High purity deoxyribonucleic acid (DNA) is a crucial tool for biological research, and has been widely used in diagnostics, bioengineering, biopharmaceuticals and biological characterization [1], [2], [3]. Analysis based on specific DNA sequences exhibits more advantages than traditional analysis based on antibody and enzyme, including earlier detection results, higher detection sensitivity and easier modification flexibility. Thus, the effective separation of DNA is a mandatory and very important stage for clinical diagnosis, mutation analysis, pathogen detection and environmental monitoring [4], [5], [6]. Although traditional liquid phase extraction methods can effectively separate DNA, these processes exhibit critical limitations, such as time-consuming, low-throughput, large sample volume required, use of hazardous organic reagents and high risk of contamination [7,8]. Therefore, many researchers are seeking new DNA separation methods that are fast, flexible, automated and high-throughput [9].

Solid-phase extraction (SPE) has the advantages of minimal use of hazardous organic reagents, easier manual operations, certain automation capabilities and enhanced throughput, resulting in higher yield and purity of DNA [10]. Currently, most available commercial DNA extraction kits are developed based on SPE [11]. Wherein, the method using magnetic nanoparticles (MN) as a solid-phase adsorbent is more widely accepted than other methods in practical applications, because the magnetic solid-phase microextraction (MSPE) exhibits inherent advantages such as flexibility, time saving, automated operation and high throughput [12]. MNs are capable of adsorption-desorption of DNA and possess magnetic responsiveness, which allows them to be evenly dispersed in the medium while quickly collected using an external magnetic field [5].

At present, research on improving the extraction performance of MNs for DNA mainly focuses on surface functional group modification of materials [13]. DNA contains abundant phosphate groups that can generate different forces with functional groups on the surface of nanoparticles, including electrostatic, hydrogen bonding, hydrophobicity and coordination [14], [15], [16]. Silane-based reagents or polymers with hydroxyl, amino or carboxyl groups were generally used to modify MN or hybrid MN [17,18]. Fortunately, hydroxyl‑modified MN captures DNA via hydrogen bonding interactions, and the release of DNA is achieved by slightly changing the pH value and salt concentration of eluent, which is beneficial for downstream analysis [13]. Moreover, the extraction performance of the MN for DNA can also be improved by optimizing the shape of MN, especially by increasing specific surface area [19]. For examples, Fe3O4 nanoparticles have been modified with metal organic framework UiO-66-NH2, which was used to extract RNA from yeast [20]. Recently, hedgehog-inspired MNs (HMN) with a magnetic core and a nanoneedle-assembled shell have been fabricated and have exhibited a high-surface-area due to the distinct burr-like structure of hedgehog. Nickel-containing and antibody-modified HMN have been used for immobilizing His-tagged enzyme [21] and capturing exosome [22,23], respectively. Similarly, a microneedle patch with high-surface-area has been used for extraction of plant pathogen DNA [24]. However, to our best knowledge, there is no report about the usage of HMN for DNA extraction.

Pathogenic bacteria can exist in the air, soil, water and food, and may cause the spread of serious diseases, which have become a global concern because of severe public health issues and significant economic losses [25]. For example, Escherichia coli (E. coli) is a typical Gram-negative bacterium and one of the most common foodborne pathogens, some of which can cause diarrhea, abdominal pain, inflammation, hemorrhagic colitis, and even death [26]. Staphylococcus aureus (S. aureus) is a typical Gram-positive bacterium and the main cause of hospital- and community-associated infections [27]. Therefore, early detection of pathogenic bacteria in food and water is the foundation for reducing disease outbreaks. In recent years, various detection methods have been developed for controlling and monitoring pathogenic bacteria. Nucleic acid amplification-based diagnostic methods exhibit excellent sensitivity and specificity, and have been widely used for the detection of pathogenic bacteria [28].

Herein, we propose the HMN-related materials for the aim of high-efficient separation of pathogenic bacteria of DNA. Silica-coated Fe3O4 nanoparticles (Fe3O4@SiO2) were heat treated in the presence of Mg2+ ions, resulting in the silica layer becoming porous and hedgehog-like shape. Benefitting from the hedgehog-like shell, HMN possessed high-surface-area to modify functional groups so that large amounts of DNA could be efficiently captured. Furthermore, the magnetic core endowed the HMN with a rapid magnetic responsiveness under an external magnetic field, which was conducive to the rapid separation of DNA. Eventually, the integrated strategy of HMN-based MSPE and nucleic acid amplification was successfully used in detection of pathogenic bacteria from real samples.