Mechanical force-induced DNA damage during AFM single-molecule manipulation

Many environmental factors can cause DNA damage, such as radiation, heat, oxygen free radical, etc., which can induce mutation during DNA replication. Meanwhile, DNA molecules are subjected to various mechanical forces in numerous biological processes. However, it is unknown whether the mechanical force would induce DNA damage and introduce mutation during DNA replication. With the combination of single-molecule manipulation based on atomic force microscopy (AFM), single molecular polymerase chain reaction (SM-PCR) and Sanger’s sequencing, we investigated the effect of mechanical force on DNA. The results show that mechanical force can cause DNA damage and induce DNA mutation during amplification.     

Single DNA molecular manipulation with atomic force microscopy

Nanomanipulation of DNA molecules or other biomolecules to form artificial patterns or structures at nanometer scale has potential applications in the construction of molecular devices in future industries. It may also lead to new insights into the interesting properties and behavior of this fantastic nature-selected molecule at the single-molecular level. Here we present a special method based on the combination of macroscopic “molecular combing” and microscopic “molecular cutting” to manipulate DNA molecules and form complex patterns at nanometer scale on solid surfaces. A possible strategy for ordered DNA sequencing based on this nanomanipulation technique has also been proposed.     

AFM studies of nonspecific binding of enzyme on DNA

Atomic force microscope(AFM) is used to study restriction endonuclease digestion of plasmid DNA,pWRr plasmid DNA is digested by Hind Ⅲ,and the specific and the nonspecific binding of the restriction endonuclease are imaged,and the biological function of the enzyme binding to nonspecific sites is discussed.In addition,it is found that nonspecific binding of Hind ǚ could not induce the DNA characteristic bending angle.     

Preparation and characterization of graphene nanoribbons

Graphene nanoribbons(GNRs) have been synthesized by unzipping oxidized multiwalled carbon nanotubes.The thickness of the GNRs synthesized is ranged from mono-layer to four layers.The morphology of prepared GNRs is strongly dependent on structure and defects of the MWCNTs.The synchrotron radiation X-ray diffractions show the d(002) spacing of the GNRs decreases with the increase of the annealing temperature.This may be caused by the removing of water molecules and oxygen-containing functional groups in the GNRs.     

基于AFM成像的DNA长度的计算机统计处理

利用计算机图像处理技术 ,对自然沉积DNA和拉直DNA分子AFM图像的长度进行了自动统计测量 ,并与DNA分子的理论长度进行了比较。该方法在DNA分子的AFM图像的基础上 ,将DNA分子拟合成曲线 ,用插值法求得DNA分子长度 ,整个过程实现了自动化。结果表明 ,该方法测得自然沉积的某DNA分子长度为 (180 .4± 16.4 )nm ,与理论长度 185 .0nm相当符合。该方法与拉直法和直接法求DNA分子长度相比是一次改进 ,也为其它基于AFM图像的线状物体求长度提供了一种新的测量方法。对另一组拉直DNA测量的结果表明 :拉直后DNA分子长度为 (34 3.6± 2 0 .7)nm ,与理论长度 30 7.0nm相比明显变长 ,这表明对自然沉积DNA进行长度测量的必要性 ,保证了DNA分子的长度不受拉直后有所伸长的影响。     

Catenary—like pattern of stretching DNA molecules：experiments and models

It Was verified that our “s-suspension bridge” model may be not only responsible for catenary-like patterns of DNA molecules which were formed in our experiments,but also for catenary-like patterns of DNA molecules in literature.     

Influencing factors on local reduction of graphene oxide with a heated AFM tip

In this paper,the factors influencing the local thermal reduction of graphene oxide (GO) sheets are investigated.The lateral force microscopy and scanning polarization force microscopy verify that the heated tips of atomic force microscope (AFM) can thermally reduce the GO into electrical conductive nanostructures.The tip temperature,heating time,and loading force applied by the AFM tip are found to have important effects on the thermal reduction of GO,while the environmental humidity is negligible.     

