GENOMES AND DNA CONFORMATION

: Genomic DNA sequences code not only for protein sequences but also for their own physical characteristics. The composition of a genome for creating particular physical characteristics is reviewed by first summarizing the conformational characteristics of short DNA fragments, and second by summarizing the combination of fragments in a genome. In this analysis the pyrimidine (Y)/purine (R) classification of the four bases is important. In genomes, there is a tendency to create YY and RR combinations rather than YR and RY combinations, with a resulting minimization of the deviation of the local DNA structure from the standard B-conformation. Among the YY combinations, TT steps are positioned with a preference for the periodicity of approximately 10 bases, which is close to the helical periodicity of the DNA. The coding regions possess another periodicity of 3 bases in addition to the approximately 10 base periodicity, which differentiates these regions from the non-coding regions in terms of the physical characteristics. It is likely that the above characteristics of genomes are designed as part of their efficient transcription mechanisms.