Poly(A) Tail Length Measurement by PCR

• US 20110059453A1
• Filed: 08/23/2010
• Published: 03/10/2011
• Est. Priority Date: 08/23/2009
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Kubu, Christopher J., Chamnongpol, Sangpen
• Application Number:
  US12/861,783
• Publication Number:
  US 20110059453A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2521/131 Terminal transferase
• CPC Class Codes: C12Q 2525/173 incorporating a polynucleotide run, e.g. polyAs, polyTs
• CPC Class Codes: C12Q 2525/204 specific length of the oligonucleotides

Abstract

Methods and kits for measuring the length of the poly(A) tail of selected target mRNA are disclosed herein. In preferred aspects the mRNA population is modified by addition of a tail comprising guanosine and inosine (G/I tailing). The added tail is used as a priming site for reverse transcription. The resulting cDNA is then amplified using one or more target specific primers and a universal primer that recognizes the tailed region. The products are separated according to size and the size is used to estimate the polyA tail length.

Claims

1. A method for estimating the length of the polyA tail of a target mRNA comprising:

adding a guanosine-inosine tail to the 3′

end of the target mRNA;

hybridizing a first primer to the guanosine-inosine tail and extending said first primer to obtain a primer extension product comprising a complement of the polyA tail of the target mRNA;

amplifying the primer extension product by PCR using a universal primer and a target specific primer to obtain a PCR product;

estimating the length of the PCR product; and

,

estimating the length of the polyA tail of the target mRNA from the estimated length of the PCR product.

2. The method of claim 1 wherein the first primer is SEQ ID NO. 1.

3. The method of claim 1 wherein the universal primer consists of SEQ ID NO. 1 and a priming sequence that is 5′

of SEQ ID NO. 1 so that the 3′

end of SEQ ID NO. 1 is the 3′

end of the universal primer.

4. The method of claim 3 wherein the priming sequence is between 15 and 30 bases.

5. The method of claim 3 wherein the priming sequence is between 18 and 26 bases.

6. The method of claim 1 wherein the guanosine-inosine tail is added by a polyA polymerase.

7. The method of claim 6 wherein the polyA polymerase is a yeast polyA polymerase.

14. The method of claim 1 wherein the polyA tail length of 2 to 50 different mRNAs are estimated.

15. The method of claim 1 wherein the universal primer is SEQ ID NO. 2.

8. A kit comprising a reverse transcription primer that comprises between 2 and 5 contiguous T bases at the 3′

end and between 8 and 15 contiguous C bases at the 3′

end.

9. The kit or claim 8 further comprising one or more components selected from a mixture of guanosine and inosine, a poly(A) polymerase, reverse transcriptase, thermostable polymerase, buffer, RNase inhibitor, nuclease free water, one or more gene specific primers, and a universal primer.

10. The kit of claim 8 comprising a plurality of target specific primers, targeting a plurality of different target mRNAs.

11. The kit if claim 9 comprising a plurality of target specific primers, targeting a plurality of different target mRNAs.

12. The kit of claim 9 comprising 3 to 50 different target specific primers each targeting a different target mRNA.

13. The kit of claim 9 wherein the reverse transcription primer is SEQ ID NO. 1 and the universal primer is SEQ ID NO. 2.