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Pairing of a consensus sequence of the precursor (pre)-mRNA intron with a short region of the U2 small nuclear (sn)RNA during assembly of the eukaryotic spliceosome results in formation of a complementary helix of seven base pairs with a single unpaired adenosine, whose 2' OH initiates the nucleophilic attack at the pre-mRNA 5' splice site during the first step of splicing. The structure of the spliceosomal branch site solved by Newby and Greenbaum showed that a highly conserved pseudouridine residue in U2 snRNA induces a dramatically altered structure compared with that of its unmodified counterpart. In this study, both modified and unmodified U2 snRNA-intron duplexes were analyzed using computer simulations including preliminary molecular dynamics (MD) simulations, electrostatic potential, surface area, and solvation free energy calculations. The preliminary MD simulations produce stable trajectories of the RNA duplexes in solution. The surface electrostatic potentials were calculated using finite difference Poisson-Boltzmann algorithm and a hybrid boundary element and finite difference Poisson-Boltzmann approach. Results show a region of exceptionally negative potential near the 2' OH of the branch site adenosine. The two RNA duplexes have similar solvent accessible surface areas, whereas the surface accessible area of the 2' OH of the branch site adenosine of the modified RNA duplex is considerably smaller than that of the unmodified RNA duplex. The solvation free energy calculation indicates that the unmodified RNA duplex is favored over the modified RNA duplex.