Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

102-POS Board 22 The Role of Dynamic Conformational Ensembles in Base Excision Repair and Triplet Repeat DNA Expansion Jens Völker 1 , Vera Gindikin 1 , G. Eric Plum 2 , Kenneth J. Breslauer 1 . 1 Rutgers, The State University of New Jersey, Piscataway, NJ, USA, 2 IBET, 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.

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