Abstract
An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA.
Highlights
The majority of natural and artificial applications involving small molecule-DNA/RNA recognition depend on several noncovalent binding modes
The synthetic routes to the new adenine–DBTAA conjugates AP3am and AP5 are summarized in Scheme 2, the details of which are given in the Experimental section
A more detailed analysis of induced CD spectrum (ICD) data revealed that ICD bands of AP3/AP3am were highly sensitive to the secondary structure of DNA/RNA and, in particular, the minor groove properties (Table S1, Supporting Information File 1)
Summary
The majority of natural and artificial applications involving small molecule-DNA/RNA recognition depend on several noncovalent binding modes. Double-stranded DNA/RNA targets chosen for this study are long (
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