Supplementary Materialsbi501534x_si_001. 3646.4, found 3647.8; calcd for DDDm [M C H]?3660.5, found 3663.4; calcd for DDDhm [M C H]?3675.5, found 3679.7; calcd for DDDf [M C H]?3674.4, found 3673.2; calcd for DDDca [M C H]?3690.4, found 3693.1). Oligodeoxynucleotides were prepared in 100 mM NaCl, 50 M Na2EDTA, in 10 mM sodium phosphate (pH 7.0), heated purchase MK-2206 2HCl at 85 C for 15 min, and annealed by cooling to space temp. Duplex concentrations were determined by UV absorbance, using extinction coefficients calculated at 260 nm.47 Thermal Denaturation The concentration of DNA was 1.2 M. Measurements were carried out in 100 mM NaCl, 50 M Na2EDTA, in 10 mM sodium phosphate (pH 7.0). The temp was improved from 10 to 80 C at 1 C/min. dimension and 1k actual points in the dimension. Spectra were zero-packed during processing to create a 2k 2k matrix. Chemical shifts were referenced to the chemical shift of water at the corresponding temp, with respect to 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). To observe exchangeable protons, samples were prepared in 9:1 H2O/D2O. For observation of imino protons, spectra were recorded at 5, 15, 25, 35, 45, and 55 C. NOESY spectra were collected at 5 C with 70 or 250 ms mixing instances and relaxation delay of 2.0 s. Water suppression was achieved by the Watergate pulse sequence.50 Data were processed with TOPSPIN (2.0.b.6, Bruker Biospin Inc., Billerica, MA). Foundation Pair Opening NMR data were collected at 500 MHz using a 5 mm cryogenic probe, at 15 C. Samples were in 180 L of 9:1 H2O/D2O purchase MK-2206 2HCl containing 100 mM NaCl, 50 M Na2EDTA, 11 mM NaN3, 1 mM triethanolamine, in 10 mM sodium phosphate (pH 8.9).51?55 The presence of triethanolamine enabled the pH of the sample to be monitored during the titration, C ?is the intensity for the em i /em th measurement of an equivalent reflection with indices em h /em , em k /em , and em l /em . Crystal Structure Determination and Refinement Structures were determined by molecular replacement using the DDD as the search model (PDB ID code 436D).39 Molecular replacement searches were completed with MOLREP67,68 in Rabbit Polyclonal to RCL1 the CCP4 suite.65 An initial model was checked and rebuilt in COOT.69 The model was rebuilt and further refined using REFMAC.70,71 Final models were refined against all reflections, except for 5% randomly selected reflections used for monitoring em R /em free. The refinement statistics are presented in Table 1. Data Deposition Complete structure factors and data coordinates were deposited in the Protein Data Bank (http://pdb.org): PDB ID code 4I9V for DDDhm, 4QC7 for DDDf, and 4PWM for DDDca. Results Stabilities of the Duplexes Containing Oxidized Cytosines The impact of placing 5hmC, 5fC, or 5caC site specifically into the 5-CG-3 sequence was investigated by incorporating each oxidized cytosine into the 5-T8X9G10-3 sequence of the DDD.37,38 The em T /em m values of the duplexes were obtained in 100 mM NaCl at pH 7. They were compared to both the unmodified DDD and also to the DDD containing 5mC in the 5-T8X9G10-3 sequence (DDDm). The em T /em m of the DDD duplex was 48 C, the em T /em m of the DDDm duplex was 46 C, the em T /em m of the DDDhm duplex was 48 C, and the em T /em m of the DDDf duplex was 46 C. purchase MK-2206 2HCl These small differences in em T /em m suggested that the presence of 5mC or of the oxidized cytosines 5hmC or 5fC in the 5-T8X9G10-3 sequence did not greatly affect the em T /em m of the DDD. In contrast, the em T /em m of the DDDca duplex increased to 54 C. NMR spectra of the exchangeable guanine N1H and thymine N3H imino protons were recorded from 5C55 C (Figure ?(Figure1).1). The resonances were assigned using standard methods.72 For the DDDca duplex, the G4 N1H proton remained sharp at 55 C, consistent with the increased em T /em m value associated with the 5caC nucleobase in the 5-T8X9G10-3 sequence. At the neighbor A5:T8 base pair, the T8 N3H resonance remained detectable at 55 C, although it exhibited broadening. At the neighbor C3:G10 base pair, the G3 N1H resonance remained detectable at 55 C, also exhibiting broadening. The stabilizing effect extended two base pairs in each direction, also including the.