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Thermodynamic Examination of the Amber/W Site in the Hepatitis Delta Virus Type III
Author(s) -
Dang Angela,
Grover Neena
Publication year - 2010
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.24.1_supplement.lb73
Subject(s) - rna , chemistry , protein secondary structure , crystallography , hepatitis a virus , stereochemistry , biology , virus , virology , biochemistry , gene
The hepatitis delta virus III (HDVIII) RNA can form two secondary structures, one branched and one unbranched. As editing requires a branched double‐hairpin structure, editing levels are determined by the fraction of RNA that folds into the correct structure and the efficiency with which ADAR (adenosine deaminase) edits. Due to the difference of only five bases in the editing region, the Peruvian and Ecuadorian isolates of the HDVIII form slightly different secondary structures and thus, exhibit different editing levels. Near the Amber/W site, the Peruvian isolate forms a 4x3 and 1x1 internal loop and is edited more efficiently than the Ecuadorian isolate, which forms a 4x2 and 0x1 internal loop. In this study, we examined the difference in the stabilities of the RNA constructs derived from the two isolates. The more efficiently edited Peruvian isolate was predicted to form a more stable secondary structure. Under 1 M KCl and varying concentrations of Mg2+ or Ca2+, the Peruvian Amber/W constructs was 1.5–2 times more stable than the Ecuadorian construct. Only a small increase in RNA stability was observed for the two isolates in the presence of divalent ions in comparison to the stability in 1 M KCl.