Polarity Sensing by Fluorescent Oligonucleotides:  First Demonstration of Sequence-Dependent Microenvironmental Changes in the DNA Major Groove

Abstract

DNA duplex recognition by macromolecules (proteins, enzymes) and small molecules (drugs, metal complexes) occurs in the major or minor grooves of DNA via hydrogen bonding and electrostatic or hydrophobic interactions, whose strengths depend on the medium. It is therefore important to understand the local environments of the major/minor grooves of DNA. It is known that small molecules bind in the minor groove that have nonpolar character (ε = 22) and are organic-like. By employing fluorescent oligonucleotides, we demonstrated recently that the major groove of DNA is more polar than the minor groove (ε = 55) and the DNA double helix has different polarity in its two grooves. Our experimentally measured values were recently validated independently by two theoretical groups, employing calculations by two different methodologies. In this paper, a hitherto unknown property of DNA double helixsequence dependent local polarity or microenvironmentis experimentally demonstrated. This is shown by fluorescence experiments using oligonucleotides containing the modified base 5-amino-dU in place of dT and the polarity varied between ε ≈ 40 and 60, in different sequences. This is the first experimental demonstration of sequence-dependent microenvironmental effects in DNA in solution, although structural effects are well-known by X-ray data. The technique used has a good potential to investigate differing microenvoronmental effects in various secondary structures, DNA polymorphs, and chemically modified DNA and their hybrids.