Chemical probes of DNA structure in chromatin

(1,4,7-trimethyl-1,4,7-triazacyclononane)iron (III)-mediated cleavage of DNA: detection of selected protein-DNA interactions

A new reagent for the oxidative cleavage of DNA, (1,4,7-trimethyl-1, 4,7-triazacyclononane)iron(III) chloride was recently introduced. We have determined the utility of this reagent for detecting protein-DNA interactions within two types of complexes. Interestingly, we find that the rates of DNA cleavage by this reagent are differentially affected by the two classes of protein-DNA interactons studied. We find that the rate of DNA cleavage by this reagent is relatively unaffected by the non-sequence-specific histone-DNA interactions within a nucleosome complex. Conversely, a clear footprint pattern is obtained with two different DNA sequence-specific protein-DNA complexes. The results suggest that (1,4,7-trimethyl-1,4,7-triazacyclononane)iron(III) chloride will be a useful reagent to probe trans -acting-factor-DNA interactions within a chromatin environment. Differences between these two types of protein-DNA interactions, which might account for this observation, are discussed.

Exciton coupled circular dichroic studies of self-assembled brevetoxin-porphyrin conjugates in lipid bilayers and polar solvents

BACKGROUND

Brevetoxins, involved in the 'red tide' as well as shellfish poisoning, are known to bind to cell membranes and membrane proteins. Brevetoxin B (BTX-B) interacts specifically with neuronal sodium channels. We recently found that BTX also induces selective ion movements across lipid bilayers through transmembrane BTX self-assemblies.

RESULTS

We examined the self-assembly of several BTX derivatives in the presence and absence of cations and lipid bilayers using the powerful porphyrin chromophores as circular dichroism labels. BTX derivatives self-assemble into tubes, which can bind to metals both when soluble and when inserted into the bilayer to form transmembrane pores. Depending on the tendency of the BTX derivative to self-aggregate (the critical 'micelle' concentration, cmc), it may aggregate in solution before membrane insertion, or may insert itself into the membrane as a monomer before assembling the pore.

CONCLUSIONS

The active BTX-B complex in lipid bilayers is a cyclic, transmembrane self-assembly consisting of antiparallel aligned BTX molecules that can mediate selective ion movement through membranes. The differences in pore formation mechanisms between BTX derivatives may be reflected in differences in pore formation by natural BTX variants, perhaps explaining their varying levels of toxicity.