BMC Genomics 2009, 10:322 http://www.biomedcentral.com/1471-2164/10/322 Table 2: Mutations of CG-dinucleotide in mouse γ-satellite DNA % of mutated CG dinucleotides Position DNA fragments (this work) 30 MnlI- fragments (Vissel and Choo [14]) 140 fragments from chromosome 9* 40 fragments from chromosome 3** 16 10/37 34 6/37 62 7/38 10/30 5/30 3/30 33.3% 16.7% 10.0% 74 6/38 0/30 0% 122 12/47 25.5% 8/30 26.7% 177 4/35 1/30 3.3% 192 7/35 2/30 6.7% 27.0% 16.2% 18.4% 15.8% 11.4% 20.0% 54/140 46/140 63/140 25/140 128/140 108/140 68/140 13/140 38.6% 32.9% 45.0% 17.9% 91.4% 77.1% 48.6% 28/40 70% 14/40 35% 20/40 50% 13/40 32.5% 38/40 95% 21/40 52.5% 10/40 25% 208 0/46 0% 6/30 20% 9.3% 16/40 40% * – region 3000003–3038419 from chromosome 9 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NT_039471.7&from=3&to=38419 ** – from chromosome 3 regions: 3000002–3004438 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NT_078380.6&from=2&to=4438 3010698–3015403 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NT_078380.6&from=10698&to=15403 3016887–3018046 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NT_078380.6&from=16887&to=18046 In our study we have observed 18,4%, 25,5% and 0% mutations of CG dinucleotide in positions 62, 122 and 208, respectively (Table 2). Data of Vissel and Choo show that all 30 sequenced fragments don't have mutations in position 74 and have only one mutation of CG dinucle- otide in position 177. On the other hand, there are 20% mutations of CG dinucleotide in position 208. An absence of CG dinucleotide mutations in position 74 may be explained, at least partially, by overlapping position 75 of this dinucleotide with MnlI recognition sequence. A discrepancy of CG dinucleotides mutations in position 208 in two works is a consequence of either a very special selection of DNA fragments in a work of Vissel and Choo (see above) or different sources of DNA (a mouse liver in our work and a cell line in the work of Vissel and Choo). Nevertheless, both works demonstrate maximum CG dinucleotides mutations in position 16 (around 30%) and in position 122 (about 26%). Moreover, there is a similar distribution of mutations in these CG dinucle- otides: mostly mutated G in position 123 and roughly equal mutated C and G in positions 16 and 17. In this work we have confirmed data on large proportion of γ-satellite DNA in a total mouse DNA preparation [7]. Vissel and Choo isolated γ-satellite DNA from a total DNA and studied its structure. According to their data γ-satellite DNA is organized into long uninterrupted arrays of between 1,000 monomers and greater than 8,000 mono- mers, likely, located near chromosome centromers [13]. So, γ-satellite DNA is a prolonged DNA and constitutes a significant part of total DNA. However, we could not find peaks of 234 bp and 468 bp in diagrams of genomic DNA digestion with restriction enzymes, which have one recog- nition site in γ-satellite DNA monomer [7]. In fact, the most of γ-satellite DNA is not presented in the known databases [7]. Nevertheless, in genomic database there are small blocks of sequenced γ-satellite DNA, which contain 10–140 monomers [14]. DNA sequences of γ-satellite monomers from two such blocks, which are located in chromosomes 3 and 9, have been aligned in this work (Additional files 3 and 4, respectively). Consensus sequences of γ-satellite DNA of these two blocks are almost identical and differ in nucleotides in positions 18 and 179. However, both of them have three identical dif- ferences from consensus sequence of arrayed γ-satellite DNA [[11] and this work]: A instead of G in positions 123 and 202, T instead of A in position 233. Besides, CG dinu- cleotide in position 178 and in position 17 has become CA dinucleotide in consensus sequences of γ-satellite DNA in chromosomes 9 and 3, respectively. A change of G for A in position 123 destroys one of three ACGT sites and consensus sequence of γ-satellite DNA in both blocks of monomers contains only two GlaI recognition sites in positions 61 and 207. A comparison of Table 2 data between rows 1, 2 and 3, 4 shows a significant difference of CG dinucleotide muta- tions in γ-satellite DNA from arrays and in small blocks of monomers. We can see more mutation in all 8 positions of CG dinucleotides in the case of blocks of γ-satellite DNA monomers if compare to CG dinucleotides in arrayed γ-satellite DNA. Table 2 shows that in arrayed γ- satellite DNA there is at least one conservative CG dinu- Page 8 of 10 (page number not for citation purposes)