Anticipation of the secondary structure of nifs and CAP2 genes using Sfold, Mfold and RNAfold softwares in Fenugreek (Trigonellafoenum-graecum L.)

It is important to find the structure and composition of biological molecules because the molecular shape determines the function of molecule in the body of living organisms. Fenugreek is a valuable medicinal herb with high potential for medicinal and oral use. Ribonucleic acid )RNA( acts as a carrier of information, catalyst and regulatory element, which indicates its importance in the early stages of evolution. RNA structures contribute to its functional mechanism, thus, it may be possible to predict its performance from its secondary structure. The secondary structure of the RNA is often predicted by minimizing the free energy of the sequence. Over the past few years, some progress has been made in estimating free energy changes, mapping the secondary structure, and implementing computer programs to predict the structure. In this study, we used Sfold, RNAfold and Mfold software to predict the secondary structure of the RNAs of the identified nifs and CAP2 genes in fenugreek (Trigonella foenum-graecum), which are involved in the activity of zinc-finger proteins. The most stable structure and the components of each structure, the minimum free energy and the number of structural components for the hairpin loop, bulge loop, internal loop, multibranched loop, single stranded regions and helix were investigated by these softwares. The minimum free energy for nifs and CAP2 genes in RNAfold software was -211.87 and -209.79, respectively, the number of multi-loop was 4, 4 respectively and The number of hairpine 13 and 14. in Sfold software had a free energy level of -201.6 and -204.9, a number of herpanics equal to 10 and 13, and a multi-loop of 6 and 8 respectively, and in software Mfold, minimum free energy was -201.6 and -202.8, The number of hairpin equaled 10 and 11, and the number of multi-loops was 6 and 7.

کلیدواژه ها:

Free Energy ، Mfold ، RNAfold ، Secondary Structure ، Sfold