Energetic signatures of single base bulges: thermodynamic consequences and biological implications.
DNA bulges are biologically consequential defects that can arise from template-primer misalignments during replication and pose challenges to the cellular DNA repair machinery. Calorimetric and spectroscopic characterizations of defect-containing duplexes reveal systematic patterns of sequence-context dependent bulge-induced destabilizations. These distinguishing energetic signatures are manifest in three coupled characteristics, namely: the magnitude of the bulge-induced duplex destabilization (DeltaDeltaG(Bulge)); the thermodynamic origins of DeltaDeltaG(Bulge) (i.e. enthalpic versus entropic); and, the cooperativity of the duplex melting transition (i.e. two-state versus non-two state). We find moderately destabilized duplexes undergo two-state dissociation and exhibit DeltaDeltaG(Bulge) values consistent with localized, nearest neighbor perturbations arising from unfavorable entropic contributions. Conversely, strongly destabilized duplexes melt in a non-two-state manner and exhibit DeltaDeltaG(Bulge) values consistent with perturbations exceeding nearest-neighbor expectations that are enthalpic in origin. Significantly, our data reveal an intriguing correlation in which the energetic impact of a single bulge base centered in one strand portends the impact of the corresponding complementary bulge base embedded in the opposite strand. We discuss potential correlations between these bulge-specific differential energetic profiles and their overall biological implications in terms of DNA recognition, repair and replication.
Minetti
Conceição A S A
CA
Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, Piscataway, NJ 08854, USA.
Remeta
David P
DP
Dickstein
Rian
R
Breslauer
Kenneth J
KJ
D002152:Calorimetry, Differential Scanning; D004247:DNA / Q000737:chemistry*; D004260:DNA Repair; D004261:DNA Replication; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry; D013816:Thermodynamics
D011687:Purines; D011743:Pyrimidines; D004247:DNA