2.4. Stopped-Flow Experiments

Stopped-flow measurements with monitoring by CD (CDSF) were carried out at 25 °C on a Chirascan spectrophotometer (Applied Photophysics) equipped with a stopped-flow accessory with a 10 mm optical path. CD was recorded at 288 nm, and the bandwidth was set to 6 nm. In all CDSF experiments, the preannealed ODN samples (rapid preannealing for Uo and U1Z and slow preannealing for other ODNs) in 50 mM sodium phosphate buffer were rapidly mixed (1: 4) with 80 mM sodium phosphate buffer of a different pH (4.5 or 9.0). There were four series of CDSF measurements:

6.8 → 5.7 pH jump (for To, T1Zg, Uo and U1Zg). The ODN solution (70 μM for To and T1Zg, 15 μM for Uo and U1Zg) in 50 mM sodium phosphate, pH 6.8, was mixed (1:4) with 80 mM sodium phosphate, pH 4.5, to a final sodium phosphate concentration of 74 mM, pH 5.7.

5.2 → 7.5 pH jump (for To, T1Zg, Uo and U1Zg). The ODN solution (70 μM for To and T1Zg, 15 μM for Uo and U1Zg) in 50 mM sodium phosphate, pH 5.2, was mixed (1:4) with 80 mM sodium phosphate, pH 9.0, to a final sodium phosphate concentration of 74 mM, pH 7.5.

8.0 → 6.0 pH jump (for Go, G1Zg, G2Zg, Mo, M1Zg and M6Zg). The ODN solution (15 μM) in 50 mM sodium phosphate, pH 8.0, containing 90 mM NaCl, was mixed (1:4) with 80 mM sodium phosphate, pH 4.5, that also contained 90 mM NaCl to a final sodium phosphate concentration of 74 mM, pH 6.0.

6.7 → 7.9 pH jump (for Go, G1Zg, G2Zg, Mo, M1Zg and M6Zg). The ODN solution (15 μM) in 50 mM sodium phosphate, pH 6.7, containing 90 mM NaCl, was mixed (1:4) with 80 mM sodium phosphate, pH 9.0, that also contained 90 mM NaCl to a final sodium phosphate concentration of 74 mM, pH 7.9.

Each experiment was performed at least in triplicate; the resulting kinetic curves were averaged and fitted to single exponentials using ProData software (Applied Photophysics, UK).