Vibrational circular dichroism and IR absorption of DNA complexes with Cu2+ ions.
Vibrational circular dichroism (VCD) spectroscopy and simultaneous IR absorption measurements are applied to study the interaction of natural calf thymus DNA with Cu2+ ions at room temperature in a Cu2+ concentration range of 0-0.4M (a Cu2+/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 Cu2+ ions bind to phosphate groups at a low metal concentration. Upon increasing the ion concentration, chelates are formed in which Cu2+ binds to the N7 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 Cu2+ 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.
Andrushchenko
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Department of Chemistry, Faculty of Science, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada.
van de Sande
J H
JH
Wieser
H
H
D000818:Animals; D001665:Binding Sites; D002417:Cattle; D002942:Circular Dichroism / Q000379:methods*; D003300:Copper / Q000737:chemistry*; D018899:CpG Islands; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D007477:Ions; D008670:Metals / Q000737:chemistry; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D013055:Spectrophotometry, Infrared / Q000379:methods*; D013696:Temperature; D013950:Thymus Gland / Q000378:metabolism
D007477:Ions; D008670:Metals; D003300:Copper; D004247:DNA