Base Spatial Pattern(BSP)of Double-strand DNA Segment——a Possible Coding Method of Genomic Regulatory Regions

Biological organisms can be viewed as a kind of special information processing systems.From this point of view, In chapter two, we give a discussion of the information coding in genomic DNA sequences, which are the biggest information resource in biological cells. Firstly, we focus on the coding methods of protein-coding regions in genomes. Secondly, after a brief review of the genes expressional regulation at transcription level, we discuss the coding methods of regulatory regions in genomes. The chapter three presents our theoretical study, by using the available open bioinformatics resource on the internet and on a possible coding method of DNA regulatory regions in genomes, which is termed BSP (Base Spatial Pattern)of double-strand DNA segment. Firstly, we have found a 4 and 20 relationship mediated by triple BSP, called 4-BSP-20 relation. We speculate that 4-BSP-20 relation might be a kind of recognition code in some DNA-protein interactions. Secondly, The study of experimental data of DNA-protein interactions in the gene transcription regulation of eukaryotic cells reveals that the specific recognition of double-helical nucleic acids by some DNA-binding proteins might involve the BSP.We have found seven sets of experimental data , which were published by other biologists, to support this hypothesis.Finally,we investigated the formal description of the BSP.We have found a formal BSP representation that is based on a mathematical model of equivalent classes, and developed a relevant computer-processing algorithm. This representation of the BSP is succinct and easy to be processed by computers. More importantly, this representation of the BSP provides a method by which the BSP or the 4-BSP-20 relation can be generalized to single-strained DNA (ssDNA) and ssDNA-protein interactions. Furthermore,the BSP or the 4-BSP-20 relation can be generalized to RNA (ssDNA) and RNA-protein interactions. In the Conclusion,the future study for the BSP is prospected.