Shiyong Ran

Morphology characterization and single-molecule study of DNA-dodecyltrimethylammonium bromide complex.

DNA compaction induced by dodecyltrimethylammonium bromide (DTAB) is studied using atomic force microscopy (AFM) and magnetic tweezers. The morphology of DNA-DTAB complex is dependent on the DTAB concentration and incubation time. With magnesium ions, the complexes show rod- and network-like structures after approximately 5 min of incubation at low DTAB concentrations. With increasing incubation time, more toroids and globules appeared, resulting in the formation of scattered condensed particles. At high DTAB concentrations, the complexes show swollen globular structures independent of the incubation time. The compaction and unraveling of the DNA-DTAB complex are also analyzed at the single-molecule level using magnetic tweezers. The extension-time curves show a staircase structure with typical sizes of ∼40, 60, 80, and 112 nm, suggesting that the complexes are well organized and more compacted than those induced by multivalent ions. Finally, the high DTAB concentration stabilized the complex and increased the unraveling energy barrier.

Field emission resonances in photodetachment of negative ions on surface

The interaction between the field emission resonance states and the photodetached electron in an electric field is studied by semiclassical theory. An analytical expression of the photodetachment cross section is derived in the framework. It is found that the Stark shifted image state modulates the photodetachment cross section by adding irregular staircase or smooth oscillation in the spectrum. When the photodetached electron is trapped in a Stark shifted image potential well, the detachment spectrum displays an irregular staircase structure which corresponds to the modified Rydberg series. While the photodetached electron is not bound by the surface potential well, the cross section contains only a smooth oscillation due to the reflection of the electronic waves by the field or the surface.

Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI.

DNA looping and aggregation induced by restriction endonuclease BspMI are studied by atomic force microscopy (AFM) and magnetic tweezers (MT). With Ca2+ substituted for the normal enzyme cofactor Mg2+ and enzyme concentration below the critical concentration of 6 units/mL, AFM images of DNA-BspMI complex show that the number of binding and looping events increases with enzyme concentration. At the critical concentration 6 of units/mL, all the BspMI binding sites are saturated. It is worth noting that nonspecific BspMI binding to DNA at saturation concentration represents more than 8% of the total BspMI-DNA complexes directly observed in AFM images. Furthermore, we used MT to prove that additional loops can form when enzyme concentration is higher than its saturation valueand the complex is incubated for a long time (>2 hrs). We ascribe this phenomenon to the aggregation of enzymes. The force spectroscopy of the BspMI-DNA complex shows that the pulling force required to open the loop of the complex at less than saturation concentration has a peak at about 3 pN, which is lower than the force required to open additional loops due to enzyme aggregation at higher than saturation concentration (>6 pN).

Helical conformations of semiflexible polymers confined between two concentric cylinders.

An off-lattice Monte Carlo method was used to study the conformational properties of semiflexible chains confined between two concentric cylinders. The conformations of confined semiflexible chains depend on the bending energy as well as the size of confinement, and the semiflexible chains with particular rigidities confined in the appropriate spaces can form helical structures under entropically driven. The inner cylinder plays a key role in the formation of helical conformations, whereas the outer cylinder affects the size of confinement. Furthermore, the helical structures keep fluctuating like a harmonic oscillation, and the clockwise or counterclockwise helical conformations will appear with the same possibility in the processes of relaxation-helix transitions. This study can help us understand the conformational behaviors of biological macromolecules in confined space.

DNA condensations on mica surfaces induced collaboratively by alcohol and hexammine cobalt

We performed systematic studies of λ-DNA condensation on mica surfaces induced by alcohol and hexammine cobalt (III) [Co(NH(3))(6)(3+)] using atomic force microscopy (AFM). The critical condensation concentration for [Co(NH(3))(6)(3+)] was found to be about 10 microM; the DNA molecules extended freely on mica when the concentration was below the critical value. The morphology of condensed DNA became more compact with increasing concentration. At about 500 microM [Co(NH(3))(6)(3+)] concentration, no condensation patterns could be observed due to charge inversion of the compact structures resulting in failure of adhesion to the positively charged surfaces. The critical concentration for alcohol was about 15% (v/v). At this concentration, a few intramolecular loops could be observed in the AFM images. With increasing ethanol concentration the condensation pattern became more complicated ranging from flower-like to pancake-like. When the solution contained both alcohol and hexammine cobalt (III), DNA condensation patterns could be observed even when the concentrations of the two condensation agents were lower than their critical values. We observed this phenomenon by adding mixtures of 10% alcohol and 8 microM hexammine cobalt (III) to DNA solutions. The condensation patterns were more compact than those of the condensation agents separately. Typical toroids were found at an appropriate alcohol and hexammine cobalt (III) concentration. The collaborative condensation phenomenon was analyzed by electrostatic interaction and charge neutralization.

