双链DNA片段的碱基空间模式BSP——基因组调控区的一种可能的信息编码方式  

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

作　　者：李许卿[1] 

机构地区：[1]中国科学院云南天文台,云南昆明650011

出　　处：《云南天文台台刊》2002年第1期66-67,共2页Publications of the Yunnan Observatoty

摘　　要：生物体可看作是一种特殊的信息处理系统 ,论文的第二章从这种观点出发讨论了生物细胞内最大的信息源基因组DNA序列的信息编码问题。首先探讨了基因组蛋白质编码区的信息编码问题 ;简要回顾转录水平的基因表达调控后 ,讨论了基因组基因表达调控区的信息编码问题。第三章介绍了我们利用internet上可获取的开放的生物信息学资源 ,对基因组DNA调控区的一种可能的编码方式所进行的理论研究。这种可能的编码方式我们称之为双链DNA上的碱基空间模式BSP (BaseSpatialPattern)。首先 ,我们发现了由三联体BSP介导的一种 4与 2 0的关系 ,称为 4 -BSP -2 0关系。并推测 4 -BSP -2 0关系也许是某些DNA—蛋白质相互作用中的一种识别密码 ;第二 ,研究真核细胞转录调控中的DNA—蛋白质相互作用的实验数据表明 :某些DNA结合蛋白质对双螺旋核酸的专一性识别可能与BSP有关。并找到了 7组由其他生物学家公开发表的实验数据支持这一猜测 ;第三 ,研究了BSP的形式化描述问题 ,找到了一种基于等价类的BSP描述方法 ,并开发了相应的计算机处理算法。该描述方法简明且便于用计算机进行处理 ,更重要的是它提供了一种研究途径 ,可把BSP和 4 -BSP -2 0关系推广到单链DNA (ssDNA)和ssDNA -蛋白质相互作用的研究中 。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.

关 键 词：BSP 编码 识别 DNA 蛋白质 生物体 碱基空间模式 

分 类 号：Q523[生物学—生物化学]