一维DNA纳米材料自组装效率的可视化测量

Visualized Measurement of Self-assembly Efficiency in One-dimensional DNA Nanomaterials

摘要

一维DNA纳米材料在诸多领域具有广泛的应用前景, 但其自组装效率的定量表征仍面临挑战. 本文以六螺旋束(six-helix bundle, 6HB) DNA纤维为模型体系, 基于已有的图像分析方法, 针对高长径比一维纤维易交叉缠绕、 难以进行单颗粒识别与计数的问题进行整合与参数化处理, 建立了一套基于原子力显微镜(AFM)图像分析的自组装效率可视化测量方法. 该方法以面积覆盖率和轮廓长度密度为量化指标, 实现了对一维DNA纤维网络结构的定量表征. 利用该方法考察了缓冲液pH(5~11)和Mg²⁺浓度(6.25~87.5 mmol/L)对6HB DNA纤维组装行为的影响. 结果表明, 6HB DNA纤维的有效组装存在明确的条件窗口: pH在6~8范围内有利于高产率形成长纤维, 其中pH=8时自组装效率达到峰值(面积覆盖率约36%, 轮廓长度密度约8 μm/μm²). 当pH偏离该范围时, 连续的一维网络逐渐转变为碎片化或无序聚集结构, 两项参数接近背景水平. 同时, 纤维自组装对Mg²⁺浓度表现出明显的阈值响应特征, 浓度高于25 mmol/L时进入快速增长区, 在50 mmol/L以上时形成稳定的长纤维产物(面积覆盖率> 20%, 轮廓长度密度> 4 μm/μm²). 这些测量结果通过可视化和定量分析, 验证了DNA纳米结构自组装对pH值和离子强度等环境条件的高度依赖性. 该研究框架有望为一维DNA纳米材料的设计、 制备与应用提供有力的定量分析工具.

Abstract

One-dimensional（1D） DNA nanomaterials exhibit broad potential for applications across multiple fields. However， quantitative evaluation of their self-assembly efficiency remains challenging. In this work， six-helix bundle（6HB） DNA fibers were employed as a model system. Building upon existing image analysis methods， we developed an integrated and parameterized approach to overcome the challenges of single-particle identification and counting in high-aspect-ratio， entangled 1D fibers， and established an AFM image-based method for visualizing and quantifying self-assembly efficiency. In this method， the area coverage ratio and contour length density extracted from AFM images were used as quantitative parameters to characterize 1D DNA fiber networks. Using this method， the effects of buffer pH（5-11） and Mg²⁺ concentration（6.25-87.5 mmol/L） on the assembly behavior of 6HB DNA fibers were investigated. The results show that efficient assembly of 6HB DNA fibers occurs within a well-defined window of conditions. Continuous long fibers are preferentially formed in the pH range of 6-8， with the highest assembly efficiency at pH=8， where the area coverage ratio reaches ca.36%， and the contour length density is ca.8 μm/μm². When the pH value deviates from this range， the continuous 1D network gradually transforms into fragmented or disordered aggregates， and both parameters decrease to background levels. Fiber assembly also shows a clear threshold response to Mg²⁺ concentration： the assembly efficiency increases rapidly above 25 mmol/L， and stable long fibers form at concentrations above 50 mmol/L， corresponding to area coverage ratios >20% and contour length densities >4 μm/μm². These results quantitatively demonstrate the strong dependence of DNA nanostructure self-assembly on environmental conditions such as pH and ionic strength. The analytical framework established here provides a useful quantitative tool for the design， assembly， and application of 1D DNA nanomaterials.

关键词

六螺旋束DNA纤维 / 原子力显微镜图像分析 / 自组装效率

Key words

Six-helix bundle DNA fibers / AFM image analysis / Self-assembly efficiency

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基金资助

国家重点研发计划项目(2023YFC3404200)

国家自然科学基金(22325406)

国家自然科学基金(22525605)

国家自然科学基金(32301185)