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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Binding of Actinomycin D to Single-stranded DNA of Sequence Motifs d(TGTCTnG) and d(TGTnGTC).

Our laboratory has recently found that actinomycin D (ACTD) binds strongly to d(CGTCGTCG) despite the absence of a preferred GpC sequence and the lack of complete self-complementarity. Binding studies with oligomers derived from base-replacements on this oligomer led to the finding that ACTD binds strongly to d(TGTCATTG), of apparent single-stranded conformation, with 1 : 1 drug to strand binding stoichiometry. A binding model was speculated in which the G base at the 3'-terminus folds back to form a base pair with the interior C to enable the 3'-sides of both G¢s to stack on opposite faces of the drug chromophore via a swing-out T base. To provide support for such a model, equilibrium binding studies were made with oligomers of sequence motifs d(TGTCTnG) and d(TGTnGTC) in which the possible formation of a dimeric duplex is considerably diminished. It was found that ACTD binds strongly to d(TGTCTnG) with n = 3 and 4 but exhibits reduced affinities for n < 3. On the other hand, ACTD binds strongly to d(TGTnGTC) with n = 4 and 5 but exhibits considerably weaker affinities for n < 4. Comparative studies with the corresponding GpC-containing oligomers were also made. These results support the hairpin-binding model and provide evidence that a strong ACTD binding requires the simultaneous stacking of 3'-sides of both G bases on the opposite faces of the drug chromophore.

Fu-Ming Chen and Feng Sha

Department of Chemistry, Tennessee State University, Nashville, Tennessee 37209-1561.
E-mail: fchen@tnstate.edu Tel: 615-963-5325 Fax: 615-963-5434.