High efficiency nucleic acid (NA) separation via magnetic nanoparticles (MNPs) is a promising technology for bioengineering, healthcare, etc. Aimed to enhance the selection of MNPs and illustrate the separation mechanism for effective isolation of NAs from complex animal samples, this study fabricated hydroxy-, amino- and carboxyl-functionalized MNPs (MNPs-OH, MNPs-NH₂ and MNPs-COOH) with different particle sizes to investigate the hybrid NA separation performance from animal tissue samples. Molecular dynamics (MD) simulation was introduced to predict the affinity action of MNPs with NA and typical impurities. The details of the kinetic separation behavior and the NA separation performance were then illustrated. MD simulation results showed MNPs-NH₂ had a stronger affinity with NA, and in most experimental separation systems, NA separation yield via three kinds of MNPs showed a following order of MNPs-NH₂ > MNPs-OH > MNPs-COOH. MNPs of different sizes had significantly different sedimentation and dispersion features, leading to diverse separation results. Combining with the proper lysis system, an optimized NA separation method at room temperature with high-throughput and low contamination risk was developed as a promising approach for large-scale samples extracted NA simultaneously. This work could provide a theoretical guidance for the fabrication strategy of advanced MNPs and the enhancement of NA separation from complex samples.

通过磁性纳米颗粒（MNP）进行高效核酸（NA）分离是一种在生物工程，医疗保健等领域很有前途的技术。该研究旨在增强MNP的选择并阐明从复杂动物样品中有效分离NA的分离机制。羟基，氨基和羧基官能化的MNP（MNPs-OH，MNPs-NH ₂和MNPs-COOH）具有不同的粒径，以研究从动物组织样品中杂交NA的分离性能。引入分子动力学（MD）模拟以预测MNP与NA和典型杂质的亲和作用。然后说明了动力学分离行为和NA分离性能的细节。MD模拟结果表明MNPs-NH ₂与NA具有更强的亲和力，并且在大多数实验分离系统中，通过三种MNP的NA分离产率显示出MNPs-NH ₂  > MNPs-OH> MNPs-COOH的顺序。不同大小的MNP具有明显不同的沉降和分散特征，从而导致不同的分离结果。结合适当的裂解系统，开发了一种在室温下具有高通量和低污染风险的优化的NA分离方法，这是一种可用于同时提取NA的大规模样品的有前途的方法。这项工作可以为高级MNPs的制备策略和从复杂样品中分离NA的方法提供理论指导。