Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Thermodynamic and Kinetic Studies of Trinucleotide Repeat (TNR) DNA

The expansion of trinucleotide repeat (TNR) DNA has been linked to several neurodegenerative diseases (McMurray, 2010). The number of repeats is usually a characteristic indication of the severity of TNR-related diseases, with longer repeats giving higher propensity to expand and earlier onset of symptoms (López, Cleary & Pearson, 2010). It is generally accepted that formation of non-canonical secondary structures, such as stem-loop hairpins or slipouts, contributes to the expansion mechanisms during aberrant DNA replication or repair processes (Mirkin, 2007). The stability of these hairpins is considered an important factor (Paiva & Sheardy, 2005). In this work, we used differential scanning calorimetry (DSC) and UV-Vis spectroscopy to study the thermodynamic and kinetic stability of a series of (CTG)n and (CAG)n TNR stem-loop hairpins and their corresponding (CTG)n/(CAG)n duplexes (n = 6-14). We found that hairpins with n = even and n = even + 1 (odd) repeats possess very similar thermodynamic stability. But when converting to the canonical duplex form, odd-repeat hairpins are more stabilized compared to their even-repeat counterparts. Within both even- and odd-repeat series, hairpins with longer repeats are thermodynamically more stabilized compared to the shorter ones. Kinetic experiments of the stem-loop hairpin to duplex conversion revealed a longer lifetime for the even-repeat hairpins, while the odd-repeat hairpins convert to duplexes 10-fold faster. Also, hairpins with increased number of repeats are more resistant to the conversion when considered within the even- or odd-repeat series individually. Taken together, although it is thermodynamically more favored that hairpins containing longer repeats convert to canonical duplex form; On the contrary, these longer hairpins are kinetically trapped during the conversion and therefore can persist the non-canonical structures, which allows TNR expansion.

This research is supported by National Institute of Environmental Health Science (ES019296).


    McMurray, C. T. (2010). Mechanisms of trinucleotide repeat instability during human development. Nat. Rev. Genet. 11, 786-799.

    Mirkin, S. M. (2007). Expandable DNA repeats and human disease. Nature 447, 932-940.

    López, C. A., Cleary, J. D. & Pearson, C. E. (2010). Repeat instability as the basis for human diseases and as a potential target for therapy. Nat. Rev. Mol. Cell Biol. 11, 165-170.

    Paiva, A. M. & Sheardy, R. D. (2005). The influence of sequence context and length on the kinetics of DNA duplex formation from complementary hairpins possessing (CNG) repeats. J. Am. Chem. Soc. 127, 5581-5585.

Ji Huang
Sarah Delaney

Department of Chemistry
Brown University Providence, RI 02912

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