37]  M. Ehrlich,et al.  Unusual properties of the DNA from Xanthomonas phage XP-12 in which 5-methylcytosine completely replaces cytosine. , 1975, Biochimica et biophysica acta.

[38]  M. Caruthers,et al.  Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis , 1981 .

[39]  C. Caskey,et al.  Methylation of the mouse hprt gene differs on the active and inactive X chromosomes , 1986, Molecular and cellular biology.

[40]  A. Riggs,et al.  Methylation of DNA in mouse early embryos, teratocarcinoma cells and adult tissues of mouse and rabbit. , 1979, Nucleic acids research.

[41]  D. Lilley.  The kinetic properties of cruciform extrusion are determined by DNA base-sequence. , 1985, Nucleic acids research.

[42]  W. Gilbert,et al.  Sequencing end-labeled DNA with base-specific chemical cleavages. , 1980, Methods in enzymology.

[43]  Howard Cedar,et al.  DNA methylation affects the formation of active chromatin , 1986, Cell.

[44]  J. Hurst,et al.  DNA methylation and the regulation of globin gene expression , 1983, Cell.

[45]  G. Felsenfeld,et al.  DNA conformation at the 5′ end of the chicken adult β-globin gene , 1983, Cell.

[46]  J. Gill,et al.  Physical studies on synthetic DANs containing 5-methylcytosine , 1974 .

[47]  D. Lilley,et al.  The mechanism of cruciform formation in supercoiled DNA: initial opening of central basepairs in salt-dependent extrusion. , 1987, Nucleic acids research.

[48]  H Yamaki,et al.  The oriC unwinding by dam methylation in Escherichia coli. , 1988, Nucleic acids research.

[49]  J. E. Larson,et al.  Methylation of cytosine in the 5-position alters the structural and energetic properties of the supercoil-induced Z-helix and of B-Z junctions. , 1988, Biochemistry.