BMC Genomics 2009, 10:322 http://www.biomedcentral.com/1471-2164/10/322 FCiogrurreesp3ondence of the sequenced GlaI DNA fragments to the mouse γ-satellite consensus sequence Correspondence of the sequenced GlaI DNA fragments to the mouse γ-satellite consensus sequence. Mono- meric γ-satellite DNA is shown in grey, sequenced GlaI-fragments – in black. Vertical lines show ACGT sites (positions are indicated at bottom). A restriction map of mouse γ-satellite DNA monomer from position 61 to +61 is provided in Figure 5B. This map includes positions of DNA cleavage with GlaI and restriction endonucleases with indication of the obtained fragments and their calculated lengths. As can be seen from Figure 5A, double digestions result in a disappear- ance of those fragments, which contain restriction enzymes' sites. A treatment of GlaI digestion products with AcsI (Figure 5C) results in hydrolysis of 60 bp, 146 bp and 234 bp DNA fragments. A new fragment 37 bp is a result of 60 bp DNA fragment cleavage. A double diges- tion with FatI (Figure 5D) destroys all upper fragment of GlaI cleavage pattern but leads to formation of 89 bp and 145 bp DNA fragments. The appearance of 89 bp and 145 bp fragments restores an original picture of 80 bp and 150 bp bands in DNA cleavage pattern and we can see a new 57 bp fragment, which is cut off 86 bp fragment. A similar picture with hydrolysis of all upper fragments of GlaI cleavage pattern is observed with BstF5I double digestion (Figure 5E). A new fragments 129 bp, 105 bp, 45 bp and 41 bp are appeared in digestion products and clearly seen in gel photo. A double digestion of γ-satellite DNA with GlaI and Bst2UI (Figure 5F) results in digestion of 88 bp fragment with formation of two small fragments 33 bp and 55 bp. So, the experimental data on double digestion of γ-satellite DNA with GlaI and restriction endonucleases are coincided with calculated positions of cleavage sites in a physical map. Primary structure of γ-satellite DNA To study a primary structure of γ-satellite DNA in detail, we have cloned additionally 234 bp fragments of AspS9I and Sse9I digestions of mouse γ-satellite DNA [7]. 10 insertions of each digestion have been sequenced. Six Sse9I fragments and seven AspS9I fragments share homol- ogy with mouse γ-satellite DNA. These 13 sequences have been aligned with a consensus sequence of monomeric γ- satellite DNA and are presented in Additional file 1, along with primary structures of GlaI hydrolysis fragments. In total, sequencing data of 52 fragments of γ-satellite DNA are provided in Additional file 1. A primary structure of consensus monomeric γ-satellite DNA is given beneath all sequences (see Additional file 1). We haven't observed a mutation of CG dinucleotide in position 208 in all 47 analyzed fragments, whereas we have 7 (from 38 analyzed fragments) mutations of CG dinucleotide in position 62 and 12 (from 47 analyzed fragments) – in position 122. Earlier, Vissel and Choo cleaved a mouse γ-satellite DNA with MnlI, cloned 30 obtained fragments of monomeric γ- satellite DNA and sequenced insertions of the correspond- ing plasmids [13]. We have aligned these sequences and provided a consensus primary structure in Additional file 2. A search for monomeric γ-satellite DNA in the reference mouse genome sequence (NCBI Build 37, [14]) has been made and two small blocks of γ-satellite DNA monomers have been revealed in chromosome 3 and 9. Locations and a primary structure of 30 sequences from the mono- mers block in chromosome 3 and 140 sequences from the monomers block in chromosome 9 are presented in Addi- tional files 3 and 4, respectively. We have determined con- sensus sequences of γ-satellite DNA monomers for both Page 4 of 10 (page number not for citation purposes)