Brownian motion of DNA confined within a two-dimensional array

Linear DNA molecules are visualized while undergoing Brownian motion inside media patterned with molecular-sized spatial constraints. The media, prepared by colloidal templating, trap the macromolecules within a two-dimensional array of spherical cavities interconnected by circular holes. Across a broad DNA size range, diffusion does not proceed by the familiar mechanisms of reptation or sieving. Rather, because of their inherent flexibility, DNA molecules strongly localize in cavities and only sporadically "jump" through holes. Jumping closely follows Poisson statistics. By reducing DNA's configurational freedom, the holes act as molecular weight-dependent entropic barriers. Sterically constrained macromolecular diffusion underlies many separation methods and assumes an important role in intracellular and extracellular transport.     

Graphite: a mimic for DNA and other biomolecules in scanning tunneling microscope studies

Highly ordered pyrolytic graphite (HOPG) is the substrate often used in scanning tunneling microscope (STM) studies of biomolecules such as DNA. All of the images presented in this article are of freshly cleaved HOPG surfaces upon which no deposition has occurred. These images illustrate features previously thought to be due to biological molecules, such as periodicity and meandering of "molecules" over steps. These features can no longer be used to distinguish real molecules from features of the native substrate. The feasibility of the continued use of HOPG as a substrate for biological STM studies is discussed.     

Theoretical studies of DNA during gel electrophoresis

A numerical study of the motion of a long-chain macromolecule in a gel has shown unexpected features. The application of a field appears to induce the chain to contract on itself. This is followed by its "unwinding" into an extended configuration. For long chains, the mobility tends toward a constant, in accord with experiments. For the parameter range used, the observed molecular motion differs strongly from assumptions made in the present theory of electrophoresis.     

Control of electron localization in molecular dissociation

We demonstrated how the subcycle evolution of the electric field of light can be used to control the motion of bound electrons. Results are presented for the dissociative ionization of deuterium molecules (D2 --> D+ + D), where asymmetric ejection of the ionic fragment reveals that light-driven intramolecular electronic motion before dissociation localizes the electron on one of the two D+ ions in a controlled way. The results extend subfemtosecond electron control to molecules and provide evidence of its usefulness in controlling reaction dynamics.     

Quantum interference device made by DNA templating of superconducting nanowires

The application of single molecules as templates for nanodevices is a promising direction for nanotechnology. We used a pair of suspended DNA molecules as templates for superconducting two-nanowire devices. Because the resulting wires are very thin, comparable to the DNA molecules themselves, they are susceptible to thermal fluctuations typical for one-dimensional superconductors and exhibit a nonzero resistance over a broad temperature range. We observed resistance oscillations in these two-nanowire structures that are different from the usual Little-Parks oscillations. Here, we provide a quantitative explanation for the observed quantum interference phenomenon, which takes into account strong phase gradients created in the leads by the applied magnetic field.     

Molecule cascades

Carbon monoxide molecules were arranged in atomically precise configurations, which we call "molecule cascades," where the motion of one molecule causes the subsequent motion of another, and so on in a cascade of motion similar to a row of toppling dominoes. Isotopically pure cascades were assembled on a copper (111) surface with a low-temperature scanning tunneling microscope. The hopping rate of carbon monoxide molecules in cascades was found to be independent of temperature below 6 kelvin and to exhibit a pronounced isotope effect, hallmarks of a quantum tunneling process. At higher temperatures, we observed a thermally activated hopping rate with an anomalously low Arrhenius prefactor that we interpret as tunneling from excited vibrational states. We present a cascade-based computation scheme that has all of the devices and interconnects required for the one-time computation of an arbitrary logic function. Logic gates and other devices were implemented by engineered arrangements of molecules at the intersections of cascades. We demonstrate a three-input sorter that uses several AND gates and OR gates, as well as the crossover and fan-out units needed to connect them.     

