Pyshnyi D V, Pyshnaya I, Levina A, Goldberg E, Zarytova V, Knorre D, Ivanova E
Siberian Branch of Russian Academy of Sciences, Novosibirsk Institute of Bioorganic Chemistry, Prospect Akad. Lavrentyeva 8, 630090, Novosibirsk, Russia.
J Biomol Struct Dyn. 2001 Dec;19(3):555-70. doi: 10.1080/07391102.2001.10506763.
Contiguous stacking hybridization of oligodeoxyribonucleotides with DNA as template was investigated using three types of complexes: oligonucleotide contiguously stacked with the stem of the preformed minihairpin (complexes I), oligonucleotide tandems containing two (complexes II) or three (complexes III) short oligomers with a common DNA template. Enthalpy Delta H degrees and entropy Delta S degrees of the coaxial stacking of adjacent duplexes were determined for GC/GpC, GT/ApC, AC/GpT, AT/ApT, CT/ApG, AG/CpT, AA/TpT and TT/ApA nicked () dinucleotide base pairs. The maximal efficiency of co-operative interaction was found for the GC/GpC interface (Delta G degrees(NN/NpN)=-2.7 kcal/mol) and the minimal one for the AA/TpT interface (Delta G degrees(NN/NpN)=-1.2 kcal/mol) at 37 degrees C. As a whole, the efficiency of the base pairs interaction Delta G degrees(NN/NpN) in the nick is not lower than that within the intact DNA helix (Delta G degrees(NN/NN)). These observed Delta G degrees(NN/N*pN) values are proposed may include the effect of the partial removal of fraying at the adjacent helix ends additionally to the effect of the direct stacking of the terminal base pairs in the duplex junction (Delta G degrees(NN/NN). The thermodynamic parameters have been found to describe adequately the formation of all tandem complexes of the II and III types with oligonucleotides of various length and hybridization properties. The performed thermodynamic analysis reveals features of stacking oligonucleotide hybridization which allow one to predict the temperature dependence of association of oligonucleotides and the DNA template within tandem complexes as well as to determine optimal concentration for formation of these complexes characterized by high co-operativity level.
以DNA为模板，研究了寡脱氧核糖核苷酸的连续堆积杂交，使用了三种类型的复合物：与预先形成的小发夹茎连续堆积的寡核苷酸（复合物I）、包含两个（复合物II）或三个（复合物III）具有共同DNA模板的短寡聚物的寡核苷酸串联体。测定了GC/GpC、GT/ApC、AC/GpT、AT/ApT、CT/ApG、AG/CpT、AA/TpT和TT/ApA切口（）二核苷酸碱基对相邻双链体同轴堆积的焓变ΔH°和熵变ΔS°。在37℃时，发现GC/GpC界面的协同相互作用效率最高（ΔG°(NN/NpN)=-2.7 kcal/mol），而AA/TpT界面的协同相互作用效率最低（ΔG°(NN/NpN)=-1.2 kcal/mol）。总体而言，切口处碱基对相互作用的效率ΔG°(NN/NpN)不低于完整DNA螺旋内的效率（ΔG°(NN/NN)）。这些观察到的ΔG°(NN/N*pN)值被认为可能包括除双链体连接处末端碱基对直接堆积的影响（ΔG°(NN/NN)）之外，相邻螺旋末端磨损部分去除的影响。已发现热力学参数能够充分描述II型和III型与各种长度和杂交特性的寡核苷酸的所有串联复合物的形成。所进行的热力学分析揭示了堆积寡核苷酸杂交的特征，这使得人们能够预测串联复合物中寡核苷酸与DNA模板缔合的温度依赖性，以及确定以高协同水平为特征的这些复合物形成的最佳浓度。
