All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic.

ABSTRACT: Given their increasingly frequent usage, understanding the chemical and structural properties which allow therapeutic nucleic acids to promote the death of cancer cells is critical for medical advancement. One molecule of interest is a 10-mer of FdUMP (5-fluoro-2'-deoxyuridine-5'-O-monophosphate) also called F10. To investigate causes of structural stability, we have computationally restored the 2' oxygen on each ribose sugar of the phosphodiester backbone, creating FUMP[10]. Microsecond time-scale, all-atom, simulations of FUMP[10] in the presence of 150 mM MgCl₂ predict that the strand has a 45% probability of folding into a stable hairpin-like secondary structure. Analysis of 16 μs of data reveals phosphate interactions as likely contributors to the stability of this folded s

SUBMITTER: Melvin RL 

PROVIDER: S-EPMC5719488 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature