Nanofluidic devices for the rapid mapping of whole genomes and related systems and methods of analysis

摘要

Devices and methods generate an ordered restriction map of genomic DNA extracted from whole cells. The devices have a fluidic microchannel that merges into a reaction nanochannel that merges into a detection nanochannel at an interface where the nanochannel diameter decreases in size by between 50% to 99%. Intact molecules of DNA are transported to the reaction nanochannel and then fragmented in the reaction nanochannel using restriction endonuclease enzymes. The reaction nanochannel is sized and configured so that the fragments stay in an original order until they are injected into the detection nanochannel. Signal at one or more locations along the detection nanochannel is detected to map fragments in the order they occur along a long DNA molecule.

主权项

1. A method of analyzing genomic DNA extracted from whole cells, comprising:
providing a device having a fluidic microchannel that merges into a reaction nanochannel that merges into a detection nanochannel at an interface where the detection nanochannel diameter decreases in size by between 50% to 99% relative to the reaction nanochannel, wherein the reaction nanochannel has width and depth dimensions that are between 1 nm and 500 nm; lysing whole cells and inducing dechromatinization of DNA with minimal fragmentation in the microchannel; then controllably introducing an intact molecule of the DNA from the fluidic microchannel into an ingress segment of the reaction nanochannel; then fragmenting the intact DNA molecule in the reaction nanochannel into ordered fragments that stay in an original order while confining the fragments within the reaction nanochannel; then transporting the ordered fragments from the reaction nanochannel into the detection nanochannel and increasing transport velocity as the ordered fragments enter the detection nanochannel, wherein there is increased spatial separation between neighboring fragments in the detection nanochannel relative to separation in the reaction nanochannel; and electrically and/or optically detecting signal in response to a presence of respective separated fragments at one or more locations along the detection nanochannel to map the fragments in the order they occur along the DNA molecule.