Bifacial Peptide Nucleic Acid Directs Cooperative Folding and Assembly of Binary, Ternary, and Quaternary DNA Complexes
Bifacial Peptide Nucleic Acid Directs Cooperative Folding and Assembly of Binary, Ternary, and Quaternary DNA Complexes
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DOI：
10.1021/bi4008963
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发表时间：
2013-09-17
期刊：
影响因子：
2.9
通讯作者：
Bong, Dennis
中科院分区：
文献类型：
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作者：
Piao, Xijun;Xia, Xin;Bong, Dennis
本文报道了通过设计的三聚氰胺-胸腺嘧啶核碱基识别，将富含胸腺嘧啶的单链DNA序列构建成肽-DNA发夹三链体结构。合成具有通式（EM*）（n）的展示三聚氰胺的α-肽，其中M* 表示用三聚氰胺衍生的赖氨酸残基侧链，三聚氰胺是胸腺嘧啶的双面氢键互补物。我们已经发现，（EM*）n肽，我们称之为双面肽核酸（bPNA），作为一个非共价模板的胸腺嘧啶丰富的DNA束。一般形式dTnCmTn的非结构化DNA与（EM*）n肽结合，并折叠成协同熔融的1：1 bPNADNA发夹复合物，其解离常数在亚微摩尔至低纳摩尔范围内，n = 410。随着界面长度（n）的减小，bPNADNA复合物的解链温度显著下降，尽管Kd增加不太显著，表明强的熵补偿。这是证明了差示扫描量热法分析，这表明pacically驱动的bPNADNA碱基堆积，成为显着减少放热的识别表面n的大小减小。识别界面容忍大量的错配，并表明如果只有1个互补的核碱基可用，则可能发生三聚氰胺和胸腺嘧啶之间的半位点或单面识别。关联与胸腺嘧啶含量分数直接相关，当TT位点的数量与三聚氰胺单位的数量相匹配时具有最佳结合。有趣的是，当DNA宿主在bPNA上具有比三聚氰胺位点更多的TT位点时，两个或三个bPNA可以与单个DNA结合，从而产生比二元（1：1）bPNADNA复合物具有更高热稳定性的三元和四元复合物，这表明协同多位点结合。相比之下，当两个不同长度的bPNA结合到相同的DNA宿主时，形成具有两个解链转变的三元复合物，对应于来自复合物的每个bPNA组分的独立解链。这些数据表明，三聚氰胺展示bPNA识别胸腺嘧啶丰富的DNA在可预测的和多方面的方式，允许结合亲和力，结构稳定性和化学计量，通过简单的bPNA长度修饰和匹配DNA长度进行调整。合成bPNA结构元件可能是生物技术的有用工具。
We report herein the structuring of single-stranded thymine-rich DNA sequences into peptideDNA hairpin triplex structures via designed melaminethymine nucleobase recognition. Melamine-displaying a-peptides were synthesized with the general form (EM*)(n), where M* denotes a lysine residue side chain derivatized with melamine, a bifacial hydrogen bond complement for thymine. We have found that (EM*)n peptides, which we term bifacial peptide nucleic acid (bPNA), function as a noncovalent template for thymine-rich DNA tracts. Unstructured DNA of the general form dTnCmTn are bound to (EM*)n peptides and fold into cooperatively melting 1:1 bPNADNA hairpin complexes with dissociation constants in the submicromolar to low nanomolar range for n = 410. As the length of the interface (n) is decreased, the melting temperature of the bPNADNA complex drops significantly, though Kd increases are less substantial, suggestive of strong enthalpyentropy compensation. This is borne out by differential scanning calorimetry analysis, which indicates enthalpically driven bPNADNA base-stacking that becomes markedly less exothermic as the recognition surface n decreases in size. The recognition interface tolerates a high number of mismatches and indicates half-site, or monofacial, recognition between melamine and thymine may occur if only 1 complementary nucleobase is available. Association correlates directly with fractional thymine content, with optimal binding when the number of TT sites match the number of melamine units. Interestingly, when a DNA host has more TT sites than melamine sites on bPNA, two or three bPNAs can bind to a single DNA, resulting in ternary and quaternary complexes that have higher thermal stability than the binary (1:1) bPNADNA complex, suggestive of cooperative multisite binding. In contrast, when two bPNAs of different lengths bind to the same DNA host, a ternary complex is formed with two melting transitions, corresponding to independent melting of each bPNA component from the complex. These data demonstrate that melamine-displaying bPNA recognize thymine-rich DNA in predictable and multifaceted ways that allow binding affinity, structure stability, and stoichiometry to be tuned through simple bPNA length modification and matching with DNA length. Synthetic bPNA structuring elements may be useful tools for biotechnology.