FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatijima-Minatomachi, Chuo-ku, Kobe 650-0047, Japan.
J Am Chem Soc. 2012 Dec 12;134(49):20060-9. doi: 10.1021/ja305384c. Epub 2012 Sep 18.
The structure and stability of long telomeric DNAs, (T(2)AG(3))(n) (n = 4-20), were studied under dilute and molecular crowding conditions in the presence of Na(+) and K(+). Structural analysis showed that the long telomeric DNAs formed intramolecular G-quadruplexes under all conditions. In the presence of Na(+), the telomeric DNAs formed an antiparallel G-quadruplex under both dilute and molecular crowding conditions. However, in the presence of K(+), molecular crowding induced a conformational change from mixed to parallel. These results are consistent with numerous structural studies for G-quadruplex units under molecular crowding conditions. Thermodynamic analysis showed that G-quadruplexes under the molecular crowding conditions were obviously more stable than under dilute condition. Interestingly, this stabilization effect of molecular crowding was reduced for the longer telomeric DNAs, indicating that the G-quadruplex structure of long telomeric DNAs is not as stable under molecular crowding conditions, as implied from the large stabilization of isolated G-quadruplex units as previously reported. Moreover, a hydration study revealed that upon structure folding, the interior of a G-quadruplex unit was dehydrated, whereas the linker between two units was more hydrated. It is thus possible to propose that the linkers between G-quadruplex units are ordered structures but not random coils, which could have an important influence on the stability of the entire structure of long telomeric DNAs. These results are significant to elucidate the biological characteristics of telomeres, and can aid in the rational design of ligands and drugs targeting the telomere and related proteins.
长端粒 DNA（(T(2)AG(3))(n)（n = 4-20））在存在 Na(+)和 K(+)的稀溶液和分子拥挤条件下的结构和稳定性进行了研究。结构分析表明，长端粒 DNA 在所有条件下均形成了分子内 G-四链体。在存在 Na(+)的情况下，端粒 DNA 在稀溶液和分子拥挤条件下均形成了反平行 G-四链体。然而，在存在 K(+)的情况下，分子拥挤诱导了从混合到平行的构象变化。这些结果与分子拥挤条件下 G-四链体单元的许多结构研究结果一致。热力学分析表明，分子拥挤条件下的 G-四链体明显比稀溶液条件下更稳定。有趣的是，这种分子拥挤的稳定效应对于较长的端粒 DNA 降低了，表明在分子拥挤条件下长端粒 DNA 的 G-四链体结构不如孤立 G-四链体单元以前报道的那样稳定。此外，水化研究表明，在结构折叠时，G-四链体单元的内部脱水，而两个单元之间的连接体则更加水化。因此，可以提出 G-四链体单元之间的连接体是有序结构而不是无规卷曲，这可能对长端粒 DNA 整个结构的稳定性产生重要影响。这些结果对于阐明端粒的生物学特性具有重要意义，并有助于针对端粒和相关蛋白质的配体和药物的合理设计。
