Bergstrom D E, Zhang P, Johnson W T
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA.
Nucleic Acids Res. 1997 May 15;25(10):1935-42. doi: 10.1093/nar/25.10.1935.
The nucleoside analogs 1-(2'-deoxy-beta-D-ribofuranosyl)- 3-nitropyrrole (9), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitropyrazole (10), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitroimidazole (11) and 1-(2'-deoxy-beta-D-ribofuranosyl)-5-nitroindole (21) were incorporated into the oligonucleotide 5'-d(CGCXAATTYGCG)-3'in the fourth position from the 5'-end. Procedures for synthesis of two of the nitroazole nucleosides, 10 and 11, were developed for this study. Each of the nitroazoles was converted into a 3'-phosphoramidite for oligonucleotide synthesis by conventional automated protocols. Four oligonucleotides were synthesized for each modified nucleoside in order to obtain duplexes in which each of the four natural bases was placed opposite (position 9) the nitroazole. In order to assess the role of the nitro group on base stacking interaction, sequences were also synthesized in which the fourth base was 1-(2'-deoxy-beta-D-ribofuranosyl)pyrazole. Corresponding sequences containing an abasic site, as well as sequences containing inosine, were synthesized for comparison. Thermal melting studies yielded T m values and thermodynamic parameters. Each nucleoside analog displayed a unique pattern of base pairing preferences. The least discriminating analog was 3-nitropyrrole, for which T m values differed by 5 degrees C and Delta G 25 degrees C ranged from -6.1 to -6.5 kcal/mol. 5-Nitroindole gave duplexes with significantly higher thermal stability, with Tm values varying from 35.0 to 46.5 degrees C and -Delta G 25 degrees C ranging from 7.7 to 8.5 kcal/mol. Deoxyinosine (22), a natural analog which has found extensive use as a universal nucleoside, is far less non-discriminating than any of the nitroazole derivatives. Tm values ranged from 35.4 degrees C when paired with G to 62.3 degrees C when paired with C. The significance of the nitro substituent was determined by comparison of the base pairing properties of a simple azole nucleoside, 1-(2'-deoxy-beta-D-ribofuranosyl)pyrazole (12). The pyrazole-containing sequences melt at 10-20 degrees C lower than the corresponding nitropyrazole-containing sequences. On average, the pyrazole-containing sequences were equivalent in stability (average Delta G = -4.8 kcal/mol) to the sequences containing an abasic site (average Delta G = -4.7 kcal/mol).
将核苷类似物1-(2'-脱氧-β-D-呋喃核糖基)-3-硝基吡咯(9)、1-(2'-脱氧-β-D-呋喃核糖基)-4-硝基吡唑(10)、1-(2'-脱氧-β-D-呋喃核糖基)-4-硝基咪唑(11)和1-(2'-脱氧-β-D-呋喃核糖基)-5-硝基吲哚(21)掺入5'-端起第四个位置的寡核苷酸5'-d(CGCXAATTYGCG)-3'中。为该研究开发了两种硝基唑核苷即10和11的合成方法。通过常规自动化方案将每种硝基唑转化为用于寡核苷酸合成的3'-亚磷酰胺。为每种修饰核苷合成了四种寡核苷酸，以获得双链体，其中四种天然碱基中的每一种都与硝基唑相对(第9位)。为了评估硝基对碱基堆积相互作用的作用，还合成了第四位碱基为1-(2'-脱氧-β-D-呋喃核糖基)吡唑的序列。合成了含无碱基位点的相应序列以及含次黄嘌呤核苷的序列用于比较。热熔解研究得出了熔点(Tm)值和热力学参数。每种核苷类似物都表现出独特的碱基配对偏好模式。区分性最小的类似物是3-硝基吡咯，其Tm值相差5℃，25℃时的ΔG范围为-6.1至-6.5kcal/mol。5-硝基吲哚形成的双链体具有明显更高的热稳定性，Tm值在35.0至46.5℃之间变化，-ΔG25℃范围为7.7至8.5kcal/mol。脱氧次黄嘌呤核苷(22)是一种已被广泛用作通用核苷的天然类似物，其区分性远低于任何一种硝基唑衍生物。Tm值在与G配对时为35.4℃，与C配对时为62.3℃。通过比较简单的唑核苷1-(2'-脱氧-β-D-呋喃核糖基)吡唑(12)的碱基配对性质来确定硝基取代基的意义。含吡唑的序列比相应的含硝基吡唑的序列低10-20℃熔解。平均而言，含吡唑的序列在稳定性上(平均ΔG=-4.8kcal/mol)与含无碱基位点的序列(平均ΔG=-4.7kcal/mol)相当。
