Thermodynamics of the Kink‐Turn Motif in RNA

Abstract

The kink‐turn is a helix‐internal loop‐helix with a three‐nucleotide bulge loop containing a canonical stem (Watson‐Crick base pairing) on one side and non‐canonical stem containing two or three G•A sheared base pairs on the other side. The sheared base pairs in the non‐canonical stem give the construct the flexibility to adopt a 120° kink between the two stems. The kink‐turn is expected to form in the presence of metal‐ions to neutralize the charges on phosphates that are in close proximity. RNA constructs were designed to mimic the Haloarcula Marismortui KT7 from the 28S ribosome. Thermodynamic properties of constructs were tested in a 1 M KCl salt buffer and a 10 mM magnesium buffer at either pH 5.5 or 7. The wild‐type construct shows a −2.36 kcal/mol gain in stability in the magnesium buffer compared to the 1 M KCl buffer at pH 7. Direct measurements of the heat released upon ion‐binding to RNA is being measured using ITC to determine the enthalpy and binding constants of RNA‐magnesium interactions.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.