From force fields to dynamics: classical and quantal paths

Reaction path methods provide a powerful tool for bridging the gap between electronic structure and chemical dynamics. Classical mechanical reaction paths may usually be understood in terms of the force field in the vicinity of a minimum energy path (MEP). When there is a significant component of hydrogenic motion along the MEP and a barrier much higher than the average energy of reactants, quantal tunneling paths must be considered, and these tend to be located on the corner-cutting side of the MEP. As the curvature of the MEP in mass-scaled coordinates is increased, the quantal reaction paths may deviate considerably from the classical ones, and the force field must be mapped out over a wider region, called the reaction swath. The required force fields may be represented by global or semiglobal analytic functions, or the dynamics may be computed "directly" from the electronic structure results without the intermediacy of potential energy functions. Applications to atom and diatom reactions in the gas phase and at gas-solid interfaces and to reactions of polyatomic molecules in the gas phase, in clusters, and in aqueous solution are discussed as examples.     

Separation of large DNA molecules by contour-clamped homogeneous electric fields

Electric fields can be manipulated by a method in which multiple electrodes are arranged along a closed contour and clamped to predetermined electric potentials. This method may be applied to a broad range of problems in the separation of macromolecules by gel electrophoresis. DNA molecules as large as 2 megabases can be well separated with a contour-clamped homogeneous electric field alternating between two orientations 120 degrees apart. The pattern of separation is independent of position in the gel, which is an advantage over previous methods. DNA less than 50 kilobases can be separated without distortion even at high voltage with a nonalternating contour-clamped homogeneous field. Decreased band broadening in DNA less than 200 bases can be achieved with a contour-clamped inhomogeneous field.     

脉冲场凝胶电泳技术及应用

脉冲场凝胶电泳(PFGE)是一种重要的用于分离大分子量线状DNA的电泳技术。介绍了PFGE的基本原理、方法、影响因素,并对其在微生物分子分型、DNA辐射损伤修复、细胞凋亡和转基因技术等研究方面的应用作了简要的综述。     

Electrophoretic separations of large DNA molecules by periodic inversion of the electric field

In gel electrophoresis, nucleic acids and protein-detergent complexes larger than a threshold size all migrate at the same rate. For DNA molecules, this effect can be overcome by the simple procedure of periodically inverting the electric field. Tuning the frequency of the field inversions from 10 to 0.01 hertz, makes it possible to resolve selectively DNA's in the size range 15 to greater than 700 kilobase pairs.     

Kinesin moves by an asymmetric hand-over-hand mechanism

Kinesin is a double-headed motor protein that moves along microtubules in 8-nanometer steps. Two broad classes of model have been invoked to explain kinesin movement: hand-over-hand and inchworm. In hand-over-hand models, the heads exchange leading and trailing roles with every step, whereas no such exchange is postulated for inchworm models, where one head always leads. By measuring the stepwise motion of individual enzymes, we find that some kinesin molecules exhibit a marked alternation in the dwell times between sequential steps, causing these motors to "limp" along the microtubule. Limping implies that kinesin molecules strictly alternate between two different conformations as they step, indicative of an asymmetric, hand-over-hand mechanism.     

Multiplex DNA sequencing

The increasing demand for DNA sequences can be met by replacement of each DNA sample in a device with a mixture of N samples so that the normal throughput is increased by a factor of N. Such a method is described. In order to separate the sequence information at the end of the processing, the DNA molecules of interest are ligated to a set of oligonucleotide "tags" at the beginning. The tagged DNA molecules are pooled, amplified, and chemically fragmented in 96-well plates. The resulting reaction products are fractionated by size on sequencing gels and transferred to nylon membranes. These membranes are then probed as many times as there are types of tags in the original pools, producing, in each cycle of probing, autoradiographs similar to those from standard DNA sequencing methods. Thus, each reaction and gel yields a quantity of data equivalent to that obtained from conventional reactions and gels multiplied by the number of probes used. To date, even after 50 successive probings, the original signal strength and the image quality are retained, an indication that the upper limit for the number of reprobings may be considerably higher.     

