The localization of the AECA target molecule on the cell surface should be an important factor for its pathogenicity in vivo, in terms of accessibility of the target molecule to AECAs.
So far, there is no tool that integrates both accessibility of the target regions in the mRNA and in the sRNA and the existence of an arbitrary seed in a general approach.
With cell lines chosen for high transfection efficiency and a molar excess of hhRz plasmid over target plasmid, the conditions of this experimental paradigm are specifically designed to evaluate for regions of accessibility of the target mRNA in cellulo.
Given the anatomical and practical limitations preventing accessibility of the target microcirculation in the organ of interest, clinicians usually have to rely on easy-to-access areas, such as the sublingual region.
Accessibility: the second component contributing to the quality of an RNA RNA interaction is the accessibility of the target sites in each sequence, which is the energy required to make them single stranded.
While MFold-derived accessibility scores may not be completely optimal, they have been used with reasonable success to predict accessibility in the siRNA targeting context, and so we use MFold here.
We use our in-house tool to predict the solvent accessibility of the target, and DSSP (Kabsch and Sander, 1983 ) to calculate the solvent accessibility of the template.
To evaluate the bioactivity/specificity of the ribozyme and the accessibility of the target site, a cleavage reaction in vitro was performed.
One possible explanation is, that transgene silencing effects [ 28] also occur in ZFHD1::miceT1 mice and that the accessibility of the target promoter is also gene locus dependent.
Accessibility to the target trees may be limited, and "monitoring may be biased by observers".
Accessibility of the target sites was evaluated based on the secondary structure of the target mRNA.
