Computer Aided Simulation of DNA Fingerprint Amplified Fragment Length Polymophism (AFLP) Using Suffix Tree Indexing and Data Mining

AFLP is one of the DNA Fingerprinting techniques which have broad application as genetic marker in various fields. Begin with the DNA sequence digestion using one or more particular restriction enzyme, ligation of the adapters to the overhanging sticky ends followed by DNA fragments amplification using PCR. The PCR reaction uses primers that match the adapter sequence and have some (1 to 3) dditional “selective” bases which could be any bases, this reduces the number of bands that will be amplified. Such technique intended to increase the amplified fragments peculiarity so the polymorphism of the organism being studied could be well visualized by gel electrophoresis. The computer aided of AFLP simulation developed in this research was aimed to predict this electrophoresis result by simulate the digestion, ligation and PCR process using some pattern recognition algorithm applied to the DNA sequence from online databases. Through this simulation the researcher could determine the best combination of restriction enzyme and selective bases for their laboratory experiment. Suffix tree indexing was conducted during the exploration process of the genome sequence (in FASTA format) to find the restriction sites rapidly and create fragments of it. Data modeling enable the system draws the fragments into virtual DNA’s electrophoresis pattern. Data mining accomplish the simulation by exploring overall possible virtual DNA’s electrophoresis pattern and determine the best restriction enzyme and selective bases combination by calculating certain quantitative criteria

The repton model of gel electrophoresis

We discuss the repton model of agarose gel electrophoresis of DNA. We review previous results, both analytic and numerical, as well as presenting a new numerical algorithm for the efficient simulation of the model, and suggesting a new approach to the model's analytic solution.Comment: 17 pages including 6 PostScript figures, typeset with LaTeX 2e using the Elsevier macro package elsart.cl

Brownian Dynamics Studies on DNA Gel Electrophoresis. I. Numerical Method and Quasi-Periodic Behavior of Elongation-Contraction Motions

Dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE) is studied by a Brownian dynamics (BD) simulation method which we have developed. The method simulates electrophoresis of DNA in a 3 dimensional (3D) space by a chain of electrolyte beads of hard spheres. Under the constraint that the separation of each pair of bonded beads is restricted to be less than a certain fixed value, as well as with the excluded volume effect, the Langevin equation of motion for the beads is solved by means of the Lagrangian multiplier method. The resultant mobilities, $\mu$, as a function of the electric field coincide satisfactorily with the corresponding experimental results, once the time, the length and the field of the simulation are properly scaled. In relatively strong fields quasi-periodic behavior is found in the chain dynamics, and is examined through the time evolution of the radius of the longer principal axis, $R_l(t)$. It is found that the mean width of a peak in $R_l(t)$, or a period of one elongation-contraction process of the chain, is proportional to the number of beads in the chain, $M$, while the mean period between two such adjacent peaks is proportional to $M^0$ for large $M$. These results, combined with the observation that the chain moves to the field direction by the distance proportional to $M$ in each elongation-contraction motion, yield $\mu \propto M^0$. This explains why CFGE cannot separate DNA according to their size $L (\propto M)$ for large $L$.Comment: 20 pages, 11 figure

Electrophoresis of a rod macroion under polyelectrolyte salt: Is mobility reversed for DNA?

By molecular dynamics simulation, we study the charge inversion phenomenon of a rod macroion in the presence of polyelectrolyte counterions. We simulate electrophoresis of the macroion under an applied electric field. When both counterions and coions are polyelectrolytes, charge inversion occurs if the line charge density of the counterions is larger than that of the coions. For the macroion of surface charge density equal to that of the DNA, the reversed mobility is realized either with adsorption of the multivalent counterion polyelectrolyte or the combination of electrostatics and other mechanisms including the short-range attraction potential or the mechanical twining of polyelectrolyte around the rod axis.Comment: 8 pages, 5 figures, Applied Statistical Physics of Molecular Engineering (Mexico, 2003). Journal of Physics: Condensed Matters, in press (2004). Journal of Physics: Condensed Matters, in press (2004

Optimizing end-labeled free-solution electrophoresis by increasing the hydrodynamic friction of the drag-tag

We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles. It is specifically shown that the label's drag coefficient is determined by its hydrodynamic size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hydrodynamic drag than the other label types. The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.Comment: 32 pages, 11 figures, submitted to Macromolecule

Stochastic modeling for the COMET-assay

We present a stochastic model for single cell gel electrophoresis (COMET-assay) data. Essential is the use of point process structures, renewal theory and reduction to intensity histograms for further data analysis

Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields

Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a simple Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the type of knot and on the electric field intensity was investigated. The results are in qualitative agreement with electrophoretic experiments done under conditions of low and high electric fields: especially the inversion of the behavior from low to high electric field could be reproduced. The knot topology imposes on the problem the constrain of self-avoidance, which is the final cause of the observed behavior in strong electric field.Comment: 17 pages, 5 figure

Separation of long DNA chains using non-uniform electric field: a numerical study

We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation demonstrates that the chain captured by an electrode escapes from the binding electric field due to thermal fluctuation. We find that the mobility of chain would depend on the chain length; the mobility sharply increases when the length of a chain exceeds a critical value, which is strongly affected by the amplitude of the applied ac field. Thus we can adjust the length regime, in which this microchannel well separates DNA molecules, without changing the structure of the channel. We also present a theoretical insight into the relation between the critical chain length and the field amplitude.Comment: 12 pages, 9 figure

Importance of hydrodynamic shielding for the dynamic behavior of short polyelectrolyte chains

The dynamic behavior of polyelectrolyte chains in the oligomer range is investigated with coarse-grained molecular dynamics simulation and compared to data obtained by two different experimental methods, namely capillary electrophoresis and electrophoresis NMR. We find excellent agreement of experiments and simulations when hydrodynamic interactions are accounted for in the simulations. We show that the electrophoretic mobility exhibits a maximum in the oligomer range and for the first time illustrate that this maximum is due to the hydrodynamical shielding between the chain monomers. Our findings demonstrate convincingly that it is possible to model dynamic behavior of polyelectrolytes using coarse grained models for both, the polyelectrolyte chains and the solvent induced hydrodynamic interactions.Comment: 5 pages, 3 figures -> published versio