Molecular Basis for the DNA Sequence Specificity of the Pluramycins. A Novel Mechanism Involving Groove Interactions Transmitted through the Helix via Intercalation To Achieve Sequence Selectivity at the Covalent Bonding Step

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Abstract

The pluramycin antitumor antibiotics, which include the altromycins, pluramycin, hedamycin, and rubiflavin, are a group of highly evolved DNA-reactive compounds that have structural features reminiscent of both nogalamycin and the aflatoxins. As such, they are characterized as “threading intercalators” with the added ability to alkylate N7 of guanine (see preceding article in this issue). In this article we have demonstrated that different members of this group of antibiotics have sequence specificities that differ for the base pair to the 5' side of the alkylated guanine and also have a range of reactivities with susceptible sequences. Subsequent experiments were designed to determine the molecular origin for both these observed contrasting sequence specificities and covalent reactivities. First, neopluramycin, an analog of pluramycin that lacks the epoxide, and thus is unable to covalently modify DNA, but is in other respects structurally similar, exhibits no discernible sequence selectivity. This suggests that the sequence selectivity of the pluramycins is determined at the covalent bonding step rather than the precovalent binding interactions. Second, using An tracts of varying length (n = 1–5) to modulate the minor groove geometry to the 5' side of the covalent alkylation site, this structural parameter has been shown to have a major effect on both sequence specificity and alkylation reactivity. Last, the electronegativity of the N7 position of the alkylated base can also affect reactivity and, to a lesser extent, sequence specificity. In order to determine the molecular details of the interactions in the minor and major grooves, which could give rise to the different sequence specificities of the nonclassical (typified by altromycin B) and classical (typified by hedamycin) pluramycins, we have used molecular models of the altromycin B and hedamycin-DNA adducts that are derived from high-field NMR data of their 10-mer duplex diadducts. These studies demonstrate that it is likely that the sequence-dependent reactivities of the epoxide of the pluramycin to N7 of guanine are dependent upon the relative extent of a “proximity effect”. The magnitude of the proximity effect is determined by a “steering reaction”, which takes place in the minor and major grooves due to the different placement of the carbohydrate substituents on the pluramycins and their hydrogen bonding and van der Waals interactions with the base pairs to the 5' side of the alkylation site. This is proposed to be a novel mechanism for sequence recognition, where cooperative interactions in the minor and major grooves transmitted via the intercalation moiety dictate the positioning of the epoxide in the major groove and, thus, sequence reactivity. Finally, we propose that the increased reactivity of the classical pluramycins in contrast to the altromycins is at least partially determined by the “reach” of the reactive epoxide in the major groove, which varies from one group to another. The molecular mechanisms for sequence recognition described here provide a new paradigm for sequence recognition by minor and major groove interactions mediated by intercalactive binding but achieved at the covalent bonding step.

Original languageEnglish (US)
Pages (from-to)2430-2440
Number of pages11
JournalJournal of the American Chemical Society
Volume117
Issue number9
DOIs
StatePublished - Jan 1 1995
Externally publishedYes

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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