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首页> 外文期刊>Biochemistry >Effect of the Number of Nucleic Acid Oligomer Charges on the Salt Dependence of Stability (DELTAG_37~o) and Melting Temperature (T_m): NLPB Analysis of Experimental Data
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Effect of the Number of Nucleic Acid Oligomer Charges on the Salt Dependence of Stability (DELTAG_37~o) and Melting Temperature (T_m): NLPB Analysis of Experimental Data

机译：核酸低聚物电荷数量对盐依赖性稳定性（DELTAG_37〜o）和熔解温度（T_m）的影响：NLPB实验数据分析

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摘要

For nucleic acid oligomers with variable chain lengths,the salt concentration ([salt]) dependences of the denaturation temperature (T_m) and of the free energy of helix formation at 37 deg C (DELTAG_37~o) are predicted using nonlinear Poisson-Boltzmann (NLPB) calculations.Analysis of experimental data reveals that the ratio of the [salt] derivative of melting temperature (ST_m = dT_m/d log [salt]) to the value for a polymer with the same base composition (ST_m/ST_(m,infinity)) is independent of base composition but strongly dependent on the number of DNA charges (|Z|) below -8 bp for two-strand helices (formed from association of two complementary strands) and below approx 18 bp for hairpin helices (formed from folding of one self-complementary strand).We interpret these ST_m/ST_(m,infinity) ratios in terms of the ratio of thermodynamic ion release from the oligomer (DELTAn_u,per charge) to that from the same oligomer embedded in polymeric DNA (DELTAn)_(n,infinity) per charge).Experimental values of ST_m/ST_(m,infinity) and its dependence on |Z| are in good agreement with NLPB predictions for a preaveraged (essential structural) model of DNA.In particular,the NLPB calculations describe the stronger |Z| dependence of ST_m observed for melting of oligomeric hairpin helices than for melting of two-strand helices.These calculations predict an experimentally detectable (>10%) difference between ST_m and ST_(m,infinity) which increases strongly with decreasing length for two-strand helix lengths of < 15 bp and for hairpin helix lengths of <30 bp.From NLPB values of DELTAn_u/DELTAn_(u,infinity),we predict AG_37~o as a function of [salt] and |Z|.Predictions of thermodynamic and thermal stabilities of oligomeric helices as functions of length and [salt] are consistent with and represent a significant refinement of the average oligomer salt effect currently in use in nearest neighbor stability predictions.
机译：对于具有可变链长的核酸寡聚物，使用非线性Poisson-Boltzmann预测了变性温度（T_m）和37摄氏度螺旋形成的自由能（DELTAG_37〜o）的盐浓度（[salt]）依赖性。实验数据分析表明，熔融温度的[salt]衍生物（ST_m = dT_m / d log [salt]）与具有相同基本组成的聚合物的值（ST_m / ST_（m，无限））与碱基组成无关，但强烈取决于DNA电荷（| Z |）的数量，对于两链螺旋（由两条互补链的结合形成）低于-8 bp，而对于发夹螺旋（形成的DNA电荷）则低于约18 bp从一条自互补链折叠而来）。我们用低聚物释放的热力学离子释放量（每电荷DELTAn_u）与嵌入聚合物DNA中的同一低聚物释放的热力学离子比率来解释这些ST_m / ST_（m，infinity）比每次充电（DELTAn）_（n，无限））。 ST_m / ST_（m，infinity）的ntal值及其对| Z |的依赖性与NLPB预测的DNA平均模型（基本结构）非常吻合。特别是，NLPB计算表明| Z |越强。计算结果表明，与低聚发夹螺旋的熔化相比，ST_m的依赖性要强于两链螺旋的熔化。这些计算预测出ST_m和ST_（m，无穷大）之间存在实验可检测到的差异（> 10％），随着两链长度的减小，该差异会显着增加螺旋长度小于15 bp，发夹螺旋长度小于30 bp。根据DELTAn_u / DELTAn_（u，infinity）的NLPB值，我们可以预测AG_37〜o是[盐]和| Z |的函数。寡聚螺旋的热稳定性作为长度和[盐]的函数，与最近邻稳定性预测中目前使用的平均低聚盐效应一致，并且代表着显着的改进。

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