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The modified duplexes were desalted by gel filtration chromatography over Sephadex G-25.
The modified duplexes were each unwound approximately 15° at the adducted sites.
The modified duplexes were each subjected to 1000 cycles of potential energy minimization.
To obtain the A-form and B-form starting structures that were used for subsequent restrained molecular dynamics (rMD) calculations, these A-form or B-form modified duplexes were energy-minimized using 200 iterations with the conjugate gradient algorithm, in the absence of experimental restraints.
To obtain the A-form and B-form starting structures that were used for subsequent restrained molecular dynamics (rMD) calculations, these A-form or B-form modified duplexes were energy minimized using 200 iterations with the conjugate gradients algorithm, in the absence of experimental restraints.
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The full-range H imino and dynamic F NMR spectra of the modified duplexes are shown in Supporting Information, Figure S1.
The temperature dependencies on the line widths for base pairs of the unmodified and modified duplexes are compared in Figure S2 of the Supporting Information.
The modified duplex was subjected to 1000 cycles of potential energy minimization.
This suggests that neither modified duplex is stabilized by hydrogen bonding interactions involving the DHB hydroxyl groups.
The Tm of the modified duplex was 40 °C in 10 mM NaH2PO4, 100 mM NaCl, and 5 μM Na2EDTA (pH 5.2).
The spectral resolution of this modified duplex was challenging because of a large number of pyrimidine aromatic resonances, e.g., T H6, T H6, C H6, C H6, T H6, and C H6, resonating between 7.35 and 7.45 ppm.
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