Methods, compositions, and kits for generating rRNA-depleted samples or isolating rRNA from samples

• US 10,435,683 B2
• Filed: 08/28/2017
• Issued: 10/08/2019
• Est. Priority Date: 08/14/2009
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Epicentre Technologies Corporation (Illumina Incorporated)
• Inventors: Sooknanan, Roy R.
• Primary Examiner(s): Thomas, David C
• Application Number:
  US15/688,600
• Publication Number:
  US 20180044660A1
• Time in Patent Office: 771 Days
• CPC Class Codes: C12N 15/1006 by means of a solid support carrier, e.g. particles, polymers
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2525/117 incorporating modified base
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin

Abstract

The present invention provides methods, compositions, and kits for generating rRNA-depleted samples and for isolating rRNA from samples. In particular, the present invention provides compositions comprising affinity-tagged antisense rRNA molecules corresponding to substantially all of at least one rRNA molecule (e.g., 28S, 26S, 25S, 18S, 5.8S and 5S eukaryotic cytoplasmic rRNA molecules, 12S and 16S eukaryotic mitochondrial rRNA molecules, and 23S, 16S and 5S prokaryotic rRNA molecules) and methods for using such compositions to generate rRNA-depleted samples or to isolate rRNA molecules from samples.

Claims

1. A composition comprising antisense rRNA molecules complementary to at least 95% of a full-length sequence of at least one rRNA molecule selected from the group consisting of 28S, 26S, 25S, 18S, 5.8S, and 5S eukaryotic cytoplasmic rRNA molecules, 12S and 16S eukaryotic mitochondrial rRNA molecules, 23S, 16S, 4.5S, and 5S eukaryotic chloroplast rRNA molecules, and 23S, 16S, and 5S prokaryotic rRNA molecules, wherein the antisense rRNA molecules comprise affinity tags at a ratio of at least eight affinity tags per every 100 nucleobases of the antisense rRNA molecules.

2. The composition of claim 1, wherein the antisense rRNA molecules are complementary to multiple different rRNA molecules.

3. The composition of claim 1, wherein the at least one rRNA molecule is selected from the group consisting of 28S, 26S, 25S, 18S, 5.8S, and 5S eukaryotic cytoplasmic rRNA molecules, 12S and 16S eukaryotic mitochondrial rRNA molecules, and 23S, 16S, 4.5S, and 5S eukaryotic chloroplast rRNA molecules.

4. The composition of claim 1, wherein the at least one rRNA molecule is selected from the group consisting of:

(a) at least four rRNA molecules selected from the group consisting of 28S, 26S, 25S, 18S, 5.8S, and 5S eukaryotic cytoplasmic rRNA molecules;

(b) two rRNA molecules consisting of 12S and 16S eukaryotic mitochondrial rRNA molecules;

(c) four rRNA molecules consisting of 16S, 23S, 4.5S, and 5S eukaryotic chloroplast rRNA molecules; and

(d) three rRNA molecules consisting of 23S, 16S, and 5S prokaryotic rRNA molecules.

5. The composition of claim 1, wherein the at least one rRNA molecule is selected from the group consisting of 28S, 26S, 25S, 18S, 5.8S, and 5S eukaryotic cytoplasmic rRNA molecules and 12S and 16S eukaryotic mitochondrial rRNA molecules.

6. The composition of claim 1, wherein the at least one rRNA molecule includes:

(a) both the 28S and 18S rRNA molecules, or

(b) (i) the 25S rRNA molecule or the 26S rRNA molecule, and (ii) the 16S rRNA molecules.

7. The composition of claim 1, wherein the at least one rRNA molecule:

(a) comprises both the 5.8S rRNA and the 5S rRNA molecules, and/or

(b) comprises both the 12S and 16S eukaryotic mitochondrial rRNA molecules, and/or

(c) is selected from the group consisting of 16S, 23S, 4.5S, and 5S eukaryotic chloroplast rRNA molecules.

8. The composition of claim 1, wherein the composition comprises antisense rRNA molecules complementary to at least one eukaryotic rRNA molecule and antisense rRNA molecules complementary to at least one prokaryotic rRNA molecule.

9. The composition of claim 1, wherein the at least one rRNA molecule comprises 18S, 5.8S, and 5S eukaryotic cytoplasmic rRNA molecules.

10. The composition of claim 1, wherein the at least one rRNA molecule comprises 23S and 16S prokaryotic rRNA molecules.

11. The composition of claim 10, wherein the at least one rRNA molecule further comprises the 5S prokaryotic rRNA molecule.

12. The composition of claim 1, wherein the at least one rRNA molecule comprises the 28S and 18S eukaryotic cytoplasmic rRNA molecules.

13. The composition of claim 1, wherein the at least one rRNA molecule comprises the 28S, 18S, 5.8S, and 5S eukaryotic cytoplasmic rRNA molecules.

14. The composition of claim 1, wherein the affinity tag comprises biotin.

15. The composition of claim 1, wherein the affinity tags are associated with at least one nucleobase selected from the group consisting of adenine, cytosine, guanine, and uracil.

16. A kit comprising:

(a) the composition of claim 1 and

(b) at least one component selected from the group consisting of;

(i) a binding matrix comprising affinity tag-binding molecules;

(ii) a control sample comprising total RNA from a cell or tissue sample;

(iii) a solution comprising an RNase inhibitor;

(iv) an RNase-free binding matrix wash solution;

(v) a volume of RNase-free water;

(vi) a hybridization buffer;

(vii) a total RNA purification reagent; and

(viii) an RNase-free binding matrix resuspension solution.

17. The kit of claim 16, wherein the at least one component comprises the binding matrix.

18. The kit of claim 16, wherein the at least one component comprises the control sample or the solution comprising the RNase inhibitor.