Comparative analysis of Helicase 3’ UTR with Hepatitis Delta Virus (HDV) ribozyme (PDB Id: 4PR6).
(a) Tertiary structure of HDV Ribozyme (4PR6). (b) Sequence alignment of Helicase 3’ UTR and HDV ribozyme. (c) Structural superimposition of HDV ribozyme (4PR6) and Helicase ribozyme where HDV ribozyme is represented in red and Helicase 3’ UTR in blue color respectively. (d) Canonical base paring are observed during the MD simulation of Helicase 3’UTR. In this we have shown the base paring between G25-C18, A23-U20, which are regular Watson-crick base pairings. (e) Non-canonical base pairing which are normally seen in RNA structures are also observed during Helicase 3’ UTR MD simulations. In this we have shown base-pairings between A35-G47, U34-U48, and U33-C49. Apart from these Hoogsteen base parings are also seen.