Amino-functionalized DNA:: the properties of C5-amino-alkyl substituted 2′-deoxyuridines and their application in DNA triplex formation
Amino-functionalized DNA:: the properties of C5-amino-alkyl substituted 2′-deoxyuridines and their application in DNA triplex formation
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DOI：
10.1093/nar/gki254
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发表时间：
2005-01-01
影响因子：
14.9
通讯作者：
Williams, DM
中科院分区：
文献类型：
--
作者：
Brazier, JA;Shibata, T;Williams, DM
将C5-氨基修饰的2'-脱氧尿苷类似物掺入DNA已在核酸标记、核酸结构的稳定、核酸适体和催化剂的功能化以及序列特异性DNA弯曲的研究中得到应用。在这项研究中，我们描述了四种不同的 C5-氨基修饰的 2'-脱氧尿苷的物理化学性质，其中氨基通过 3-碳烷基、Z-或 E-烯基或炔基连接体连接到碱基上。使用 H-1 NMR 推导出核苷的构象参数及其 pK(a) 值。它们都显示出预期的核苷与脱氧核糖环的 2'-内糖褶皱的反构象。发现Z-烯基类似物优选顺式构象，而E-烯基类似物仅以其反式构象存在。 pKa 值范围从具有脂肪族丙基连接基的类似物的 10.0 到炔丙基氨基类似物的 8.5。这些类似物已用于合成三螺旋形成寡核苷酸 (TFO)，其中它们取代了天然序列中的胸苷。含有炔丙基氨基类似物的寡核苷酸显示出最高的稳定性，尤其是在低pH下，而含有具有丙基、特别是Z-烯基连接体的类似物的寡核苷酸在很大程度上不稳定。含有带有 E-烯基连接基的类似物的 TFO 具有与未修饰结构相似的稳定性。含有中性但极性侧链的类似物5-(3-羟基丙-1-炔基)-2'-脱氧尿苷的TFO的化学合成显示出显着的稳定性，其稳定性高于所有含有烷氨基或烯基氨基类似物的TFO，仅略低于含有炔氨基类似物的TFO。相对于含有C5-丙炔基-2'-脱氧尿苷的类似序列，羟基和炔丙基氨基取代均赋予增强的三螺旋稳定性。此外，在含有羟丙炔基修饰的 TFO 和含有炔丙氨基侧链的 TFO 之间发现了类似的稳定性对 pH 的依赖性。这表明稳定这种三螺旋的主要因素是由于带有连接的负电基团的炔的存在。
The incorporation of C5-amino-modified2 '-deoxyuridine analogues into DNA have found application in nucleic acid labelling, the stabilization of nucleic acid structures, functionalization of nucleic acid aptamers and catalysts, and the investigation of sequence-specific DNA bending. In this study, we describe the physicochemical properties of four different C5-amino-modified2 '-deoxyuridines in which the amino group is tethered to the base via a 3-carbon alkyl, Z- or E-alkenyl or alkynyl linker. Conformational parameters of the nucleosides and their pK(a) values were deduced using H-1 NMR. All of them display the expected anti-conformation of the nucleoside with 2 '-endo sugar puckers for the deoxyribose ring. A preference for the cisoid conformation for the Z- alkenyl analogue is found, while the E-alkenyl analogue exists exclusively as its transoid conformation. The pKa values range from 10.0 for the analogue with an aliphatic propyl linker to 8.5 for the propargylamino analogue. The analogues have been used for the synthesis of triple-helix forming oligonucleotides (TFOs) in which they replace thymidine in the natural sequence. Oligonucleotides containing the propargylamino analogue display the highest stability especially at low pH, while those containing analogues with propyl and especially Z-alkenyl linkers are destabilized to a great extent. TFOs containing the analogue with the E-alkenyl linker have stability similar to the unmodified structures. The chemical synthesis of TFOs containing the analogue, 5-(3-hydroxyprop-1-ynyl)-2 '-deoxyuridine that possesses neutral but polar side chain show a remarkable stability, which is higher than that of all TFOs containing the alkylamino or alkenylamino analogues and only slightly lower than that of TFOs containing the propargylamino analogue. Both the hydroxyl and propargylamino substitutions impart enhanced triple-helix stability relative to the analogous sequences containing C5-propynyl-2 '-deoxyuridine. Furthermore, a similar dependence of stability on pH is found between TFOs containing the hydroxypropynyl modifications and those containing the propargylamino side chains. This suggests that the major factor responsible for stabilizing such triple helices is due to the presence of the alkyne with an attached electronegative group.