Self-assembly of nanorods on soft elastic shells

The self-assembly behavior of nanorods (NRs) on soft elastic shells is investigated using the molecular dynamics (MD) simulation method. The self-assembly structures of the adsorbed nanorods depend on the length of the nanorods as well as the bending energy of the soft elastic shells. For short nanorods, the aggregates consist of regular pentagons around the gibbosity at low bending energies, and the ordered structures are gradually broken when the bending energy increases. In the meantime, the adsorption ability of the nanorods on the elastic shells decreases when the binding energy increases. For long nanorods, the binding energy can induce the nanorods to aggregate in clusters on shells with low or moderate bending energy, and each cluster is formed by several parallel long nanorods. However, the self-assembly structures of long nanorods disappear for shells with high bending energy because the adsorption becomes isotropic for nanorods on a rigid shell. Meanwhile, the adsorption of nanorods on the shell can also affect the shape of the soft elastic shell, especially for long nanorods. This investigation can help us understand the complexity of the self-assembly of nanorods on an elastic shell.

Single DNA Condensation Induced by Hexammine Cobalt with Molecular Combing

We investigated the interaction between DNA and hexammine cobalt III [Co(NH3)6]3+ by a simple molecular combing method and dynamic light scattering. The average extension of λ-DNA-YOYO-1 complex is found to be 20.9 μm, about 30% longer than the contour length of the DNA in TE buffer (10 mmol/L Tris, 1 mmol/L EDTA, pH=8.0), due to bis-intercalation of YOYO-1. A multivalent cation, hexammine cobalt, is used for DNA condensation. We find that the length of DNA-[Co(NH3)6]3+ complexes decrease from 20.9 μ to 5.9 μ as the concentration of the [Co(NH3)6]3+ vary from 0 to 3 μmol/L. This observation provides a direct visualization of single DNA condensation induced by hexammine cobalt. The results from the molecular combing studies are supported by dynamic light scattering investigation, where the average hydrodynamic radius of the DNA complex decreases from 203.8 nm to 39.26 nm under the same conditions. It shows that the molecular combing method is feasible for quantitative conformation characterization of single bio-macromolecules.

Quantum coherence and electric field control of the photodetached electron on elastic surface

The quantum dynamics of the photodetached electron of H(-) in electric field near a surface are studied in the time domain. The evolution of wave packet for different manifold eigenstates with limited lifetimes is obtain analytically. It is found that the quantum coherence and temporal evolution of surface electronic wave packet can be controlled by the laser central energy and electric field. The correspondence between classical and quantum mechanics is shown explicitly in the system. Numerical simulation shows that the temporal evolution of photodetached electronic wave packet on elastic surface exhibits some similar properties of time-resolved two-photon photoemission signal of surface electron.

Two-stage DNA compaction induced by silver ions suggests a cooperative binding mechanism

The interaction between silver ions and DNA plays an important role in the therapeutic use of silver ions and in related technologies such as DNA sensors. However, the underlying mechanism has not been fully understood. In this study, the dynamics of Ag+-DNA interaction at a single-molecule level was studied using magnetic tweezers. AgNO3 solutions with concentrations ranging from 1 μM to 20 μM led to a 1.4-1.8 μm decrease in length of a single λ-DNA molecule, indicating that Ag+ has a strong binding with DNA, causing the DNA conformational change. The compaction process comprises one linear declining stage and another sigmoid-shaped stage, which can be attributed to the interaction mechanism. Considering the cooperative effect, the sigmoid trend was well explained using a phenomenological model. By contrast, addition of silver nanoparticle solution induced no detectable transition of DNA. The dependence of the interaction on ionic strength and DNA concentration was examined via morphology characterization and particle size distribution measurement. The size of the Ag+-DNA complex decreased with an increase in Ag+ ionic strength ranging from 1 μM to 1 mM. Morphology characterization confirmed that silver ions induced DNA to adopt a compacted globular conformation. At a fixed [AgNO3]:[DNA base pairs] ratio, increasing DNA concentration led to increased sizes of the complexes. Intermolecular interaction is believed to affect the Ag+-DNA complex formation to a large extent.