Conformational Ensembles from Experimental Data and Computer Simulations

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Conformational Ensembles from Experimental Data
and Computer Simulations Poster Abstracts
139
102-POS Board 22
The Role of Dynamic Conformational Ensembles in Base Excision Repair and Triplet
Repeat DNA Expansion
Jens Völker1, Vera Gindikin1, G. Eric Plum2, Kenneth J. Breslauer1.
1Rutgers, The State University of New Jersey, Piscataway, NJ, USA, 2IBET, Inc, Columbus, OH,
USA.
Trinucleotide repeat DNA sequences of type (CNG)n can undergo uncontrolled expansion
resulting in debilitating neurological diseases such as Huntington’s and Myotonic dystrophy type
I. DNA expansion appears inevitable when the repeat length exceeds a threshold value, n~35. It
has been postulated that uncontrolled expansion occurs as a consequence of the propensity of
large repeat DNA sequences to adopt alternative single strand structures, such as bulge loops, in
competition with normal duplex DNA, thereby leading to aberrant metabolic processes during
DNA replication, recombination, and repair. Using a combination of calorimetric and
spectroscopic techniques in conjunction with modeling, we present evidence that a bulge loop
structure forming within the confines of larger repeat domains can occupy multiple, nearly
isoenergetic loop positions, called rollamers, thereby creating an ensemble of metastable loop
isomers in dynamic exchange. Such dynamic ensembles of bulge loops provide an intriguing
thermodynamic basis for the unexplained threshold phenomenon associated with expansion of
DNA repeat domains. We further demonstrate how a common mutagenic, oxidative DNA lesion
(8oxodG) and its base excision repair (BER) intermediate (abasic site), both implicated in repeat
DNA expansion in mouse models of Huntington’s disease, each alter the rollamer ensemble. Our
prior studies on static, lesion-containing repeat bulge loops revealed the preferred lesion
containing repeat loop isomers to be poor substrates for APE1, a key BER enzyme. Based on
these collective observations, we postulate that the impact of DNA damage on ensemble
distribution and dynamics of DNA bulge loops is a significant factor in aberrant repair outcomes
leading to DNA expansion, and ultimately disease states. Our results emphasize the importance
of considering dynamic conformational ensembles in DNA repair outcomes, thereby providing a
biophysical basis for an observed biological outcome.