相关实验视频
Updated: Jul 20, 2026

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Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
一个循环聚胺-DNA复合物的NMR结构.
Qing Zhang1, Tammy J Dwyer, Vickie Tsui
1Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.
Journal of the American Chemical Society
|June 24, 2004
概括
这项研究使用NMR和分子动力学揭示了与DNA结合的循环聚胺的结构. 连接体结合得很紧,显示了DNA的灵活性,尽管结构改变.
科学领域:
- 结构生物学 结构生物学
- 生物化学 生物化学
- 分子生物物理学 分子生物物理学
背景情况:
- 循环聚胺被研究为DNA结合剂.
- 了解配体-DNA相互作用对于药物设计至关重要.
研究的目的:
- 为了确定与特定DNA寡合体复合的循环聚胺的溶液结构.
- 分析聚胺-DNA复合物的结合相互作用和动态.
主要方法:
- 核磁共振 (NMR) 光谱法被用来获得2D (1)H NMR数据.
- 距离限制来自NOESY使用MARDIGRAS的交叉峰强度.
- 使用溶剂模型进行受限分子动力学计算,以生成结构.
主要成果:
- 确定了复合到DNA复合体的循环聚胺 (cyclo-gamma-ImPyPy-gamma-PyPyPy-) 的溶液结构.
- 连接体表现出DNA结合的纳米分离常数.
- 结构显示了一些DNA扭曲和因循环化而改变的连接环堆叠,但与未连接的复合体相比,仍然保持了类似的DNA相互作用.
- 观察到缓慢的连接体解离和减少的DNA开放波动.
结论:
- 循环聚胺稳定地与DNA结合,诱导轻微的结构变化.
- 循环化会影响连接体构造,但不会影响整体的DNA相互作用概况.
- 连接体-DNA复合体表明了连接体结合和DNA灵活性之间的动态相互作用.
相关概念视频
The DNA Helix
Overview
¹H NMR: Complex Splitting
A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
The DNA Helix
Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
Nucleic Acid Structure
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
DNA Structure
DNA has a double-helix structure. The...

