Kunitsyn A, Kochetkova S, Timofeev E, Florentiev V
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation.
J Biomol Struct Dyn. 1996 Oct;14(2):239-44. doi: 10.1080/07391102.1996.10508114.
Earlier we showed that reported in literature nearest-neighbor thermodynamic parameters describe poorly the thermal-induced behavior of DNA duplexes immobilized in gel. Here we present a complete set of partial thermodynamic parameters for all 10 nearest-neighbor interactions specially developed for duplexes immobilized in gel. This thermodynamic library allows to predict dissociation enthalpy and free energy of DNA duplex immobilized in gel matrix from its base sequence. The predicted values are in good agreement with the experimental ones. Dissociation enthalpy and free energy are needed for such application as (i) predicting relative stability of duplexes formed by DNA with oligonucleotides immobilized in cells of gel matrix; (ii) selecting optimal conditions for hybridization experiment; (iii) predicting washing curves and washing temperatures at irreversible temperature-stepped wash of DNA out of oligonucleotide gel matrix; (iv) selecting optimal conditions for washing gel matrix.
我们之前表明，文献中报道的近邻热力学参数难以描述固定在凝胶中的DNA双链体的热诱导行为。在此，我们给出了专门为固定在凝胶中的双链体开发的所有10种近邻相互作用的完整部分热力学参数集。这个热力学库能够根据DNA双链体的碱基序列预测其固定在凝胶基质中的解离焓和自由能。预测值与实验值吻合良好。解离焓和自由能可用于以下应用：（i）预测DNA与固定在凝胶基质细胞中的寡核苷酸形成的双链体的相对稳定性；（ii）选择杂交实验的最佳条件；（iii）预测从寡核苷酸凝胶基质中不可逆温度梯度洗脱DNA时的洗脱曲线和洗脱温度；（iv）选择洗涤凝胶基质的最佳条件。
