Abstract:
:Small RNA-mRNA binding is an essential step in RNA interference, an important cellular regulatory process. Calculations of binding free energy have been used in binding site prediction, but the cost of stretching the mRNA loop when the small RNA-mRNA duplex forms requires further exploration. Here, using both polymer physics theory and simulations, we estimate the free energy of a stretched mRNA loop. We find loop stretching significantly increases the free energy of 3' supplementary/compensatory miRNA binding and siRNA binding to mRNA hairpin loops. We also make the observation that sites where 3' supplementary binding is available may bind at the seed only, and that loop stretching often favors seed-only binding over seed plus 3' supplementary binding in mRNA hairpins.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Meng Y,Aalberts DPdoi
10.1016/j.bpj.2012.12.017subject
Has Abstractpub_date
2013-01-22 00:00:00pages
482-7issue
2eissn
0006-3495issn
1542-0086pii
S0006-3495(12)05129-6journal_volume
104pub_type
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