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• W2914355379 abstract "RNA thermodynamics play an important role in determining the two- and three-dimensional structures of RNA. Internal loops of the sequence 5′-GMNU/3′-UNMG are relatively unstable thermodynamically. Here, five duplexes with GU-flanked 2 × 2 nucleotide internal loops were structurally investigated to reveal determinants of their instability. The following internal loops were investigated: 5′-GCAU/3′-UACG, 5′-UUCG/3′-GCUU, 5′-GCUU/3′-UUCG, 5′-GUCU/3′-UCUG, and 5′-GCCU/3′-UCCG. Two-dimensional nuclear magnetic resonance spectra indicate the absence of GU wobble base pairing in 5′-GCUU/3′-UUCG, 5′-GUCU/3′-UCUG, and 5′-GCCU/3′-UCCG. The 5′-GCUU/3′-UUCG loop has an unusual conformation of the GU base pairs, in which U’s O2 carbonyl forms a bifurcated hydrogen bond with G’s amino and imino protons. The internal loop of 5′-GUCU/3′-UCUG displays a shifted configuration in which GC pairs flank a U-U pair and several U’s are in fast exchange between positions inside and outside the helix. In contrast, 5′-GCAU/3′-UACG and 5′-UUCG/3′-GCUU both have the expected GU wobble base pairs flanking the internal loop. Evidently, GU base pairs flanking internal loops are more likely to display atypical structures relative to Watson–Crick base pairs flanking internal loops. This appears to be more likely when the G of the GU pair is 5′ to the loop. Such unusual structures could serve as recognition elements for biological function and as benchmarks for structure prediction methods." @default.
• W2914355379 created "2019-02-21" @default.
• W2914355379 creator A5013801926 @default.
• W2914355379 creator A5020257959 @default.
• W2914355379 creator A5052987216 @default.
• W2914355379 date "2019-01-31" @default.
• W2914355379 modified "2023-10-14" @default.
• W2914355379 title "Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures" @default.
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• W2914355379 doi "https://doi.org/10.1021/acs.biochem.8b01027" @default.
• W2914355379 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6559796" @default.
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• W2914355379 hasPublicationYear "2019" @default.
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