Selection and characterization of RNA aptamer against Newcastle disease virus hemagglutinin protein RNA aptamer

Aptamers have higher resolution than monoclonal antibody;it could recognize tiny difference of a group between the ligands and needs smaller active site to bind.By using the SELEX technology,we could get three of RNA aptamers which can combine with the Newcastle disease virus F48E9strain through in vitro 12rounds of selection.Named FHN12-45-3,FHN12-36-6 and FHN12-19-9.The result of RNA aptamers secondary structure prediction showed that the spatial structures of selected RNA aptamers are mainly external loop,interior loop,hairpin loop, and bulge loop.The result of specificity experiment showed that the aptamer FHN-12-42-6could distinguish different strains of Newcastle disease virus through ELISA and Dot-blot test.Result of biology activity experiment showed that the aptamer FHN-12-42-6could reduce 4units of hemagglutination titer of virus F48E9strain.Virus possible of aptamer and F48E9strain active sites was preliminary considered to be on the hemagglutinin protein.In the chicken embryo fibroblast culture system,it can also reduce virus plaque of F48E9strain by 84.62%;using fluorescent quantitation RT-PCR method to test aptamer,virus load in the culture system could reduce 77.73%. It is concluded that selected RNA aptamers at the cellular level can inhibit Newcastle disease virus F48E9strain replication.