BMC Genomics 2009, 10:322 http://www.biomedcentral.com/1471-2164/10/322 Table 1: DNA fragments with mutated or uncleaved ACGT sites (Continued) A234-4b A234-3 S234-13N S234-1 234 233 234 234 4 – +4 4 – +4 98 – +98 98 – +98 Number of fragments with non-hydrolyzed ACGT and their percentage Number of mutated ACGT sites blocks and placed them in Additional files 3 and 4 as well. In Table 2 we have summarized data on mutations of CG dinucleotide in all 8 positions in a) 52 fragments of γ-sat- ellite DNA from Additional file 1, b) 30 monomers of γ- satellite DNA from Additional file 2), c) 140 monomers in chromosome 9 from Additional file 3 and d) 40 mono- mers in chromosome 3 from Additional file 4. ACAT ACAT ACAT ACGT 2/29 6,9% 14/47 29,8% ACGT ACGT ACGT ACGT 13/26 50% 1/46 2,2% ACGT ACAT ACAT ACAT 1/34 3,3% 9/38 23,7% Discussion According to a primary structure of consensus sequence of γ-satellite DNA [11], there are three GlaI recognition sites 5'-A(5mC)GT-3'/3'-TG(5mC)A-3' within monomeric DNA in positions 61, 121 and 207. Patterns of a total DNA hydrolysis with AspS9I and BstSCI have shown that products of γ-satellite DNA digestion have a molar con- centration at least 20 times more than a concentration of LINE1 repeats digestions [7]. Because of such difference in DNA concentration we have used a total mouse DNA preparation in study of γ-satellite DNA cleavage with GlaI. The obtained cleavage pattern corresponds to a limited hydrolysis of γ-satellite DNA with GlaI due to mutations of ACGT sites and undermethylation of CG dinucleotides. Results of double digestion of γ-satellite DNA with GlaI and restriction endonucleases AcsI, Bst2UI, BstF5I and FatI have confirmed positions of enzymes' recognition sites and locations of small (60 bp, 86 bp and 88 bp) and intermediate (146 bp, 148 bp and 174 bp) GlaI digestion fragments in monomeric γ-satellite DNA. Hydrolysis of γ-satellite DNA with HpyCH4IV and SspI has provided similar patterns of evenly distributed DNA fragments, which are monomers, dimers, trimers, etc. (Figure 4). However, the reasons of such specific digestion of γ-satellite DNA with these restriction enzymes are dif- ferent. Incomplete hydrolysis of γ-satellite DNA with SspI is explained by mutation of the enzyme recognition sequence [7], whereas HpyCH4IV cleaves γ-satellite DNA due to undermethylation of ACGT site in position 207 (Table 1). Consensus sequences of γ-satellite DNA fragments obtained in our work (Additional file 1) and published earlier [11] are coinciding. Surprisingly, a consensus sequence, which has been determined for 30 monomeric γ-satellite DNA fragments sequenced in the work of Vissel and Choo (Additional file 2), differs in two positions Page 6 of 10 (page number not for citation purposes) FHMipogyuuCsreHeg44eIVnoamndic SDspNI A cleavage with enzymes GlaI, Mouse genomic DNA cleavage with enzymes GlaI, HpyCH4IV and SspI. M – DNA marker SE 1 kbp.