Rotation-dependent transcriptional sequencing systems and methods of using

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

(a) combining an RNA polymerase, a target nucleic acid molecule, a solid substrate, and a rotation tag, to form a combination for sequencing in which the target nucleic acid molecule is bound to the rotation tag and the RNA polymerase is immobilized on the solid substrate and complexed with the target nucleic acid molecule;

(b) exposing the combination produced in step (a) to sequencing conditions, wherein the sequencing conditions comprise contacting the combination of step (a) with at least one nucleoside triphosphate;

(c) detecting the rotational pattern of the rotation tag;

(d) repeating the contacting and detecting steps a plurality of times; and

(e) determining the sequence of the target nucleic acid molecule based, sequentially, on the presence or absence of a change in the rotational pattern as a result of each exposure to the sequencing conditions.

2. The method of claim 1 , wherein step (a) comprises immobilizing the RNA polymerase on the solid substrate followed by binding the rotation tag to the target nucleic acid molecule followed by complexing the rotation tagged-target nucleic acid molecule with the immobilized RNA polymerase.

3. The method of claim 1 , wherein step (a) comprises immobilizing the RNA polymerase on the solid substrate followed by complexing the target nucleic acid molecule with the immobilized RNA polymerase followed by binding the rotation tag to the target nucleic acid molecule.

4. The method of claim 1 , wherein step (a) comprises binding the rotation tag to the target nucleic acid molecule followed by immobilizing the RNA polymerase on the solid substrate followed by complexing the rotation tagged-target nucleic acid molecule with the immobilized RNA polymerase.

5. The method of claim 1 , wherein step (a) comprises binding the rotation tag to the target nucleic acid molecules followed by complexing the rotation tagged-target nucleic acid molecule with the RNA polymerase followed by immobilizing the RNA polymerase of the complex on the solid substrate.

6. The method of claim 1 , wherein step (a) comprises complexing the target nucleic acid molecule with the RNA polymerase followed by binding the rotation tag to the target nucleic acid molecule followed by immobilizing the RNA polymerase of the complex on the solid substrate.

7. The method of claim 1 , wherein step (a) comprises complexing the target nucleic acid molecule with the RNA polymerase followed by immobilizing the RNA polymerase of the complex on the solid substrate followed by binding the rotation tag to the target nucleic acid molecule.

8. The method of claim 1 , wherein the total diameter of the rotation tag is about 50 nm to about 5 microns.

9. The method of claim 8 , wherein the rotation tag comprises a single tag.

10. The method of claim 8 , wherein the rotation tag comprises a first tag and a second tag.

11. The method of claim 10 , wherein the first tag is about 2 microns in diameter.

12. The method of claim 11 , wherein the first tag and second tag are about the same size.

13. The method of claim 10 , wherein the first tag is larger than the second tag.

14. The method of claim 10 , wherein the first tag is attached to the target nucleic acid molecule and the second tag is attached to the first tag.

15. The method of claim 10 , wherein the first tag is magnetic.

16. The method of claim 10 , wherein the second tag is magnetic.

17. The method of claim 10 , wherein the second tag is an electric tag.

18. The method of claim 1 , wherein the rotation tag comprises a non-spherical tag.

19. The method of claim 18 , wherein the non-spherical tag comprises a single tag.

20. The method of claim 19 , wherein the non-spherical tag has a shape selected from the group consisting of a tapered rod, triangular, conical, and egg-shaped.

21. The method of claim 18 , wherein the non-spherical tag comprises a first tag and a second tag.

22. The method of claim 21 , wherein the first tag is about 2 microns in diameter.

23. The method of claim 22 , wherein the first tag and second tag are about the same size.

24. The method of claim 21 , wherein the first tag is larger than the second tag.

25. The method of claim 21 , wherein the first tag is attached to the target nucleic acid molecule and the second tag is attached to the first tag.

26. The method of claim 21 , wherein the first tag is magnetic.

27. The method of claim 21 , wherein the second tag is magnetic.

28. The method of claim 21 , wherein the second tag is an electric tag.

29. The method of claim 1 , wherein the rotation tag comprises a spherical tag.

30. The method of claim 29 , wherein the spherical tag comprises a single tag having a non-uniform feature.

31. The method of claim 30 , wherein the non-uniform feature is selected from the group consisting of shape, surface coating and material composition.

32. The method of claim 29 , wherein the tag comprises a first spherical tag and a second spherical tag.

33. The method of claim 32 , wherein the first tag is about 2 microns in diameter.

34. The method of claim 33 , wherein the first tag and second tag are about the same size.

35. The method of claim 32 , wherein the first tag is larger than the second tag.

36. The method of claim 32 , wherein the first tag is attached to the target nucleic acid molecule and the second tag is attached to the first tag.

37. The method of claim 32 , wherein the first tag is magnetic.

38. The method of claim 32 , wherein the second tag is magnetic.

39. The method of claim 32 , wherein the second tag is an electric tag.

40. The method of claim 1 , wherein the rotation tag comprises at least a first tag, a second tag, and a third tag.

41. The method of claim 1 , wherein the RNA polymerase is a multi-subunit RNA polymerase.

42. The method of claim 1 , wherein the RNA polymerase is a single-subunit RNA polymerase.

43. The method of claim 1 , wherein the RNA polymerase exhibits a duration of rotation, per nucleotide incorporated, of from a sub-microsecond to about 100 milliseconds.

44. The method of claim 1 , wherein the RNA polymerase exhibits a duration of rotation, per nucleotide incorporated, of from about 100 milliseconds up to several seconds.