title: Structure and stability of alkane-linked DNA hairpin conjugates.
abstract: The synthesis and properties of three related families of alkane-linked DNA hairpins are reported. The first possesses a dodecane linker (C12) and 2-8 AT base pairs. The second possesses six AT base pairs and straight chain alkane linkers having 8-16 methylenes. The third has three alkane linkers of different length and a constant six base-pair stem with alternating A-T bases and a single TT step. The spectroscopic properties (UV, CD, and (1)H NMR) and molecular modeling are consistent with the formation of base-paired B-DNA structures for all hairpins having four or more AT base pairs. The thermal stability of hairpins having a C12 linker is greater than that of the commonly used hexa(ethylene glycol) linker but less than that of the stilbenediether linker having the same AT base-pair domain. Hairpin stability is related to both hydrophobic interactions between the linker and the adjacent base pair (stilbene > alkane > glycol) and the overall length of the linker. The stability of the alkane-linked hairpins having six AT base pairs is greater for a tetradecane linker than for either shorter or longer linkers. The good thermal stability of alkane-linked hairpins and absence of a chromophore which absorbs in the UV region makes them well-suited for studies of the electronic spectra and photochemistry of short hairpins having variable base-pair sequences.
authors.affiliation: School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India 695 016. mahesh@iisertvm.ac.in
authors.forename: Mahesh
authors.initials: M
authors.lastname: Hariharan
authors.forename: Karsten
authors.initials: K
authors.lastname: Siegmund
authors.forename: Frederick D
authors.initials: FD
authors.lastname: Lewis
mesh_terms: D000473:Alkanes / Q000737:chemistry*; D020029:Base Pairing; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure; D013696:Temperature
chemical_list: D000473:Alkanes; D004247:DNA