UNASSIGNED: @entity3918 1 ( @entity6045 ) is a @entity74 caused by expansion of CTG repeats in DNA. Once transcribed, these repeats form RNA hairpins with repeating 1*1 @entity4334 UU internal loop motifs, r(CUG)n, which attract @entity48973 ( @entity48973 ) protein leading to the disease. In @entity6045 CUG can be repeated thousands of times, so these structures are intractable to characterization using structural biology. However, inhibition of @entity48973 -r(CUG)n binding requires a detailed analysis of the 1*1 UU internal loops. In this contribution we employ regular and umbrella sampling @entity74 ( @entity74 ) simulations to describe the structural and thermodynamic properties of 1*1 UU internal loops. Calculations were run on a reported crystal structure and a designed system, which mimics an infinitely long RNA molecule with continuous CUG repeats. Two-dimensional (2D) potential of mean force (PMF) surfaces were created by umbrella sampling, and the discrete path sampling (DPS) method was utilized to investigate the energy landscape of 1*1 UU RNA internal loops, revealing that 1*1 UU base pairs are dynamic and strongly prefer the anti-anti conformation. Two 2D PMF surfaces were calculated for the 1*1 UU base pairs, revealing several local minima and three syn-anti     anti-anti transformation pathways. Although at room temperature the syn-anti     anti-anti transformation is not observed on the @entity74 time scale, one of these pathways dominates the dynamics of the 1*1 UU base pairs in temperature jump @entity74 simulations. This mechanism has now been treated successfully using the DPS approach. Our results suggest that local minima predicted by umbrella sampling calculations could be stabilized by small molecules, which is of great interest for future drug design. Furthermore, distorted GC/CG conformations may be important in understanding how @entity48973 binds to RNA CUG repeats. Hence we provide new insight into the dynamic roles of RNA loops and their contributions to presently incurable diseases.

Computational Investigation of RNA CUG Repeats Responsible for XXXX 1.

@entity6045 :: ('1760', 'Gene') :: ['DM1'] @entity74 :: ('MESH:D030342', 'Disease') :: ['molecular dynamics', 'genetic disease', 'MD'] @entity3918 :: ('MESH:D009223', 'Disease') :: ['Myotonic Dystrophy'] @entity4334 :: ('D009711', 'Chemical') :: ['nucleotide'] @entity48973 :: ('4154', 'Gene') :: ['muscleblind-like 1', 'MBNL1']
@entity3918 :: (MESH:D009223,Disease) :: ['Myotonic Dystrophy']
