Restraints for structure calculations
This protocol is extracted from research article:
Encoding canonical DNA quadruplex structure
Sci Adv, Aug 31, 2018; DOI: 10.1126/sciadv.aat3007

Distance restraints were typically derived from NOESY experiments in “100%” 2H2O at three to five mixing times, and distances estimated from the initial buildup rates of the NOE curves by the two-spin approximation rij = rref(Rij/Rref)1/6, where rij is the distance between protons i and j, rref is a reference distance, and Rij and Rref are the initial buildup rates. Interproton distances were estimated using the average of the volume integral of the distance between H5-methyl in thymine residues, that is, 2.46 Å. Only two limiting mixing times (60 and 200 ms) were used to derive distance restraints from the exchangeable protons collected with jump-and-return NOESY spectra at 5°C in 90% H2O, 10% 2H2O. Distances were assumed to be 3.0 ± 0.8 Å for strong peaks observed in the 60-ms mixing time spectrum, 4.0 ± 1.2 Å for medium cross-peaks observed in the 200-ms mixing time spectrum, and 5.0 ± 1.8 Å for cross-peaks not observed in a 60-ms mixing time spectrum.

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