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DNA Translocation Trajectories of Poly(A-T) and Poly(G-C) Sequences (.mpg-at, 8M; .mpg-gc, 8.4M)
Deoxyribonucleic acid (DNA) is the molecule that carries almost all of the genetic information of an organism. Distinguishing between A-T and G-C sequences in DNA is crucial to decoding the DNA sequence. The movie shows that the A-T sequence (shown in red) gets stretched to a higher degree than the G-C sequence (shown in blue).
Threading DNA through the Nanopore Needle (.mpg, 2.3M)
DNA (deoxyribonucleic acid) is the molecule that carries almost all of the genetic information of an organism. The genetic information stored in DNA can be read by electronic currents when the DNA (blue cartoon) molecule threads itself through graphene nanopore (cyan color sheet). Being able to rapidly sequence DNA in this fashion is critical to unraveling the human genome.
Analyzing DNA with a Bacterial Toxin (.mpg, 3.9M)
The movie shows a computer simulation of a molecule of DNA (in orange) pulled by an electric field through alpha-hemolysin (in cyan), a toxin manufactured by bacteria that forms a pore in the membrane (in gold). While in the pore, the DNA blocks electrical current through it, allowing the DNA to be detected, its length to be measured, and whether it consists of A's, T's, C's, or G's to be determined.
Confining DNA (.mpg, 4.2M)
This movie illustrates a molecular dynamics simulation of poly(dA11) strand in a shrinking pore.
Stretching DNA (.mpg, 4.4M)
This movie illustrates the stretching of a poly(dA11) strand by a constant force applied to its 5' (bottom) end.
The Lock Opening in LacI (.mp4, 3.0M)
Opening of the lock of LacI, where three groups of interacting residues keep lacI in the ''V'' configuration when wrestling the DNA loop.
DNA Forced Forced Through Small Nanopore (.mpg, 3.8M)
A high electric field forced dsDNA through a 2.0 nm diameter pore that is impermeable at smaller fields. The 6.5 V bias deformed the DNA helix, shifting one of the strands relative to the multiscale by approximately one nucleotide, while preserving the hydrogen bonds between strands.
Determining Voltage Threshold for Translocation of dsDNA (.mpg, 13.3M)
This video is from a simulation done to establish the threshold field required to drive dsDNA through a 2.0 nanometer diameter pore. Here, a 3.9 V path caused the partial unzipping of the DNA strands prior to reaching the center of the membrane.
Opening Simulation of LacI-DNA Complex (.mov, 2.4M)
Forces are applied to the ends of the protein-bound DNA segments in order to mimic the opening of the lac repressor in vivo and in experiment. The color scale of the elastic rod model of DNA corresponds to the energy stored along the loop (red showing high density of elastic energy, and blue, low energy density).