Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings.


Journal Article

We present a protocol for determining the relative orientation and dynamics of A-form helices in 13C/15N isotopically enriched RNA samples using NMR residual dipolar couplings (RDCs). Non-terminal Watson-Crick base pairs in helical stems are experimentally identified using NOE and trans-hydrogen bond connectivity and modeled using the idealized A-form helix geometry. RDCs measured in the partially aligned RNA are used to compute order tensors describing average alignment of each helix relative to the applied magnetic field. The order tensors are translated into Euler angles defining the average relative orientation of helices and order parameters describing the amplitude and asymmetry of interhelix motions. The protocol does not require complete resonance assignments and therefore can be implemented rapidly to RNAs much larger than those for which complete high-resolution NMR structure determination is feasible. The protocol is particularly valuable for exploring adaptive changes in RNA conformation that occur in response to biologically relevant signals. Following resonance assignments, the procedure is expected to take no more than 2 weeks of acquisition and data analysis time.

Full Text

Duke Authors

Cited Authors

  • Bailor, MH; Musselman, C; Hansen, AL; Gulati, K; Patel, DJ; Al-Hashimi, HM

Published Date

  • 2007

Published In

Volume / Issue

  • 2 / 6

Start / End Page

  • 1536 - 1546

PubMed ID

  • 17571061

Pubmed Central ID

  • 17571061

Electronic International Standard Serial Number (EISSN)

  • 1750-2799

Digital Object Identifier (DOI)

  • 10.1038/nprot.2007.221


  • eng

Conference Location

  • England