A physical map of human Alu repeats cleavage by restriction endonucleases

<p>Abstract</p> <p>Background</p> <p>Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction endonucleases. We have proposed a method of restriction analysis of Alu repeats sequences <it>in silico</it>.</p> <p>Results</p> <p>Simple software to analyze Alu repeats database has been suggested and Alu repeats digestion patterns for several restriction enzymes' recognition sites have been constructed. Restriction maps of Alu repeats cleavage for corresponding restriction enzymes have been calculated and plotted. Theoretical data have been compared with experimental results on DNA hydrolysis with restriction enzymes, which we obtained earlier.</p> <p>Conclusion</p> <p>Alu repeats digestions provide the main contribution to the patterns of human chromosomal DNA cleavage. This corresponds to the experimental data on total human DNA hydrolysis with restriction enzymes.</p

GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation

Abstract Background Patterns of mouse DNA hydrolysis with restriction enzymes are coincided with calculated diagrams of genomic DNA digestion in silico, except presence of additional bright bands, which correspond to monomer and dimer of γ-satellite DNA. Only small portion of mouse γ-satellite DNA sequences are presented in databases. Methyl-directed endonuclease GlaI cleaves mouse DNA and may be useful for a detailed study of primary structure and CG dinucleotides methylation in γ-satellite DNA. Results We have constructed a physical map and produced experimental patterns of mouse γ-satellite DNA hydrolysis with unique site-specific methyl-directed endonuclease GlaI and several restriction endonucleases. Fifty two DNA fragments of γ-satellite DNA have been cloned and sequenced. We have not observed any mutations of CG dinucleotide in position 208 of monomeric γ-satellite DNA and confirmed 50% methylation of this CG dinucleoitide. A comparison of consensus sequences of arrayed γ-satellite DNA and small blocks of satellite DNA (140 monomers and less) has shown a higher level of mutations and an absence of conserved CG dinucleotide in last ones. A replacement of CG dinucleotide by CA-dinucleotide in positions 178 and 17 in chromosomes 9 and 3, respectively, has been observed in blocks of monomers. Conclusion Arrayed γ-satellite DNA from mouse has at least one conservative CG-dinucleotide. Consensus sequences of this DNA and γ-satellite DNA in small blocks of monomers are differing. The last one displays a higher level of CG dinucleotides mutations and an absence of conservative CG-dinucleotide. Presence of conservative and half-methylated CG-dinucleotide supports an idea of importance of this CG dinucleotide methylation/demethylation in arrayed γ-satellite DNA functioning.</p

A physical map of human Alu repeats cleavage by restriction endonucleases-4

Wn at top, whereas those for the complete set of annotated Alu repeats are shown at bottom. The highest peak values are indicated.<p><b>Copyright information:</b></p><p>Taken from "A physical map of human Alu repeats cleavage by restriction endonucleases"</p><p>http://www.biomedcentral.com/1471-2164/9/305</p><p>BMC Genomics 2008;9():305-305.</p><p>Published online 26 Jun 2008</p><p>PMCID:PMC2443384.</p><p></p

A physical map of human Alu repeats cleavage by restriction endonucleases-3

Electrophoregrams of human genomic DNA enzymatic cleavage (8% PAAG) and lengths of fragments are shown at left. A correspondence of predicted DNA fragments (arrows) to the bands in electrophoregrams is shown by dotted lines. M – DNA ladder pUC19/MspI (the lengths of visible fragments are: 501, 489, 404, 331, 242, 190, 147, 111+110, 67 and 34 bp, from top to bottom). "sat" – α-satellite DNA cleavage products.<p><b>Copyright information:</b></p><p>Taken from "A physical map of human Alu repeats cleavage by restriction endonucleases"</p><p>http://www.biomedcentral.com/1471-2164/9/305</p><p>BMC Genomics 2008;9():305-305.</p><p>Published online 26 Jun 2008</p><p>PMCID:PMC2443384.</p><p></p

Distribution diagrams of AluI and AsuHPI recognition sites in all Alu repeats sequences

<p><b>Copyright information:</b></p><p>Taken from "A physical map of human Alu repeats cleavage by restriction endonucleases"</p><p>http://www.biomedcentral.com/1471-2164/9/305</p><p>BMC Genomics 2008;9():305-305.</p><p>Published online 26 Jun 2008</p><p>PMCID:PMC2443384.</p><p></p

A physical map of human Alu repeats cleavage by restriction endonucleases-0

Wn at top, whereas those for the complete set of annotated Alu repeats are shown at bottom. The highest peak values are indicated.<p><b>Copyright information:</b></p><p>Taken from "A physical map of human Alu repeats cleavage by restriction endonucleases"</p><p>http://www.biomedcentral.com/1471-2164/9/305</p><p>BMC Genomics 2008;9():305-305.</p><p>Published online 26 Jun 2008</p><p>PMCID:PMC2443384.</p><p></p