Role of electrostatic complementarity between perylenediimide and porphyrin in highly stabilized GNA

Abstract

Relatively electron-deficient perylenediimide (PDI) and relatively electron-rich porphyrin (Por) were introduced into the middle of 16-mer glycol nucleic acid (GNA), and up to five consecutive chromophores were arranged in the zipper-like interstrand alternating fashion. Remarkable variation for the CD spectra ascribed to chromophores was observed, and bathochromic shift in the UV/Vis absorption region of chromophores occurred upon duplex formation. Interestingly, zipper-like heteroaggregates of chromophores inside had marvelous positive effects on the stabilization of the duplex, T_m of Por-PDI-Por sandwich-type modified GNA duplex was increased by 24°C in comparison with three A-T base pairs, moreover, Por-PDI-Por-PDI-Por interstrand modified GNA duplex was even stabilized by 25°C in replacement of five A-T base pairs. The specificity of high duplex stability might be driven by the strong hydrophobic electrostatic complementarity between PDI and Por face-centered stacking.

Keywords: Complementarity; Oligonucleotide; Self-assembly; Stability; Stacking.