Restricted puckering of mineralized RNA-like riboses.

The pseudorotational motions of highly hydroxylated pentafuranose sugars in the free state and tethered to hydroxyapatite have been compared. The conformation pentafuranose ring remains restricted at the North region of the pseudorotational wheel, which is the one typically observed for nucleosides and nucleotides in the double helix A-RNA, when the phosphate-bearing sugar is anchored to the mineral surface. Results indicate that the severe restrictions imposed by the mineral are responsible of the double helix preservation when DNA and RNA are encapsulated in crystalline nanorods.

Self-assembly of a designed amyloid peptide containing the functional thienylalanine unit.

The self-assembly of a peptide based on a sequence from the amyloid beta peptide but incorporating the non-natural amino acid beta-2-thienylalanine (2-Thi) has been investigated in aqueous and methanol solutions. The peptide AAKLVFF was used as a design motif, replacing the phenylalanine residues (F) with 2-Thi units to yield (2-Thi)(2-Thi)VLKAA. The 2-Thi residues are expected to confer interesting electronic properties due to charge delocalization and pi-stacking. The peptide is shown to form beta-sheet-rich amyloid fibrils with a twisted morphology, in both water and methanol solutions at sufficiently high concentration. The formation of a self-assembling hydrogel is observed at high concentration. Detailed molecular modeling using molecular dynamics methods was performed using NOE constraints provided by 2D-NMR experiments. The conformational and charge properties of 2-Thi were modeled using quantum mechanical methods, and found to be similar to those previously reported for the beta-3-thienylalanine analogue. The molecular dynamics simulations reveal well-defined folded structures (turn-like) in dilute aqueous solution, driven by self-assembly of the hydrophobic aromatic units, with charged lysine groups exposed to water.