AFM Imaging Study Of DNA Alignment Induced By Magnetic Nanoparticles

Double stranded DNA is a kind of flexible biomacromolecules, it has a wide rangeof applications including biomedical and DNA nanotechnology. Atomic forcespectroscopy (AFM) imaging has been used widely in the investigation of theinteractions between DNA and other molecules, because of its nanometer resolution,easy operation, and friendly working environment (in air or liquid), providing theinformation at single molecular level. However, long dsDNA tends to form a randomcoiled structure, which prevents the direct observation of subtle DNA structure.Therefore, the ability to reproducibly creat aligned DNA, manipulating them fromrandom-coiled state into extended conformation, is not only important for elucidatingthe interaction mechanism between DNA and other molecules, but also forapplications in DNA nanotechnology.In our research, the dumbbell-like5.5-10nm Au-Fe3O4magnetic nanoparticlesmodified with oleylamine and oleic acid were synthesized by thermolysis of ferricacetylacetonate (Fe(acac)3), the nanoparticles could be transferred from oil phase intowater with mPEG-COOH as ligand transfer agent. Based on the results oftransmission electron microscope (TEM), ultraviolet spectroscopy (UV-vis), Fourierinfrared spectroscopy (FTIR), X-ray powder diffraction (XRD), dynamic lightscattering (DLS), vibrating sample magnetometer (VSM), we know that theoil-to-water phase transfer showed no obvious changes in the size and shape ofAu-Fe3O4nanoparticle. And the nanoparticles could be dispersed well in aqueoussolution because of the modification of PEG molecules on the surface, and showedthe superparamagnetism at room temperature. The characterization by DLS showedthat the nanoparticles carried positive charge after the transfer. The hydrophilicmagnetic nanoparticles were used in the conjugation with double stranded DNA. Weobtained a5‘-thioled and5‘-amino-labeled linear dsDNA (2000base pair) by polymerase chain reaction (PCR), and the DNA molecule was linked directly onto theAu-Fe3O4nanoparticles through Au-S covalent bond, the amino end of DNA wascoupled to the silicon surface via-NH2/NHS reaction. Then, we used atomic forcespectroscopy (AFM) imaging to study the alignment of stretched DNA induced by theapplied magnetic field. It turned out the DNA molecules can be stretched and highlyoriented due to the movement of the magnetic nanoparticles driven by the externalmagnetic field. The aligned DNA molecules relaxed to their random coiled state uponrinsing and removal of the magnetic field. Such alignment and relaxation can berepeated, which demonstrated that the DNA can be induced to be stretched repeatedlyby controlling the magnetic field.