Provided herein are nanostructure-based sequencing methods and systems. Such methods and systems include contacting an immobilized RNA polymerase with a double-stranded target nucleic acid molecule under sequencing conditions, where the sequencing conditions include the presence of four nucleoside triphosphates, where one of the nucleoside triphosphates is present in a rate-limiting amount; detecting the movement of the target nucleic acid molecule and/or one or more nascent strand(s) through, on or over a nanostructure; repeating the contacting and detecting steps a plurality of times; and determining the sequence of the target nucleic acid molecule based, sequentially, on the presence or absence of a change in the movement in the presence of the at least one nucleoside triphosphate.