Vibrational circular dichroism and IR absorption of DNA complexes with Cu 2+ ions

Vibrational circular dichroism (VCD) spectroscopy and simultaneous IR absorption measurements are applied to study the interaction of natural calf thymus DNA with Cu 2+ ions at room temperature in a Cu 2+ concentration range of 0–0.4 M (a Cu 2+ /phosphate molar ratio [Cu]/[P] of 0–0.7). In some important instances, VCD provides more detailed insights than previous IR investigations whereas in several others it leads to the same interpretations. The Cu 2+ ions bind to phosphate groups at a low metal concentration. Upon increasing the ion concentration, chelates are formed in which Cu 2+ binds to the N 7 of guanine (G) and a phosphate group. Detectable only by VCD, significant distortion of most guanine‐cytosine (GC) base pairs occurs at a [Cu]/[P] ratio of 0.5 with only a minor affect on adenine‐thymine (AT) base pairs, which favors a “sandwich” complex in which a Cu 2+ ion is inserted between two adjacent guanines in a GpG sequence. The AT base pairs become significantly distorted when the metal concentration is increased to 0.7 [Cu]/[P]. A number of GC base pairs, which are possibly involved in sandwich complexes, remain stacked and paired even at 0.7 [Cu]/[P], preventing complete strand separation. The DNA secondary structure changes considerably from the standard B‐form geometry at a [Cu]/[P] ratio of 0.4 and higher. A further transition to some intermediate conformation that is inconsistent with either the A‐ or Z‐form or a completely denatured state is suggested in agreement with other works. In general, VCD proves to be a reliable indicator of the 3‐dimensional structure of the DNA–metal ion complexes, which reveals structural details that cannot be deduced from the IR absorption spectra alone. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 374–390, 2003