Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
Chembiochem. 2009 Oct 12;10(15):2530-8. doi: 10.1002/cbic.200900434.
In a functioning genetic system, the information-encoding molecule must form a regular self-complementary complex (for example, the base-paired double helix of DNA) and it must be able to encode information and pass it on to new generations. Here we study a benzo-widened DNA-like molecule (yDNA) as a candidate for an alternative genetic set, and we explicitly test these two structural and functional requirements. The solution structure of a 10 bp yDNA duplex is measured by using 2D-NMR methods for a simple sequence composed of T-yA/yA-T pairs. The data confirm an antiparallel, right-handed, hydrogen-bonded helix resembling B-DNA but with a wider diameter and enlarged base-pair size. In addition to this, the abilities of two different polymerase enzymes (Klenow fragment of DNA pol I (Kf) and the repair enzyme Dpo4) to synthesize and extend the yDNA pairs T-yA, A-yT, and G-yC are measured by steady-state kinetics studies. Not surprisingly, insertion of complementary bases opposite yDNA bases is inefficient due to the larger base-pair size. We find that correct pairing occurs in several cases by both enzymes, but that common and relatively efficient mispairing involving T-yT and T-yC pairs interferes with fully correct formation and extension of pairs by these polymerases. Interestingly, the data show that extension of the large pairs is considerably more efficient with the flexible repair enzyme (Dpo4) than with the more rigid Kf enzyme. The results shed light on the properties of yDNA as a candidate for an alternative genetic information-encoding molecule and as a tool for application in basic science and biomedicine.
在一个功能正常的遗传系统中，信息编码分子必须形成规则的自我互补复合物（例如，DNA 的碱基配对双链），并且它必须能够编码信息并将其传递给新一代。在这里，我们研究了一种苯并加宽的 DNA 类似物（yDNA）作为替代遗传物质的候选物，并明确测试了这两个结构和功能要求。通过使用二维 NMR 方法测量由 T-yA/yA-T 对组成的简单序列的 10 bp yDNA 双链体的溶液结构。数据证实了一种类似 B-DNA 的反平行右手氢键螺旋，但直径更大，碱基对尺寸更大。除此之外，两种不同聚合酶（DNA pol I 的 Klenow 片段（Kf）和修复酶 Dpo4）的能力通过稳态动力学研究测量来合成和扩展 yDNA 对 T-yA、A-yT 和 G-yC。毫不奇怪，由于碱基对尺寸较大，插入互补碱基对 yDNA 碱基的效率不高。我们发现两种酶都在几种情况下发生了正确配对，但常见且相对有效的 T-yT 和 T-yC 错配会干扰这些聚合酶完全正确的形成和扩展。有趣的是，数据表明，与更刚性的 Kf 酶相比，大对的延伸在灵活的修复酶（Dpo4）中效率更高。这些结果揭示了 yDNA 作为替代遗传信息编码分子的候选物以及在基础科学和生物医学中的应用工具的特性。
