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Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states

Author

Listed:
  • Yanjiao Wang

    (Tsinghua University)

  • Ge Han

    (Tsinghua University)

  • Xiuying Jiang

    (Tsinghua University)

  • Tairan Yuwen

    (Peking University)

  • Yi Xue

    (Tsinghua University)

Abstract

NH groups in proteins or nucleic acids are the most challenging target for chemical shift prediction. Here we show that the RNA base pair triplet motif dictates imino chemical shifts in its central base pair. A lookup table is established that links each type of base pair triplet to experimental chemical shifts of the central base pair, and can be used to predict imino chemical shifts of RNAs to remarkable accuracy. Strikingly, the semiempirical method can well interpret the variations of chemical shifts for different base pair triplets, and is even applicable to non-canonical motifs. This finding opens an avenue for predicting chemical shifts of more complicated RNA motifs. Furthermore, we combine the imino chemical shift prediction with NMR relaxation dispersion experiments targeting both 15N and 1HN of the imino group, and verify a previously characterized excited state of P5abc subdomain including an earlier speculated non-native G•G mismatch.

Suggested Citation

  • Yanjiao Wang & Ge Han & Xiuying Jiang & Tairan Yuwen & Yi Xue, 2021. "Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21840-x
    DOI: 10.1038/s41467-021-21840-x
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    Cited by:

    1. Ge Han & Yi Xue, 2022. "Rational design of hairpin RNA excited states reveals multi-step transitions," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Yanyan Xue & Jun Li & Dian Chen & Xizhu Zhao & Liang Hong & Yu Liu, 2023. "Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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