Ribosome binding of DNA analogs of tRNA requires base modifications and supports the "extended anticodon".

The efficiency of translation depends on correct tRNA-ribosome interactions. The ability of chemically synthesized yeast tRNA(Phe) anticodon domains to effectively inhibit the binding of native yeast tRNA(Phe) to poly(U)-programmed Escherichia coli 30S ribosomal subunits was dependent on a Mg(2+)-stabilized stem and an open anticodon loop, both facilitated by base modifications. Analysis of tRNA sequences has revealed that base modifications which negate canonical hydrogen bonding are found in 95% of those tRNA anticodon loop sequences with the potential to form two Watson-Crick base pairs across the loop. Therefore, we postulated that a stable anticodon stem and an open loop are prerequisites for ribosome binding. To test this hypothesis, DNA analogs of the yeast tRNA(Phe) anticodon domain were designed to have modification-induced, Mg(2+)-stabilized stems and open loops. The unmodified DNA analog neither bound to poly(U)-programmed 30S ribosomal subunits nor inhibited the binding of native tRNA(Phe). However, specifically modified DNA analogs did bind to ribosomal subunits and effectively inhibited tRNA(Phe) from binding. Thus, modification-dependent Mg(2+)-stabilized anticodon domain structures with open loops have evolved as the preferred anticodon conformations for ribosome binding.

翻译的效率取决于正确的转运RNA（transfer RNA, tRNA）-核糖体相互作用。化学合成的苯丙氨酸酵母转运RNA（yeast tRNA(Phe)）反密码子结构域，有效抑制天然苯丙氨酸酵母转运RNA与多聚U编程的大肠杆菌30S核糖体亚基结合的能力，依赖于镁离子（Mg²+）稳定的茎环结构与开放的反密码子环，二者均通过碱基修饰得以稳定。对转运RNA序列的分析显示，在95%具有跨环形成两组沃森-克里克碱基对（Watson-Crick base pairs）潜力的转运RNA反密码子环序列中，均存在可破坏经典氢键的碱基修饰。因此，我们提出假设：稳定的反密码子茎环结构与开放的反密码子环是核糖体结合的必要前提。为验证该假设，我们设计了苯丙氨酸酵母转运RNA反密码子结构域的DNA类似物，使其具备修饰诱导、镁离子稳定的茎环结构与开放环结构。未修饰的DNA类似物既无法与多聚U编程的30S核糖体亚基结合，也不能抑制天然苯丙氨酸酵母转运RNA的结合。然而，经过特异性修饰的DNA类似物则可与核糖体亚基结合，并有效抑制苯丙氨酸酵母转运RNA的结合。由此可见，依赖修饰且经镁离子稳定、带有开放环的反密码子结构域，已演化成为核糖体结合的最优反密码子构象。