Method for synthesizing selectively labeled RNA

1. A method for synthesizing a RNA, comprising performing an initiation stage, an elongation stage, and a termination stage, wherein:

(a) the initiation stage comprises:

(i) providing a solid phase comprising a DNA template, wherein the DNA is attached to a solid substrate;

(ii) providing a first liquid phase comprising a RNA polymerase and ribonucleoside triphosphates (rNTPs);

(iii) mixing the solid phase and first liquid phase;

(iv) incubating the solid phase and first liquid phase at 4-37° C. for 5-30 minutes to initiate synthesis of the RNA;

(v) pausing the RNA synthesis by incubating the solid phase and first liquid phase at 0-5° C., whereupon the solid phase comprises the RNA polymerase and the RNA being synthesized; and

(vi) separating the solid phase from the first liquid phase;

(b) the elongation stage comprises:

(i) providing a second liquid phase comprising rNTPs;

(ii) mixing the solid phase and second liquid phase;

(iii) incubating the solid phase and second liquid phase at 4-37° C. for 5-20 minutes to elongate the RNA;

(iv) pausing the RNA synthesis by incubating the solid phase and second liquid phase at 0-5° C. for 5-30 minutes;

(v) separating the solid phase from the second liquid phase; and

(vi) repeating steps (i)-(v) of part (b) n times, wherein n is equal to 1-100, and wherein the rNTPs in the second liquid phase are the same or different in each repeat;

(c) the termination stage comprises:

(i) providing a third liquid phase comprising rNTPs;

(ii) mixing the solid phase with the third liquid phase;

(iii) incubating the solid phase and third liquid phase at 4-37° C. for 5-30 minutes; and

(iv) pausing the RNA synthesis by incubating the solid phase and third liquid phase at 0° C. for 5-30 minutes; wherein steps (a)-(c) are repeated multiple times, and wherein rNTPs of at least one of the first liquid phase, the second liquid phase, or third liquid phase comprise a label.

2. The method of claim 1 , wherein the solid substrate is a bead comprising a gel, glass, or a synthetic polymer.

3. The method of claim 2 , wherein the bead has a diameter of 5-100 μm.

4. The method of claim 1 , wherein the ratio of concentration of rNTPs to DNA is 1-100.

5. The method of claim 1 , wherein the RNA polymerase is T7 RNA polymerase.

6. The method of claim 1 , wherein the label is selected from the group consisting of 13 C/ 15 N, 2 H, Cy3, Cy5, a fluorophore, a heavy atom, and a chemical modification.

7. The method of claim 1 , wherein any one of the mixing steps is performed under an inert atmosphere.

8. The method of claim 1 , wherein the mixing does not cause the liquid phases to form bubbles.

9. The method of claim 8 , wherein the mixing comprises rotating the reaction 360 degrees.

10. The method of claim 1 , wherein the RNA synthesis is carried out in a reaction vessel of an automated platform.

11. The method of claim 10 , wherein the reaction vessel is in operative association with a motor that manipulates the reaction vessel through a gear arrangement that is operatively engaged with the motor, and wherein the motor is in operative association with a computer processor for controlling the automated platform and for manipulation of the reaction vessel.

12. The method of claim 11 , wherein the apparatus comprises a holder for receiving and manipulating the reaction vessel.

13. The method of claim 12 , wherein the holder manipulates the reaction vessel to mix the liquid phases during the RNA synthesis.

14. The method of claim 13 , wherein the mixing does not stir, shake, or bubble the liquid phases of the RNA synthesis.

15. The method of claim 14 , wherein the reaction vessel is rotated 360 degrees by the holder.