Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
复制标题
DOI：
10.1021/ja0386546
复制
发表时间：
2004-03-10
影响因子：
15
通讯作者：
Chattopadhyaya, J
中科院分区：
文献类型：
--
作者：
Acharya, P;Cheruku, P;Chattopadhyaya, J
为了理解为什么 RNA-RNA 双链体通常比相应的 DNA-DNA 双链体具有更高的热力学稳定性，我们测量了核苷 3',5'-双乙基磷酸 [Etp(d/rN)pEt] 和核苷 3'-乙基磷酸 [(d/rN)pEt]（N = A、G、C 或 T/U）的 pK(a) 值，建模为供体和双链体中碱基对的受体。 3',5'-双磷酸酯 Etp(d/rN)pEt 模拟 DNA 和 RNA 的核苷酸间单体单元，其中完全不存在堆积作用，而 3'-乙基磷酸酯 (d/rN)pEt 模拟 5' 端的核苷酸。这些模型核苷磷酸中的每一种核苷碱基的 pK(a) 值均通过 H-1 NMR（500 MHz）确定，具有低 pK(a) 误差（sigma = +/-0.01 至 0.02），对每种化合物进行 20-33 次不同的 pH 测量。这项研究使我们得出以下结论：（1）所有单体 DNA 核碱基在其各自的 Etp(d/rN)pEt 和 (d/rN)pEt 中都比相应的 RNA 核碱基更碱性。 (2) 单体核苷酸块的 pKa 值以及供体和受体之间的 DeltapK(a) 值可用于了解 RNA 和 DNA 系列中寡聚双链体的相对碱基配对强度。 (3) 双链体中碱基对的供体和受体的 DeltaG 度 (pKa) 能够定性分析 RNA-RNA 中碱基配对和堆积相对于 DNA-DNA 双链体的相对强度。 (4)还发现，随着％A-T/U含量的增加或减少，RNA-RNA中碱基配对强度和核碱基堆积相对于DNA-DNA的相对贡献是相互补偿的。堆叠和氢键的这种相互依赖性对于碱基对模拟的分子设计以扩展遗传密码的字母表可能具有潜在的重要意义。
To understand why the RNA-RNA duplexes in general has a higher thermodynamic stability over the corresponding DNA-DNA duplexes, we have measured the pK(a) values of both nucleoside 3',5'-bis-ethyl phosphates [Etp(d/rN)pEt] and nucleoside 3'-ethyl phosphates [(d/rN)pEt] (N = A, G, C, or T/U), modeling as donors and acceptors of base pairs in duplexes. While the 3',5'-bis-phosphates, Etp(d/rN)pEt, mimic the internucleotidic monomeric units of DNA and RNA, in which the stacking contribution is completely absent, the 3'-ethyl phosphates, (d/rN)pEt, mimic the nucleotide at the 5'-end. The pK(a) values of the nucleobase in each of these model nucleoside phosphates have been determined with low pK(a) error (sigma = +/-0.01 to 0.02) by H-1 NMR (at 500 MHz) with 20-33 different pH measurements for each compound. This study has led us to show the following: (1) All monomeric DNA nucleobases are more basic than the corresponding RNA nucleobases in their respective Etp(d/rN)pEt and (d/rN)pEt. (2) The pKa values of the monomeric nucleotide blocks as well as DeltapK(a) values between the donor and acceptor can be used to understand the relative base-pairing strength in the oligomeric duplexes in the RNA and DNA series. (3) The DeltaGdegrees(pKa) of the donor and acceptor of the base pair in duplexes enables a qualitative dissection of the relative strength of the base-pairing and stacking in the RNA-RNA over the DNA-DNA duplexes. (4) It is also found that the relative contribution of base-pairing strength and nucleobase stacking in RNA-RNA over DNA-DNA is mutually compensating as the % A-T/U content increases or decreases. This interdependency of stacking and hydrogen bonding can be potentially important in the molecular design of the base-pair mimicks to expand the alphabet of the genetic code.