1 research outputs found
Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes
The assembly of stacked dyes on DNA
is of interest for electron
transfer, light harvesting, sensing, and catalysis applications. A
combination of UV/vis absorption, linear dichroism (LD), and circular
dichroism (CD) was applied to characterize thoroughly the aggregation
with DNA of the phenothiazine dyes methylene blue, azure B, and thionine.
Aggregates of each dye with [poly(dG-dC)]<sub>2</sub>, [poly(dA-dT)]<sub>2</sub>, and calf thymus DNA were explored at high dye:DNA binding
ratios, where excess dye groove-binds after all intercalation sites
are filled. The organization of the aggregates (dimers, trimers, and
multimers) with polydeoxynucleotides displays a structural diversity
that depends on DNA sequence, extent of methylation of dye exocyclic
amine groups, and ionic strength. The dyes typically form right-handed
H-aggregates having negative LD, consistent with stepped stacking
along the minor groove. However, aggregates in some dye:DNA aggregates
show left-handed chirality or positive LD, indicating unusual modes
of aggregation such as formation of adventitious dimers between intercalated
and minor groove bound dye. In terms of sequence-dependence, methylene
blue shows more extensive aggregation with [poly(dA-dT)]<sub>2</sub>, while thionine aggregates more with [poly(dG-dC)]<sub>2</sub>.
Azure B has distinctive behavior that is unlike either other dyes.
Thus, although these phenothiazine dyes possess a common tricyclic
framework, the organization of their polynucleotide-facilitated aggregates
depends sensitively on the extent of methylation of the exocyclic
amines