English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

The RNA “GAGU” duplex, (5′GAC GAGU GUCA) 2 , contains the internal loop (5′-GAGU-3′) 2  , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of  trans -Watson–Crick/Hoogsteen GG pairs, A residues stacked on each other, U residues bulged outside the helix, and all sugars with a C2′- endo  conformation. This differs markedly from the internal loops, (5′-G AG C-3′) 2 , (5′-A AG U-3′) 2 , and (5′-UAGG-3′) 2 , which all have  cis -Watson–Crick/Watson–Crick AG “imino” pairs flanked by  cis -Watson–Crick/Watson–Crick canonical pairs resulting in maximal hydrogen bonding. Here, molecular dynamics was used to test whether the Amber force field (ff99 + bsc0 + OL3) approximates molecular interactions well enough to keep stable the unexpected conformation of the GAGU major duplex structure and the NMR structures of the duplexes containing (5′-G AG C-3′) 2 , (5′-A AG U-3′) 2 , and (5′-U AG G-3′) 2  internal loops. One-microsecond simulations were repeated four times for each of the duplexes starting in their NMR conformations. With the exception of (5′-UAGG-3′) 2 , equivalent simulations were also run starting with alternative conformations. Results indicate that the Amber force field keeps the NMR conformations of the duplexes stable for at least 1 µsec. They also demonstrate an unexpected minor conformation for the (5′-GAGU-3′) 2  loop that is consistent with newly measured NMR spectra of duplexes with natural and modified nucleotides. Thus, unrestrained simulations led to the determination of the previously unknown minor conformation. The stability of the native (5′-GAGU-3′) 2  internal loop as compared to other loops can be explained by changes in hydrogen bonding and stacking as the flanking bases are changed.

Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation