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Original Articles

Determination of The Solution Conformation of A Non-Uniformly Deuterium Labelled (Uppsala ‘Nmr-Window’) 21Mer Rna Hairpin by Nmr Spectroscopy And Computational Methods.

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Pages 743-750 | Published online: 22 Aug 2006

REFERENCES

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  • Distance constraints were divided into the following four reions: (i)1.8–3.0 Å (strong volumes), (ii) 1.8–4.0 Å (medium), (iii) 1.8–5.0 Å (weak) and (iv) 1.8–7.0 Å (very weak volumes). The volume for the H5-H6 crosspeak of C9 at each mixing time was used as reference volume with a corresponding distance of 2.46 Å
  • Additional distance constraints: 20 hydrogen bond constraints for the seven basepairs in the stem, 12 distance constraints involving the H1-H1′ crosspeaks (see Fig. 1) in the stem, six planarity constraints to ensure planarity of the basepairs, and 122 dihedral constraints (α, β, γ, ε, ζ, χ and V0-V4) to keep the stem nucleotides in an A-RNA conformation
  • Borgias , B. A. , Thomas , P. D. , Liu , H. , Kumar , A. , Tonelli , M. and James , T. L. 1995 . MARDIGRAS 5.1 , San Fransisco , CA : University of California .
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  • All AMBER calculations were performed in vacuo with a constant dielectric of 4.0 (ε=4.0) and infinite non–bonded cutoffs. Shake17 was used for bonds involving hydrogen atoms and the time step was 1 fs for all MDs. The Berendsen algorithm18 was used to control the temperature with τ=0.2 ps
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  • Force constants: 40 kcal.mol−1.Å−2 for distances derived from NOESY spectra, 80 kcal.mol−1.Å−2 for hydrogen bond distances, 160 kcal.mol−1.Å−2 for the two H1-H1′ distances, and 400 kcal.mol−1.rad−2 for torsions
  • Force constants: 5 kcal.mol−1.Å−2 for distances derived from NOESY spectra, 10 kcal.mol−1.Å−2 for hydrogen bond distances, 2.5 kcal.mol−1.Å−2 for the twelve H1-H1′ distances, and 50 kcal.mol−1.rad−2 for torsions
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  • González , C. , Stec , W. , Reynolds , M. A. and James , T. L. 1995 . Biochemistry , 34 : 4969 – 4982 .

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