A nanofluidic analysis system, comprising: a reaction nanochannel that is between 500 μm and 10 cm long and that merges into a detection nanochannel at an interface position therebetween where the detection nanochannel diameter reduces in size by between 50% to 99% relative to the reaction nanochannel; a microfluidic channel in communication with an ingress portion of the reaction nanochannel; a first electrode in communication with the micro fluidic channel; a first transverse fluidic channel extending from and in fluid communication with the reaction nanochannel at a location that is spaced apart from but proximate the ingress portion of the reaction nanochannel; a second electrode in communication with the first transverse fluidic channel; a second transverse fluidic channel extending from and in fluid communication with the reaction nanochannel downstream of the first transverse fluidic channel; a third electrode in communication with the second transverse fluidic channel; a fourth electrode in communication with the detection nanochannel; a circuit configured to control operation of the first, second, third and fourth electrodes to controllably thread, load and digest DNA within the reaction nanochannel to thereby prevent fragment disordering; and at least one electrical or optical detector in communication with the detection nanochannel configured such that the spatially and temporally resolved fragments are detected downstream in the detection nanochannel using imaging or single point or multiple point detection and a resulting signal analyzed to thereby allow an ordered restriction map of chromosomal DNA in real time or near real time. a reaction nanochannel that is between 500 μm and 10 cm long and that merges into a detection nanochannel at an interface position therebetween where the detection nanochannel diameter reduces in size by between 50% to 99% relative to the reaction nanochannel; a microfluidic channel in communication with an ingress portion of the reaction nanochannel; a first electrode in communication with the micro fluidic channel; a first transverse fluidic channel extending from and in fluid communication with the reaction nanochannel at a location that is spaced apart from but proximate the ingress portion of the reaction nanochannel; a second electrode in communication with the first transverse fluidic channel; a second transverse fluidic channel extending from and in fluid communication with the reaction nanochannel downstream of the first transverse fluidic channel; a third electrode in communication with the second transverse fluidic channel; a fourth electrode in communication with the detection nanochannel; a circuit configured to control operation of the first, second, third and fourth electrodes to controllably thread, load and digest DNA within the reaction nanochannel to thereby prevent fragment disordering; and at least one electrical or optical detector in communication with the detection nanochannel configured such that the spatially and temporally resolved fragments are detected downstream in the detection nanochannel using imaging or single point or multiple point detection and a resulting signal analyzed to thereby allow an ordered restriction map of chromosomal DNA in real time or near real time.