Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA).
Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA).
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化学修饰对凝血酶结合适体（TBA）的结构和结合作用。
DOI：
10.3390/molecules26154620
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发表时间：
2021-07-30
期刊：
影响因子：
--
通讯作者：
Sheng J
中科院分区：
文献类型：
--
作者：
Valsangkar V;Vangaveti S;Lee GW;Fahssi WM;Awan WS;Huang Y;Chen AA;Sheng J
凝血酶结合适体（TBA）是一种很有前途的核酸抗凝剂。我们研究了化学修饰，如树状大分子Trebler和NHS羧基，对TBA的结构和凝血酶结合亲和力的影响。采用固相寡核苷酸合成方法，在TBA的5′端将这两种树突状修饰物结合到TBA g -四联体（T4、T13和T4/T13）凝血酶结合位点的胸腺嘧啶残基上添加NHS羧基。圆二色性（CD）光谱证实了所有这些修饰的TBA变体折叠成稳定的g -四重体。用表面等离子体共振（SPR）测定TBA变异体与凝血酶的结合亲和力。改性TBA的结合模式和平衡解离常数（KD）与天然TBA非常相似。分子动力学模拟研究表明，由于tba -凝血酶相互作用的破坏或适体中其他地方的不稳定，修饰引入的额外相互作用或稳定性增强被最小化，这为我们的实验数据提供了合理的解释。总的来说，本研究确定了TBA上可以在不影响其结构和凝血酶结合偏好的情况下进行修饰的潜在位置，这可能有助于设计和开发更功能的TBA类似物。
The thrombin binding aptamer (TBA) is a promising nucleic acid-based anticoagulant. We studied the effects of chemical modifications, such as dendrimer Trebler and NHS carboxy group, on TBA with respect to its structures and thrombin binding affinity. The two dendrimer modifications were incorporated into the TBA at the 5′ end and the NHS carboxy group was added into the thymine residues in the thrombin binding site of the TBA G-quadruplex (at T4, T13 and both T4/T13) using solid phase oligonucleotide synthesis. Circular dichroism (CD) spectroscopy confirmed that all of these modified TBA variants fold into a stable G-quadruplex. The binding affinity of TBA variants with thrombin was measured by surface plasmon resonance (SPR). The binding patterns and equilibrium dissociation constants (KD) of the modified TBAs are very similar to that of the native TBA. Molecular dynamics simulations studies indicate that the additional interactions or stability enhancement introduced by the modifications are minimized either by the disruption of TBA–thrombin interactions or destabilization elsewhere in the aptamer, providing a rational explanation for our experimental data. Overall, this study identifies potential positions on the TBA that can be modified without adversely affecting its structure and thrombin binding preference, which could be useful in the design and development of more functional TBA analogues.
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DOI：
10.1111/jth.12217
发表时间：
2013-06
期刊：
Journal of thrombosis and haemostasis : JTH
影响因子：
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作者：
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Yang X
影响因子：
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通讯作者：
Orozco M
DOI：
10.1039/c0cp00111b
发表时间：
2010-07-28
期刊：
Physical chemistry chemical physics : PCCP
影响因子：
--
作者：
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通讯作者：
Cieplak P