A combinatorial approach to the restriction of a mouse genome

BMC Research Notes

Leonid V Bystrykh¹ 

[1] Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9700 AD, Groningen, The Netherlands

关键词: Randomness of genome;    Genome restriction;    DNA fragmentation;   

Others  :  1142116
DOI  :  10.1186/1756-0500-6-284

 received in 2012-09-10, accepted in 2013-07-16,  发布年份 2013

【 摘 要 】

Background

A fragmentation of genomic DNA by restriction digestion is a popular step in many applications. Usually attention is paid to the expected average size of the DNA fragments. Another important parameter, randomness of restriction, is regularly implied but rarely verified. This parameter is crucial to the expectation, that either all fragments made by restriction will be suitable for the method of choice, or only a fraction of those will be effectively used by the method. If only a fraction of the fragments are used, we often should know whether the used fragments are representative of the whole genome. With a modern knowledge of mouse, human and many other genomes, frequencies and distributions of restriction sites and sizes of corresponding DNA fragments can be analyzed in silico. In this manuscript, the mouse genome was systematically scanned for frequencies of complementary 4-base long palindromes.

Findings and conclusions

The study revealed substantial heterogeneity in distribution of those sites genome-wide. Only few palindromes showed close to random pattern of distribution. Overall, the distribution of frequencies for most palindromes is much wider than expected by random occurrence. In practical terms, accessibility of genome upon restriction can be improved by a selective combination of restrictases using a few combinatorial rules. It is recommended to mix at least 3 restrictases, their recognition sequences (palindrome) should be the least similar to each other. Principles of the optimization and optimal combinations of restrictases are provided.

【 授权许可】

   
2013 Bystrykh; licensee BioMed Central Ltd.

【 图 表 】

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