Tris(tetramethylphenanthroline)ruthenium(II): a chiral probe that cleaves A-DNA conformations.

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Abstract
.LAMBDA.-Tris(3,4,7,8-tetramethyl-1,10-phenanthroline)ruthenium(II) [.LAMBDA.-Ru(TMP)32+] was found to be a distinctive molecular tool to examine the local variation in conformation along the strand. The metal complex binds cooperatively to A-form helices of various base sequences under conditions where little or no binding was found to analogous B-form DNAs. Photoactivate DNA cleavage may be coupled to this conformation-secific binding by taking advantage of the photophysical properties of ruthenium(II) complexes. .LAMBDA.-Ru(TMP)32+ cleaves preferentially 3H-labeled A-form polynucleotides upon irradiation with visible light. The photoinduced DNA strand scission is likely to be mediated by singlet oxygen, which leads to a preferential cleavage of guanine residues. Comparative mapping of cleavage sites on a linear pBR322 fragment for tris(phenanthroline)ruthenium(II), which binds to B-DNA and cleaves also by sensitization of singlet oxygen, and for Ru(TMP)32+ shows the selective binding of .LAMBDA.-Ru(TMP)32+ to conformationally distinct sites along the fragment. These sites correspond to 5- to 13-base-pair homopyrimidine stretches.