Energetics, Ion, and Water Binding of the Unfolding of AA/UU Base Pair Stacks and UAU/UAU Base Triplet Stacks in RNA,The Journal of Physical Chemistry B

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Energetics, Ion, and Water Binding of the Unfolding of AA/UU Base Pair Stacks and UAU/UAU Base Triplet Stacks in RNA
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2018-07-06 , DOI: 10.1021/acs.jpcb.8b05575
Carolyn E. Carr ₁ , Irine Khutsishvili ₁ , Luis A. Marky ₁

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Triplex formation occurs via interaction of a third strand with the major groove of double-stranded nucleic acid, through Hoogsteen hydrogen bonding. In this work, we use a combination of temperature-dependent UV spectroscopy and differential scanning calorimetry to determine complete thermodynamic profiles for the unfolding of polyadenylic acid (poly(rA))·polyuridylic acid (poly(rU)) (duplex) and poly(rA)·2poly(rU) (triplex). Our thermodynamic results are in good agreement with the much earlier work of Krakauer and Sturtevant using only UV melting techniques. The folding of these two helices yielded an uptake of ions, Δn_Na⁺ = 0.15 mol Na⁺/mol base pair (duplex) and 0.30 mol Na⁺/mole base triplet (triplex), which are consistent with their polymer behavior and the higher charge density parameter of triple helices. The osmotic stress technique yielded a release of structural water, Δn_W = 2 mol H₂O/mol base pair (duplex unfolding into single strands) and an uptake of structural water, Δn_W = 2 mol H₂O/mole base pair (triplex unfolding into duplex and a single strand). However, an overall release of electrostricted waters is obtained for the unfolding of both complexes from pressure perturbation calorimetric experiments. In total, the ΔV values obtained for the unfolding of triplex into duplex and a single strand correspond to an immobilization of two structural waters and a release of three electrostricted waters. The ΔV values obtained for the unfolding of duplex into two single strands correspond to the release of two structural waters and the immobilization of four electrostricted water molecules.

中文翻译：

RNA中AA / UU碱基对堆栈和UAU / UAU碱基三重堆栈的展开的能量，离子和水结合

三链体的形成是通过Hoogsteen氢键结合，使第三条链与双链核酸的主要凹槽相互作用。在这项工作中，我们结合使用依赖于温度的紫外光谱和差示扫描量热法来确定聚腺苷酸（poly（rA））·聚尿苷酸（poly（rU））（duplex）和poly（ rA）·2poly（rU）（三重）。我们的热力学结果与仅使用紫外线熔融技术的Krakauer和Sturtevant的早期工作非常吻合。这两个螺旋的折叠产生的离子的摄取，Δ Ñ_{的Na ⁺} = 0.15摩尔的Na ⁺ /摩尔碱基对（双链体）和0.30摩尔的Na ⁺摩尔基三重态（三重态），这与它们的聚合物行为和三重螺旋的较高电荷密度参数一致。渗透胁迫技术得到的结构水，Δ释放Ñ _{w ^} = 2摩尔ħ ₂ O /摩尔碱基对（双链体展开成单链）和结构水的摄取，Δ Ñ _{w ^} = 2摩尔ħ ₂ O /摩尔碱对（三链体展开为双链体和单链）。然而，从压力摄动量热实验中，两种络合物的展开都获得了电致伸缩水的整体释放。总的来说，ΔV将三链体展开成双链体和单链所获得的值对应于两个结构水的固定化和三个电致伸缩水的释放。的Δ V为双链体的解折叠成两条单链而得到的值对应于两个结构水域的释放和四个electrostricted水分子的固定。

更新日期：2018-07-08

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