Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure–function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for ‘phase 1’ amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the ‘GADV world’ hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase 1 set, showing a series of decreasing triplet propensity with evolutionary newness. The weak form of our observation provides a physical mechanism to minimise read frame and recombination alignment errors in the early evolution of the genetic code.

中文翻译：

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在有机阳离子存在下，DNA 在张力下分裂为三联体，序列进化年龄预测三联体相的稳定性

使用原子模拟，我们展示了在有机盐存在的情况下，当特定的富含 GC 的 DNA 双链在溶液中延伸数百纳秒的时间尺度时，稳定的三重态结构的形成。我们将平面堆叠的三重歧化 DNA (Σ DNA) 作为张力下双螺旋的可能溶液相，受序列和稳定辅助因子的影响。考虑到将双链体分割成碱基对三联体作为 RecA 等重组酶操作的第一步，我们强调了 Σ DNA 中的结构-功能关系。我们用热力学论证补充原子计算，以表明“阶段 1”氨基酸（在进化早期出现的那些）的密码子比低熵富含 GC 的序列更有可能在张力下形成三联体。我们进一步观察到，假设（在“GADV 世界”假设中）构成产生功能性球状蛋白的最小组的四种氨基酸在第一阶段组中具有最强的三联体形成倾向，显示出一系列随着进化而降低的三联体倾向新鲜感。我们观察的弱形式提供了一种物理机制，可以在遗传密码的早期进化中最小化读取框和重组比对错误。