Minqian Li

Nanobubbles on solid surface imaged by atomic force microscopy

Gas bubbles of nanometer size were produced on atomically flat solid surfaces and imaged by atomic force microscopy (AFM) in tapping mode in water. In AFM images, nanobubbles appeared like blight spheres. Some of the bubbles remained stable for hours during the experiments. The bubbles were disturbed under high load during AFM imaging. A related mechanism is discussed

Molecular patterns by manipulating DNA molecules

Manipulating DNA molecules to form molecular patterns on a nanometer scale is a subject with wide prospects. By applying a modified “molecular combing” technique and imaging in air with atomic force microscope, we aligned DNA molecules on a mica surface which was chemically modified with a small organic molecule, (3-aminopropyl)-triethanoxysilane. Two-dimensional patterns of DNA molecules were also constructed.

Study on the chain structure of starch molecules by atomic force microscopy

Starch molecules were stretched and aligned by a special method on a mica surface and imaged with atomic force microscopy (AFM). The AFM images have shown the “chain” structure of the starch molecules. The results also show that there exist complicated structures in the molecules of natural starch and that the glucose units may form thicker “chains.” The length of the chains may reach 1–2 μm.

Single-base resolution and long-coverage sequencing based on single-molecule nanomanipulation

We show new approaches towards a novel single-molecule sequencing strategy which consists of high-resolution positioning isolation of overlapping DNA fragments with atomic force microscopy (AFM), subsequent single-molecule PCR amplification and conventional Sanger sequencing. In this study, a DNA labelling technique was used to guarantee the accuracy in positioning the target DNA. Single-molecule multiplex PCR was carried out to test the contamination. The results showed that the two overlapping DNA fragments isolated by AFM could be successfully sequenced with high quality and perfect contiguity, indicating that single-base resolution and long-coverage sequencing have been achieved simultaneously.

Stretching and imaging studies of single DNA molecules

DNA molecules were stretched on silanized mica surface with the molecular combing technique, and detected with fluorescence microscopy and atomic force microscopy. Meantime, DNA molecules were stretched with a modified dynamic molecular combing technique and studied with atomic force microscopy. The results indicate that, compared with the dynamic molecular combing technique, the modified dynamic molecular combing technique has advantages of less-sample demand and less contamination to sample; as compared with the molecular combing technique, it has better aligning effect and reproducibility. Combination of this kind of DNA molecular manipulating technique with the single DNA molecule detecting technique by atomic force microscopy and fluorescence microscopy will play an important role in the basic research of molecular dynamics and the application of gene research.

Height measurement of dsDNA and antibodies adsorbed on solid substrates in air by vibrating mode scanning polarization force microscopy

A method of height measurement based on vibrating mode scanning polarization force microscopy is developed and applied to soft molecules such as dsDNA and antibodies. In the experiment, a bias voltage is applied to a conductive atomic force microscopy (AFM) tip to maintain it farther from the surface during imaging in vibrating mode. By changing amplitude setpoint (A(sp)) the tip can be lowered from the top of a molecule to the substrate, and the displacement of the tip in the z direction (D-Z) approximates the true height of this molecule. This method is first applied to rigid colloidal gold particles and then to dsDNA and antibodies. The measured heights of gold particles are consistent with those in normal tapping mode AFM (TM-AFM). However, the measured heights of dsDNA molecules and antibodies CA125 are much larger than the results in TM-AFM. We deduce that tip pressure might have caused large deformation on soft biomolecules when imaging is performed in ITM-AFM

Imaging bacteriorhodopsin-like molecules of claret-membranes from Tibet halobacteria xz515 by atomic force microscope

HalobacteriaH.sp.xz 515 was isolated from a salt lake in Tibet. Although proton release-and-uptake across claret membrane is in reverse order compared to bacteriorhodopsin in purple membrane fromHalobacterium Salinarum, and its efficiency of proton pump is much lower, AFM image shows that the molecules are still arranged in a two-dimensional hexagonal lattice of trimers. Primary structure of Cto G-helix of the archaerhodopsin shows that it has only 56% homology with bacteriorhodopsin. But the interactive amino acid residues at the interface between B and D-helixes are conserved. These amino acid residues are believed to play a significant role in the stability of protein oligomers.

Stretch and align virus in nanometer scale on an atomically flat surface

Manipulation of macromolecules in nanometer scale is becoming an interesting research field. An approach to manipulate supramolecular assemblies is reported in this article. Linear phage viruses were aligned in one direction on atomically flat surfaces by a special method called “molecular combing.” Atomic force microscopy was used to check the results. Most of the phage strands were found to be stretch straight from one end to another. A related mechanism is also discussed.

Combined-dynamic mode "dip-pen" nanolithography and physically nanopatterning along single DNA molecules

Atomic force micriscope (AFM)-based dip-pen nanolithography (DPN) is an emerging approach for constructing nanostructures on material surfaces such as gold, silicon and silicon oxide. Although DPN is a powerful technique, it has not shown its ability of direct-writing and patterning of nanostructures on surfaces of soft materials, for example biomacromolecules. Direct depositing on soft surfaces becomes possible with the introduction of a combined-dynamic mode DPN rather than mostly used contact mode DPN or tapping mode DPN. In this report, the combined dynamic mode DPN is used for direct depositing protein ink on DNA molecules at the nanometer scale.

Real time observation of the photocleavage of single DNA molecules

A method for real time observation of photocleavage of stretched λDNA at single molecular level by a fluorescent microscope coupled with CCD is developed. DNA molecules stained with YOYO-1 are stretched by the molecular combing technique and fixed on a modified slide. Then the process of photocleavage and relaxation of DNA under radiation of blue light is observed. We speculate that the conformation change of stretched DNA and the effect of water are likely to facilitate the effect of YOYO photocleavage DNA molecules. The photocleavage effect of YOYO for stretched DNA may be useful to study DNA elasticity, cancer research as well as the interaction between DNA and dyes.