Rotation-dependent transcriptional sequencing systems and methods of using

A method of determining the sequence of a target nucleic acid molecule having an unknown sequence, comprising:

• providing a solid substrate onto which RNA polymerase is immobilized;
• contacting the RNA polymerase with the target nucleic acid molecule under first sequencing conditions, wherein the target nucleic acid molecule comprises a rotation tag that is about 50 nm to about 2 microns in diameter, wherein the first sequencing conditions comprise the presence of four nucleoside triphosphates, where a first nucleoside triphosphate of the four nucleoside triphosphates is present in a rate-limiting amount;
• detecting the rotational pattern of the rotation tag under the first sequencing conditions;
• contacting the RNA polymerase with the target nucleic acid molecule comprising the rotation tag under second sequencing conditions, wherein the second sequencing conditions comprise the presence of four nucleoside triphosphates, where a second nucleoside triphosphate of the four nucleoside triphosphates is present in a rate-limiting amount;
• detecting the rotational pattern of the rotation tag under the second sequencing conditions;
• and
• contacting the RNA polymerase with the target nucleic acid molecule comprising the rotation tag under third sequencing conditions, wherein the third sequencing conditions comprise the presence of four nucleoside triphosphates, where a third nucleoside triphosphate of the four nucleoside triphosphates is present in a rate-limiting amount;
• detecting the rotational pattern of the rotation tag under the third sequencing conditions;
• determining positional information of the first, second and third nucleoside triphosphates along the target nucleic acid molecule based on the changes in the rotational pattern under the first, second and third sequencing conditions;
• and
• repeating the contacting and detecting steps under first sequencing conditions, second sequencing conditions and third sequencing conditions at least one hundred times.

A method of determining the sequence of a target nucleic acid molecule having an unknown sequence, comprising:

• contacting an RNA polymerase with a target nucleic acid molecule under sequencing conditions, wherein the sequencing conditions comprise the presence of one nucleoside triphosphate or the presence of four nucleoside triphosphates with one of the four nucleoside triphosphates present in a rate-limiting amount, wherein said RNA polymerase is immobilized on a solid substrate, wherein the target nucleic acid molecule comprises a rotation tag that is about 50 nm to about 2 microns in diameter;
• detecting the rotational pattern of the rotation tag;
• repeating the contacting and detecting steps at least twenty times;
• and
• determining the sequence of the target nucleic acid molecule based, sequentially, on the presence or absence of a change in the rotational pattern in the presence of the one nucleoside triphosphate or the presence of the four nucleoside triphosphates with the one of the four nucleoside triphosphates present in a rate-limiting amount.