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Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.

Völker J, Gindikin V, Klump HH, Plum GE, Breslauer KJ - J. Am. Chem. Soc. (2012)

Bottom Line: In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature.These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery.We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA.

ABSTRACT
DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.

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Related in: MedlinePlus

Excess heat capacity curves measured for a repeat loopconstructcomposed of four CAG repeats located in a fixed position (black) ordistributed between three (red) or five (blue) equivalent loop positions.Similar results were obtained for different CAG loop sizes and forCTG repeat loops in multiple equivalent loop positions.
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fig1: Excess heat capacity curves measured for a repeat loopconstructcomposed of four CAG repeats located in a fixed position (black) ordistributed between three (red) or five (blue) equivalent loop positions.Similar results were obtained for different CAG loop sizes and forCTG repeat loops in multiple equivalent loop positions.

Mentions: Figure 1 shows typical DSC thermograms obtained for a bulge loop oligonucleotidecomprising four CAG repeats in either a fixed loop position (blacktrace) or a distribution of three (red trace) or five (blue trace)potential loop positions. Whereas the repeat loop in a fixed positiongives rise to a single cooperative melting transition, as describedpreviously,34,48 the possibility probed here forthe repeat loop to occupy multiple positions results in more complexmelting curves, yielding two visually resolved, overlapping transitions.As the number of possible loop positions increases, these two transitionsbecome more resolved while shifting progressively to higher temperaturesand manifesting higher melting enthalpies. This observed split intotwo melting transitions is of particular interest. If the loop occupiesa fixed position, simply extending the upstream and downstream duplexarms by an additional 3n base pairs should maintaina single transition, albeit a more cooperative one with a higher enthalpyand a higher Tm. In contrast, we observedtwo transitions that became better resolved with increasing chainlength. This experimental reality suggests that the bulge loop islocated, either statically or dynamically, in multiple positions relativeto the upstream and downstream arms and that interchangeability withinthe distribution alters the melting behavior of these constructs relativeto equivalent loops in “frozen” constructs that limitthe loop to a single fixed position. The complementary fluorescence,absorption, and calorimetric data described below are consistent withsuch a rollamer model.


Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.

Völker J, Gindikin V, Klump HH, Plum GE, Breslauer KJ - J. Am. Chem. Soc. (2012)

Excess heat capacity curves measured for a repeat loopconstructcomposed of four CAG repeats located in a fixed position (black) ordistributed between three (red) or five (blue) equivalent loop positions.Similar results were obtained for different CAG loop sizes and forCTG repeat loops in multiple equivalent loop positions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3318849&req=5

fig1: Excess heat capacity curves measured for a repeat loopconstructcomposed of four CAG repeats located in a fixed position (black) ordistributed between three (red) or five (blue) equivalent loop positions.Similar results were obtained for different CAG loop sizes and forCTG repeat loops in multiple equivalent loop positions.
Mentions: Figure 1 shows typical DSC thermograms obtained for a bulge loop oligonucleotidecomprising four CAG repeats in either a fixed loop position (blacktrace) or a distribution of three (red trace) or five (blue trace)potential loop positions. Whereas the repeat loop in a fixed positiongives rise to a single cooperative melting transition, as describedpreviously,34,48 the possibility probed here forthe repeat loop to occupy multiple positions results in more complexmelting curves, yielding two visually resolved, overlapping transitions.As the number of possible loop positions increases, these two transitionsbecome more resolved while shifting progressively to higher temperaturesand manifesting higher melting enthalpies. This observed split intotwo melting transitions is of particular interest. If the loop occupiesa fixed position, simply extending the upstream and downstream duplexarms by an additional 3n base pairs should maintaina single transition, albeit a more cooperative one with a higher enthalpyand a higher Tm. In contrast, we observedtwo transitions that became better resolved with increasing chainlength. This experimental reality suggests that the bulge loop islocated, either statically or dynamically, in multiple positions relativeto the upstream and downstream arms and that interchangeability withinthe distribution alters the melting behavior of these constructs relativeto equivalent loops in “frozen” constructs that limitthe loop to a single fixed position. The complementary fluorescence,absorption, and calorimetric data described below are consistent withsuch a rollamer model.

Bottom Line: In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature.These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery.We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA.

ABSTRACT
DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.

Show MeSH
Related in: MedlinePlus