Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, Piscataway, NJ 08854, USA.
Nucleic Acids Res. 2010 Jan;38(1):97-116. doi: 10.1093/nar/gkp1036. Epub 2009 Nov 27.
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.
DNA 凸起是生物上有重要意义的缺陷，可能是由于复制过程中模板-引物的不对准而产生的，并对细胞的 DNA 修复机制构成挑战。含有缺陷的双链体的量热法和光谱学特性揭示了序列上下文依赖性凸起诱导的不稳定性的系统模式。这些有区别的能量特征表现在三个耦合特性中，即：凸起诱导的双链体不稳定性的幅度（DeltaDeltaG（凸起））；DeltaDeltaG（凸起）的热力学起源（即焓变与熵变）；以及双链体熔解转变的协同性（即二态与非二态）。我们发现中等程度不稳定的双链体经历二态解离，并表现出与局部、近邻扰动一致的 DeltaDeltaG（凸起）值，这些扰动来自不利的熵贡献。相反，强烈不稳定的双链体以非二态方式熔解，并表现出与近邻预期值相超出的 DeltaDeltaG（凸起）值，这些值起源于焓变。重要的是，我们的数据揭示了一个有趣的相关性，即一个链上的单个凸起碱基的能量影响预示着嵌入相反链上的相应互补凸起碱基的影响。我们讨论了这些凸起特异性的差分能量分布与 DNA 识别、修复和复制方面的整体生物学意义之间的潜在相关性。
