Distribution of "intrastrand annealing" sequences in lambda bacteriophage genome

Our computer programme which is originally developed for calculating distribution of folding structures in single stranded nucleic acids was applied for analysis of lambda phage DNA. We found that we have to choose an optimum condition of calculation depending upon what kind of structures we are looking for, for example secondary structure of transcripts or clover-leaf structures in the double stranded DNA molecules. In one calculation condition, the lambda genome was divided into two distinct regions, i.e., capsid genes with high folding probabilities. In this condition, the clover-leaf structure previously indicated in the replication origin was not detected. Calculation in the condition which included annealings with higher free energies (lower stabilities) revealed the presence of the clover-leaf structure in the DNA replication origin in the middle of the gene O.