title: Synthesis, structure, and photochemistry of exceptionally stable synthetic DNA hairpins with stilbene diether linkers.
abstract: The structure and properties of 18 hairpin-forming bis(oligonucleotide) conjugates possessing stilbene diether linkers are reported. Conjugates possessing bis(2-hydroxyethyl)stilbene 4,4'-diether linkers form the most stable DNA hairpins reported to date. Hairpins with as few as two T:A base pairs or four noncanonical G:G base pairs are stable at room temperature. Increasing the length of the hydroxyalkyl groups results in a decrease in hairpin thermal stability. On the basis of the investigation of their circular dichroism spectra, all of the hairpins investigated adopt B-DNA structures, except for a hairpin with a short poly(G:C) stem which forms a Z-DNA structure. Both the strong fluorescence of the stilbene diether linkers and their trans-cis photoisomerization are totally quenched in hairpins possessing neighboring T:A and G:C base pairs. Quenching is attributed to an electron-transfer mechanism in which the singlet stilbene serves as an electron donor and T or C serves as an electron acceptor. In contrast, in denatured hairpins and hairpins possessing neighboring G:G base pairs the stilbene diether linkers undergo efficient photoisomerization.
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA. lewis@chem.northwestern.edu
authors.forename: Frederick D
authors.initials: FD
authors.lastname: Lewis
authors.forename: Yansheng
authors.initials: Y
authors.lastname: Wu
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Liu
mesh_terms: D002942:Circular Dichroism; D003432:Cross-Linking Reagents / Q000737:chemistry*; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D007536:Isomerism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D009943:Organophosphorus Compounds / Q000737:chemistry; D010777:Photochemistry; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D013267:Stilbenes / Q000737:chemistry*
chemical_list: D003432:Cross-Linking Reagents; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D013267:Stilbenes; C434331:phosphoramidite; D004247:DNA