基于原子力显微术的DNA折纸弹性模量的研究

原子力显微术(Atomic force microscopy,AFM)的力学成像模式可在高分辨成像的同时,定量测量材料的力学性质。然而,对尺度小、质地薄而软的生物分子的弹性模量的测量仍然是一个挑战。本文以脱氧核糖核酸(Deoxyribonucleic acid,DNA)折纸为检测样品,将峰值力定量纳米力学模式(Peak Force Quantitative Nanomechanical Mapping,PF-QNM)作为测量手段研究了DNA分子的力学性质,探索不同作用力对DNA折纸弹性模量的影响。结果表明,当峰值力控制在80-100 p N时,峰值力成像稳定,获得的杨氏模量维持在约10 MPa。与传统力曲线阵列模式(Force volume mapping,FV)相比较,在小力区(100 p N),两种方法符合性较好。这种峰值力定量纳米力学模式为DNA分子定量力学性质研究提供了一种简便而有效的研究方法。     

单能电子诱发DNA损伤的理论计算

利用径迹结构的方法模拟了单能电子从入射DNA水溶液到最终产生DNA损伤的早期物理和化学变化过程。着重研究了直接能量沉积导致碱基损伤的判断方法、DNA损伤穷举分类的定义及计算机实现方法,以及确定自由基产生位置的随机抽样方法。结果表明：物理、化学径迹与DNA的反应主要以NB（nobreak）的形式存在,而在链断裂中,主要也以易修复的单链断裂(SSB)为主;在为数不多的双链断裂（DSB）中,复杂DSB占到相当数量的份额。验证了DNA是辐射作用主要“靶”的假定。     

原子力显微镜在聚合物膜研究中的应用

原子力显微镜（AFM）已被用来研究膜的孔径和孔径分布、膜孔的结构、表面粗糙度、表面接点结构、膜的表面整体形态、膜污染机制和膜材料的选择等7个方面。原子力显微镜作为一种崭新的、有效的物理观测工具，在聚合物膜研究方面仍具有应用潜力。     

高LET的7Li离子致DNA损伤的直接和间接作用研究

在HI-13串列加速器加速的具有高LET值的7Li离子辐照不同浓度的pUC19质粒DNA水溶液、加自由基清除剂(甘露醇)的DNA水溶液以及干状DNA样品,利用高分辨的原子力显微镜技术,研究7Li致DNA损伤的直接作用和间接作用.结果显示,在相同剂量下,7Li离子比低LET辐射能诱发更多的双链断裂,形成更多的集团损伤,使DSB的分布更局部和更密集.对于水溶液DNA,7Li离子的水辐解产生的自由基的间接作用在DNA分子链断裂的产生方面发挥着重要作用,而且自由基清除剂甘露醇能有效地保护DNA分子.     

Sulfonated polyetherketone （SPEK-C） films investigated by positron annihilation lifetime spectroscopy and atomic force microscopy

The characterization of sulfonated polyetherketone （SPEK-C） films was investigated by using positron annihilation lifetime spectroscopy （PALS） and atomic force microscopy （AFM）. It was found that free volume radius and intensity depend on the variation of sulfonation degree and solvent evaporation time of the films. Pore size and distribution determined from PALS and AFM measurements showed reasonable agreement.     

DNA double-strand breaks induced along the trajectory of particles

It is well-known that the DNA damage caused by charged particles considerably differs from damage due to electromagnetic radiation. In the case of irradiation by charged particles the DNA lesions are more complex and clustered. Such clustered damage is presumed difficult to be repaired, and is potentially lethal. In this study, we utilize a 90°-scattering system and related imaging techniques to investigate the accumulation of γ-H2AX along the trajectory of charged particles. By immunostaining the γ-H2AX protein, optical images of corresponding double strand breaks were observed using a high resolution confocal microscope. We demonstrate the difference in the accumulation of γ-H2AX from irradiation by 1 MeV protons and that of 150 keV X-rays. The acquired images were arranged and reconstructed into a 3D image using ImageJ software. We discovered that the γ-H2AX foci, following irradiation by protons, have a tendency to extend in the beam direction, while those from X-ray irradiation tend to be smaller and more randomly distributed. These results can be explained by the physical model of energy deposition.     

Nano-manipulation of single DNA molecules

Nano-manipulation of single atoms and molecules is a critical technique in nanoscience and nanotech-nology. This review paper will focus on the recent development of the manipulation of single DNA molecules based on atomic force microscopy (AFM). Precise manipulation has been realized including varied manipulating modes such as “cutting”, “pushing“, “folding”, “kneading”, “picking up”, “dipping”, etc. The cutting accuracy is dominated by the size of the AFM tip, which is usually 10nm or less. Single DNA fragments can be cut and picked up and then amplified by single molecule PCR. Thus positioning isolation and sequencing can be performed.     

