Determinaon of secondary and terary structures of cervical cancer lncRNA diagnosc and siRNA therapeuc biomarkers

Abstract

Cervical cancer is one of the primary causes of mortality in women due to human papilloma virus (HPV) infec-on. The fingerprint of an HPV infecon could be detected using a long non-coding RNA (lncRNA) biomarker, enabling it to be ulized in molecular diagnoscs. The primary structure or sequences of RNA should be annotated within convenonal bioinformacs tools. Therefore, this study aimed to determine the fine-grained 2D and 3D structures of lncRNA PVT1 and its respecve siRNA inhibitors. lncRNA PVT1 sequences from Homo sapiens, Mus musculus, and Raus norvegicus were retrieved from Genbank (NCBI). Predicon of the 2D structure and analysis of the interacons of the lncRNA and siRNA were performed using the Vienna RNA package. The 3D structure of the RNA was computed using the SimRNA and ModeRNA soware programs. The results showed that lncRNA PVT1 from H. sapiens and M. musculus had a conserved region. However, the lncRNA from both H. sapiens and M. musculus showed a low conserved region, and the 2D structure could not be determined; thus, the annotaon and 2D model focused only on H. sapiens. Both of their lncRNA PVT1 also had a short half-life in the cell. Based on the 3D modeling pipeline, the 3D model of lncRNA PVT1 showed the stability and possible funcon as molecules, while the PVT1 siRNA-lncRNA interacon analysis revealed that the molecules could bind well. Based on these findings, the structures of both lncRNA PVT1 and its siRNA have the potenal to be ulized as biomarkers.