Synthesis and binding of proflavine diazides as functional intercalators for directed assembly on DNA

Abstract

Proflavine diazide (PD) with amido-azide substituents on the amine groups and its N-methylated analogue (MePD) bind strongly to DNA by nearest-neighbour intercalation with little sequence selectivity, presenting reactive azide groups in the major groove. PD is neutral in aqueous solution but experiences binding-coupled protonation on interaction with DNA with an apparent pK a shift of 2.5 units. MePD can be click modified in situ on DNA with alkyne-functionalised thienyl-pyrrole as a precursor for conducting polymer synthesis, and remains intercalated after reaction with the substituents aligned in the groove.

Click Modification of Diazido Acridine Intercalators: A Versatile Route towards Decorated DNA Nanostructures

“…Conditions for full loading of the DNA are described in the Supporting Information and were designed to ensure quantitative binding of 1 or 2 (i.e., minimal unbound material) up to the intercalation saturation limit. We previously postulated that the intercalators 1 and 2 remain effectively locked into the DNA helix after click functionalization as supported by linear dichroism spectroscopy (LD) of the [DNA⊃ 2 ]+ 5 complex (see the Supporting Information) 8. In addition, LD studies also indicated that the click product [ 2 + 5 ] did not intercalate into DNA if added as a presynthesized unit, possibly due to hydrophobic and steric barriers.…”

“…Similarly, in further non‐intercalated control experiments, the synthesis of [ 1+3 ], [ 1+4 ], [ 1+5 ], and [ 2+5 ] was clean and in all cases the products were double‐clicked (NMR and MS data, presented in the Supporting Information). Therefore, having previously reported that 1 and 2 intercalate into DNA with association constants between 10 4 –10 6 M −1 ,8 and now demonstrated that 1 and 2 undergo the click reaction at both azido sites, we reasoned that the DNA‐azido intercalator complexes, [DNA⊃ 1 ] and [DNA⊃ 2 ] are sufficiently stable to allow for “click” functionalization, that is, in situ modification.…”

“…Therefore, the observation that [DNA⊃ 1 ]+ 5 is conductive indicates that the monomer units 5 are sufficiently exposed along the DNA helix for them to be able to polymerize with nearby intra‐ or interstrand units within the bundled DNA. In the LD spectrum of [DNA⊃ 2 ]+ 5 (see Figure S1 in the Supporting Information), a magnitude of the negative signal below 350 nm suggests that the two pentynyl‐thienyyl‐pyrrole groups are not constrained and have sufficient flexibility to align for polymerization 8…”

“…The synthesis of the diazidoacridine derivatives 1 and 2 , and their binding to DNA through intercalation have been reported 8. After intercalation, the two azido groups present themselves in the major groove and provide attractive sites for further chemical functionalization through click chemistry (see Scheme ) 9.…”

From Interaction to Function in DNA‐Templated Supramolecular Self‐Assemblies

“…Tuite, Pike and co‐workers reported the DNA‐templated self‐assembly of multiple proflavine‐derived compounds (Figure ). Binding to DNA was shown to occur following the nearest‐neighbor intercalation, as evidenced by negative induced circular dichroism signals as well as linear dichroism, with association constants in the range 10 4 –10 6 m − 1 and little sequence selectivity . λ‐DNA was used as a template onto which up to 24251 intercalators can bind per helix.…”