Hwang Gil Tae, Romesberg Floyd E
Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
Nucleic Acids Res. 2006 Apr 14;34(7):2037-45. doi: 10.1093/nar/gkl049. Print 2006.
As part of an effort to develop stable and replicable unnatural base pairs, we have evaluated a large number of unnatural nucleotides with predominantly hydrophobic nucleobases. Despite its limited aromatic surface area, a nucleobase analog scaffold that has emerged as being especially promising is the simple phenyl ring. Modifications of this scaffold with methyl and fluoro groups have been shown to impact base pair stability and polymerase recognition, suggesting that nucleobase shape, hydrophobicity and electrostatics are important. To further explore the impact of heteroatom substitution within this nucleobase scaffold, we report the synthesis, stability and polymerase recognition of nucleoside analogs bearing single bromo- or cyano-derivatized phenyl rings. Both modifications are found to generally stabilize base pair formation to a greater extent than methyl or fluoro substitution. Moreover, polymerase recognition of the unnatural base pairs is found to be very sensitive to both the position and nature of the heteroatom substituent. The results help identify the determinants of base pair stability and efficient replication and should contribute to the effort to develop stable and replicable unnatural base pairs.
作为开发稳定且可复制的非天然碱基对工作的一部分，我们评估了大量主要带有疏水核碱基的非天然核苷酸。尽管其芳香表面积有限，但一种特别有前景的核碱基类似物支架是简单的苯环。已表明用甲基和氟基团对该支架进行修饰会影响碱基对稳定性和聚合酶识别，这表明核碱基形状、疏水性和静电作用很重要。为了进一步探索该核碱基支架内杂原子取代的影响，我们报告了带有单溴或氰基衍生化苯环的核苷类似物的合成、稳定性和聚合酶识别情况。发现这两种修饰通常比甲基或氟取代更能稳定碱基对的形成。此外，发现聚合酶对非天然碱基对的识别对杂原子取代基的位置和性质都非常敏感。这些结果有助于确定碱基对稳定性和有效复制的决定因素，并应为开发稳定且可复制的非天然碱基对的工作做出贡献。
