RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates

RNA is a functionally
rich molecule with multilevel, hierarchical
structures whose role in the adsorption to molecular substrates is
only beginning to be elucidated. Here, we introduce a multiscale simulation
approach that combines a tractable coarse-grained RNA structural model
with an interaction potential of a structureless flat adsorbing substrate.
Within this approach, we study the specific role of stem-hairpin and
multibranch RNA secondary structure motifs on its adsorption phenomenology.
Our findings identify a dual regime of adsorption for short RNA fragments
with and without the secondary structure and underline the adsorption
efficiency in both cases as a function of the surface interaction
strength. The observed behavior results from an interplay between
the number of contacts formed at the surface and the conformational
entropy of the RNA molecule. The adsorption phenomenology of RNA seems
to persist also for much longer RNAs as qualitatively observed by
comparing the trends of our simulations with a theoretical approach
based on an ideal semiflexible polymer chain.