SIMPLIFIED SAMPLE PREPARATION FOR RNA ANALYSIS

• US 20100159533A1
• Filed: 11/24/2009
• Published: 06/24/2010
• Est. Priority Date: 11/24/2008
• Status: Abandoned Application

• Current Assignee: Fluidigm Corporation
• Original Assignee: Helicos Biosciences Corporation
• Inventors: Lipson, Doron, Raz, Tal, Thompson, John F.
• Application Number:
  US12/625,115
• Publication Number:
  US 20100159533A1
• Time in Patent Office: Days
• US Class Current: 435/91.510
• 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 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 2521/107 RNA dependent DNA polymerase,(i.e. reverse transcriptase)
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2525/204 specific length of the oligonucleotides

Abstract

Methods and kits for selective preparing cDNA relatively free of sequences found in rRNA and subcellular RNAs are disclosed. The methods and kits utilize approximately 200 hexamer sequences which target messenger RNA. The methods and kits are useful in preparing samples for sequencing analysis, especially when performing single molecule sequencing by synthesis.

Claims

1. A method for selective priming during reverse transcription of RNA to cDNA, comprising contacting an RNA sample with one or more primer oligonucleotides, wherein said primer oligonucleotides are comprised of one or more oligonucleotide sequences which hybridize specifically to mRNA.

2. The method of claim 1, wherein the RNA sample is total RNA or polyA RNA.

3. The method of claim 1, wherein the oligonucleotide sequences comprise a set of random sequence oligonucleotides.

4. The method of claim 3, wherein the oligonucleotide sequences are 6-12 bases in length.

5. The method of claim 4, wherein the G+C content of the oligonucleotide sequences is less than 70% of the entire sequence length.

6. The method of claim 1, wherein the oligonucleotide sequences are a subset of random sequence hexamers.

7. The method of claim 6, wherein the oligonucleotide sequences comprises those sequences containing no greater than 4 C+G'"'"'s.

8. The method of claim 6, wherein the hexamers are comprised of those sequences provided in Table 1 when the sample is of human origin.

9. The method of claim 6, wherein the oligonucleotide sequences are at least 2 base edit distance to nearest sequences found in rRNA, mitochondrial RNA or chloroplast RNA.

10. The method of claim 9, wherein the rRNA is human 28S RNA, 18S RNA, 5.8S RNA, or 5S RNA.

11. The method of claim 1, wherein the oligonucleotide sequences additionally have a moiety which anchors to the substrate.

12. The method of claim 11, wherein the moiety is additional base sequence complementary to surface attached primers.

13. The method of claim 11, wherein the moiety is one member of a binding pair, the other member of the binding pair be anchored on the substrate.

14. The method of claim 13, wherein the binding pair is biotin and streptavidin.

15. The method of claim 11, wherein the moiety comprises a 5′

-amine, 5′

-azide, or 5′

-alkynyl.

16. The method of claim 11, wherein the substrate comprises an epoxide.

17. A kit for selective priming during reverse transcription of RNA to cDNA, comprising one or more primer oligonucleotides, wherein said primer oligonucleotides are comprised of one or more oligonucleotide sequences which hybridize specifically to mRNA.

18. A pre-selected mixture of random hexamer sequences, comprising a plurality of hexamer sequences comprising those sequences containing no greater than 4 C+G per hexamer;

or a plurality of hexamer sequences provided in Table 1 when the sample is of human origin.

19. The mixture of claim 18, wherein the random hexamer sequences comprise a portion or all of the hexamer sequences provided in Table 1.