Molecular Modeling And Docking Studies Of MBL, Genomic Cloning Of NAC Genes From Dendrobium Candidum Wall, Ex Lindl.

Monocots mannose-binding lectin (MBL) has an important role in plants against pathogens, pests and herbivorous animals. Based on the importance of MBL in plants, MBL deduced from DOL gene in Dendrobium candidum Wall ex Lindl was analyzed by homology modeling, molecular docking and dynamic simulations for further studying about the structure, characteristics and mannose-binding mechanism of DOL, which will provide more useful informations in studying the drug efficacy and breeding new varieties of Dendrobium.NAC is one of the plant-specific transcriptional factor families, which is involved in more biological processes. D. candidum is one of important ornamental and medicinal plants which is absent of whole-genome sequencing data. In order to clarify the binding and regulatory mechanisms of NAC to its target, it is very important that the structures and characteristics should be analyzed after they are cloned.Some commonly used genomic cloning techniques are compared and 21 fragments of NAC family in D. candidum have been achieved through an improved genomic cloning method, in which the length among the fragments is 117bp-3859bp, the content of G+C 35%-53%, deduced amino acids 39-821. Many fragments have a conserved sequence at their 5’end. Phylogenetic analysis shows that they can be divided into four branches, named as A, B, C and D. NAC1, NAC3, NAC4, NAC9, NAC16, NAC21, NAC43 may be associated with the organ boundaries and meristem formation; NAC29 associated with stressing; and NAC13 related to cell division. NAC2, NAC11, NAC17, NAC22, NAC45 and NAC6, NAC12 are separately clustered to B and C branch, and find that they have no association with some biological processes which is linked with A and D branches, so it indicates that there may have been new functions in NAC family.4 of the most similar fragments, NAC3, NAC4, NAC16, NAC21, are clustered to a same group which is associated with organ boundaries and meristem formation, are chosen for codon preference analysis. The results show that these genes prefer to use the codons ended with U/A. Codon usage bias of NACs in Arabidopsis thaliana, rice and tomato are also compared for successfully cloning of NACs in D. candidum afterwards.