Long-range cooperativity in molecular recognition of RNA by oligodeoxynucleotides, with multiple C5-(1-propynyl) pyrimidines
Long-range cooperativity in molecular recognition of RNA by oligodeoxynucleotides, with multiple C5-(1-propynyl) pyrimidines
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DOI：
10.1021/ja003208t
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发表时间：
2001-05-09
影响因子：
15
通讯作者：
Turner, DH
中科院分区：
文献类型：
--
作者：
Barnes, TW;Turner, DH
由C5-（1-丙炔基）嘧啶（Y-p）组成的七聚体是针对SV 40大T抗原的mRNA的有效且特异的反义剂（瓦格纳，R. W的; Matteucci，M. D，; Grant，D.;黄，T.; Froehler，B. C，Nat. Biotechnol. 1996，14，840-844）。为了表征丙炔基在分子识别中的作用，已经通过UV熔解实验测量了与DNA：RNA双链体中的取代相关的热力学增量，例如5 ' -dCCUCCUU-3 '：3 ' -r（GA）相对于bar GGAGGAA（Au）相对于bar-5'。对于检测的核苷酸。未配对的悬挂末端类似地稳定未修饰的和丙炔化的双链体：除了添加5 ′未配对的rA在丙炔化的PODN：RNA双链体上比在DNA：RNA双链体上更稳定1.4kcal/mol。添加单个丙炔基的自由能增量范围为0至-4.0千卡/摩尔，取决于取代的最终数目和位置。提出了一个预测含Y-p杂合双链体稳定性的初步模型。通过用肌苷（I）取代鸟苷（G）来消除一个氨基，从而消除氢键，得到5 ′-dC（p）C（p）U（p）C（p）C（p）U（p）U（p）-3 ′：3 ′ =r（GA），在条GIAGGAAAU-5 ′上，使双链体不稳定3.9千卡/摩尔，相比之下，在未丙炔化的双链体中相同变化为1.7千卡/摩尔。通过除去三个碱基对以外的单个丙炔基消除了2.2千卡/摩尔的差异。CD光谱表明，单丙炔基缺失，内的PODN：RNA双链体的螺旋几何形状的位置依赖性的影响。结果表明，丙炔基团之间的长程协同性，并提供见解，合理编程寡核苷酸增强结合和特异性。这可以用于开发依赖于基于核酸的分子识别的技术。
A heptamer composed of C5-(1-propynyl) pyrimidines (Y-p's) is a potent and specific antisense agent against the mRNA of SV40 large T antigen (Wagner, R. W.; Matteucci, M. D,; Grant, D.; Huang, T.; Froehler, B. C, Nat. Biotechnol. 1996, 14, 840-844). To characterize the role of the propynyl groups in molecular recognition, thermodynamic increments associated with substitutions in DNA:RNA duplexes, such as 5 ' -dCCUCCUU-3 ' :3 ' -r (GA) over bar GGAGGAA (AU) over bar -5 ', have been measured by UV melting experiments. For nucleotides tested. an unpaired dangling end stabilizes unmodified and propynylated duplexes similarly: except that addition of a 5 ' unpaired rA is 1.4 kcal/mol more stabilizing on the propynylated, PODN:RNA, duplex than on the DNA:RNA duplex. Free energy increments for addition of single propynyl groups range from 0 to -4.0 kcal/mol, depending on the final number and locations of substitutions. A preliminary model for predicting the stabilities of Y-p-containing hybrid duplexes is presented. Eliminating one amino group, and therefore a hydrogen bond, by substituting inosine (I) for guanosine (G), to give 5 ' -dC(p)C(p)U(p)C(p)C(p)U(p)U(p)-3 ' :3 ' =r (GA) over bar GIAGGAAAU-5 ' , destabilizes the duplex by 3.9 kcal/mol, compared to 1.7 kcal/mol for the same change within the unpropynylated duplex, This 2.2 kcal/mol difference is eliminated by removing a single propynyl group three base pairs away. CD spectra suggest that single propynyl deletions, within the PODN:RNA duplex have position-dependent effects on helix geometry. The results suggest long-range cooperativity between propynyl groups and provide insights for rationally programming oligonucleotides with enhanced binding and specificity. This can be exploited in developing technologies that are dependent upon nucleic acid-based molecular recognition.