DNA-templated organic synthesis and selection of a library of macrocycles

The translation of nucleic acid libraries into corresponding synthetic compounds would enable selection and amplification principles to be applied to man-made molecules. We used multistep DNA-templated organic synthesis to translate libraries of DNA sequences, each containing three "codons," into libraries of sequence-programmed synthetic small-molecule macrocycles. The resulting DNA-macrocycle conjugates were subjected to in vitro selections for protein affinity. The identity of a single macrocycle possessing known target protein affinity was inferred through the sequence of the amplified DNA template surviving the selection. This work represents the translation, selection, and amplification of libraries of nucleic acids encoding synthetic small molecules rather than biological macromolecules.     

Femtosecond pulse sequences used for optical manipulation of molecular motion

Optical control over elementary molecular motion is enhanced with timed sequences of femtosecond (10(-15) second) pulses produced by pulse-shaping techniques. Appropriately timed pulse sequences are used to repetitively drive selected vibrations of a crystal lattice, in a manner analogous to repetitively pushing a child on a swing with appropriate timing to build up a large oscillation amplitude. This process corresponds to repetitively "pushing" molecules along selected paths in the lattice. Amplification of selected vibrational modes and discrimination against other modes are demonstrated. Prospects for more extensive manipulation of molecular and collective behavior and structure are clearly indicated.     

Scissors-grip model for DNA recognition by a family of leucine zipper proteins

C/EBP is a sequence-specific DNA binding protein that regulates gene expression in certain mammalian cells. The region of the C/EBP polypeptide required for specific recognition of DNA is related in amino acid sequence to other regulatory proteins, including the Fos and Jun transforming proteins. It has been proposed that these proteins bind DNA via a bipartite structural motif, consisting of a dimerization interface termed the "leucine zipper" and a DNA contact surface termed the "basic region." An evaluation of the properties of conserved amino acids within the basic region of 11 deduced protein sequences, coupled with the observation that they are located at an invariant distance from the leucine zipper, has led to the formulation of a "scissors-grip" model for DNA binding. The architectural features of this model are well suited for interaction with directly abutted, dyadsymmetric DNA sequences. Data supportive of the model were obtained with chemical probes of protein: DNA complexes.     

A novel instrument for separating large DNA molecules with pulsed homogeneous electric fields

A new instrument has been developed for the electrophoretic separation of large DNA molecules that can independently regulate the voltage of each of 24 electrodes and allow the magnitude, orientation, homogeneity, and duration of the electric field to be precisely controlled. Each parameter can be varied at any time during the electrophoretic process. Thus distinct sets of conditions can be combined to optimize the separation of various fragment sizes in a single run. Independent control of electrode voltage allows all of the fields to be generated with electrodes arranged in a closed contour, independent of a particular geometry. This device increases both the resolution in any size range and the speed of separation, especially for DNA molecules larger than 3 megabases.     

Removal of contaminants from soils by electric fields

Application of a direct-current electric field in soils that contain contaminated liquid is expected to produce an important in situ means of environmental restoration. The electric field induces a motion of the liquid and dissolved ions that transports the contaminant to wells for removal. Electrode chemistry plays an important role, and reagents can be introduced at the electrodes to enhance contaminant removal rates. Experiments and modeling demonstrate high degrees of contaminant removal, propagation of sharp acid and base wave fronts from the electrodes, and a "focusing" effect by which metals accumulate in regions of the soil.     

Late cretaceous polar wander of the pacific plate: evidence of a rapid true polar wander event

We reexamined the Late Cretaceous-early Tertiary apparent polar wander path for the Pacific plate using 27 paleomagnetic poles from seamounts dated by (40)Ar/(39)Ar geochronology. The path shows little motion from 120 to 90 million years ago (Ma), northward motion from 79 to 39 Ma, and two groups of poles separated by 16 to 21 degrees with indistinguishable mean ages of 84 +/- 2 Ma. The latter phenomenon may represent a rapid polar wander episode (3 to 10 degrees per million years) whose timing is not adequately resolved with existing data. Similar features in other polar wander paths imply that the event was a rapid shift of the spin axis relative to the mantle (true polar wander), which may have been related to global changes in plate motion, large igneous province eruptions, and a shift in magnetic field polarity state.