Structure and stability of alkane-linked DNA hairpin conjugates

Mahesh Hariharan*, Karsten Siegmund, Frederick D Lewis

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Figure presented. 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 1H 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.

Original languageEnglish (US)
Pages (from-to)6236-6243
Number of pages8
JournalJournal of Organic Chemistry
Issue number18
StatePublished - Sep 17 2010

ASJC Scopus subject areas

  • Organic Chemistry

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