Hydrophobic ionic liquids/water interfacial phase transfer induced by direct current electric field

To investigate the affect of direct current electric field (DCEF) on the interfacial phase,in this paper,a hydrophobic ionic liquid (HIL)/water as liquid-liquid two-phase binary system is established by using the deioned water and l-butyl-3-methyl imidazolium hexafluorophosphate,and the topographies of the HIL nanodroplets and nanolayers in ambient water are observed by atomic force microscope (AFM).The results show the AFM exerting the DCEF can enhance the intersolubility of the HIL/water binary system and...     

AFM characterization of model nuclear fuel oxide multilayer structures modified by heavy ion beam irradiation

This work explored a potential new model dispersion fuel form consisting of an actinide material embedded in a radiation tolerant matrix that captures fission products (FPs) and is easily separated chemically as waste from the fuel material. To understand the stability of this proposed dispersion fuel form design, an idealized model system composed of a multilayer film was studied. This system consisted of a tri-layer structure of an MgO layer sandwiched between two HfO₂ layers. HfO₂ served as a surrogate fissile material for UO₂ while MgO represented a stable, fissile product (FP) getter that is easily separated from the fissile material. This type of multilayer film structure allowed us to control the size of and spacing between each layer. The films were grown at room temperature by e-beam deposition on a Si(1 1 1) substrate and post-annealed annealing at a range of temperatures to crystallize the HfO₂ layers. The 550 °C annealed sample was subsequently irradiated with 10 MeV Au³⁺ ions at a range of fluences from 5 × 10¹³ to 3.74 × 10¹⁶ ions/cm². Separate single layer constituent films and the substrate were also irradiated at 5 × 10¹⁵ and 8 × 10¹⁴ and 2 × 10¹⁶, respectively. After annealing and irradiation, the samples were characterized using atomic force imaging techniques to determine local changes in microstructure and mechanical properties. All samples annealed above 550 °C cracked. From the AFM results we observed both crack healing and significant modification of the surface at higher fluences.     

UVC诱导的枯草芽孢杆菌DNA双链断裂及影响因素探讨

为探讨短波紫外线（Ultraviolet C,UVC）对枯草芽孢杆菌基因组DNA的损伤效应,探讨研究方法和材料对结果的影响,以枯草芽孢杆菌为研究材料,分别对其菌体样品及DNA样品进行不同剂量的UVC辐照,采用8h、16h、24h脉冲场凝胶电泳分离DNA片段。结果发现,16h脉冲场凝胶电泳最能反映DNA的双链断裂程度。对16h电泳图进行数据分析发现,随UVC辐照剂量的增大DNA释放百分比递增;菌体样品在辐照剂量17．8J／cm^2处其DNA双链断裂产额最大,而DNA样品的最大双链断裂产额出现在辐照剂量为72．7J／cm^2处;另外,同辐照剂量下菌体样品的释放百分比和菌体DNA双链断裂产额均高于DNA样品。结果表明,UVC诱导的枯草芽孢杆菌DNA双链断裂程度与辐照剂量及辐照样品密切相关。     

单细胞凝胶电泳法检测研究同步辐射软X射线辐照引起的DNA损伤

本实验采用单细胞凝胶电泳方法定量检测了不同辐照剂量的同步辐射软X射线对小麦根尖细胞造成的DNA单链损伤.通过测定核DNA的迁移效应表明,在剂量为0-288 J·cm-2范围内的软X射线辐照下,有20%-92%的小麦根尖细胞产生了DNA单链的损伤效应,同时DNA的损伤程度也与辐照剂量呈显著正相关.     

碳微集团束的产生及其在CR-39中径迹的AFM观测

在HI－13串行加速器上实现了对碳微集团的加速，得到了MeV级的碳微集团束，对产生的碳的微集团束进行了测量并用它对CR＝－39塑料核径迹探测器进行了辐照，利用先进的原子力显微镜对C1和C2在CR－39中的径迹进行了观测。     

Radiotoxicity induced by Auger electron emitters in human osteosarcoma cell line using comet assay

The comet assay (single cell gel electrophoresis assay) was used to evaluate the radiotoxicity of Auger electron emitters in the human osteosarcoma cell line (HOS-8603). After internal exposure to 67Ga-EDTMP, the sarcoma cell has been injured severely. The comet length was longer along with the increase of dose, the appearance of comet tail was different from that with respect to the 60Co r-ray irradiation. DNA damage of cell was mainly due to the radiation effect of Auger electrons. The 67Ga may be a therapeutic radionuclide with good prospect for tumor treatment and palliation of bone pain induced by metastasis.