METHODS FOR PREPARING TAGGING OLIGONUCLEOTIDES

• US 20190309363A1
• Filed: 06/09/2017
• Published: 10/10/2019
• Est. Priority Date: 06/10/2016
• Status: Active Grant

• Current Assignee: Seegene, Inc.
• Original Assignee: Seegene, Inc.
• Inventors: CHUN, Jong Yoon, YOON, Gi-Seck
• Granted Patent: US 11,066,704 B2
• Time in Patent Office: Days
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation

Abstract

The present invention relates to technologies for preparing a tagging oligonucleotide. By analyzing exquisitely a non-complementarity level of a first tagging part, the first aspect of the present invention permits to more efficiently and easily select a suitable tagging sequence among a multitude of sequences generated theoretically. In addition, according to the second aspect of the present invention, when a nucleotide sequence for a tagging portion is first selected, one or more regions in a target nucleic acid sequence having a non-complementarity level to the nucleotide sequence for the tagging portion are found, and then a nucleotide sequence for a targeting portion is determined, tagging oligonucleotides for detecting various target nucleic acid sequences can prepared by using the fewest number of nucleotide sequences for the tagging portion and a third template.

Claims

1. A method for preparing a tagging oligonucleotide comprising a targeting portion comprising a hybridizable-complementary nucleotide sequence to a target nucleic acid sequence and a tagging portion comprising a non-hybridizable-non-complementary nucleotide sequence to the target nucleic acid sequence, comprising:

(a) selecting the hybridizable-complementary nucleotide sequence to the target nucleic acid sequence for the targeting portion and the non-hybridizable-non-complementary nucleotide sequence to the target nucleic acid sequence for the tagging portion;

wherein the tagging portion comprises a first tagging part of 3-8 nucleotides in length adjacent to the targeting portion and a second tagging part of 4-40 nucleotides in length adjacent to the first tagging part;

the non-hybridizable-non-complementary nucleotide sequence for the tagging portion is selected not to be hybridized with the target nucleic acid sequence;

wherein a non-hybridizable-non-complementary nucleotide sequence of the first tagging part is selected by an independent non-complementarity level such that a sequence with a non-complementarity level satisfying a predetermined threshold value criterion is selected as the non-hybridizable-non-complementary nucleotide sequence of the first tagging part; and

(b) preparing the tagging oligonucleotide comprising (i) the targeting portion comprising the selected hybridizable-complementary nucleotide sequence and (ii) the tagging portion comprising the selected non-hybridizable-non-complementary nucleotide sequence.

3. The method according to claim 1, wherein the non-hybridizable-non-complementary nucleotide sequence in the tagging portion, the hybridizable-complementary nucleotide sequence in the targeting portion, or the non-hybridizable-non-complementary nucleotide sequence in the tagging portion and the hybridizable-complementary nucleotide sequence in the targeting portion is selected or provided from a pre-established dataset of tagging portion candidates or a pre-established dataset of targeting portion candidates.

7. The method according to claim 1, wherein the non-complementarity level is evaluated by unfavorability between nucleotide bases.

8. The method according to claim 1, wherein the non-complementarity level is scores given depending on unfavorability of the bonds between nucleotide bases A, T, G and C.

12. The method according to claim 1, wherein the non-hybridizable-non-complementary nucleotide sequence of the tagging portion is selected from sequences that satisfy one or more of the following criteria:

(i) exclusion of a mononucleotide run sequence, (A)_n, (T)_n, (G)_n or (C)_n, in which n is at least 4;

(ii) inclusion of a sequence with 30-80% GC content;

(iii) exclusion of a sequence of the tagging portion immediately adjacent to the targeting portion in which G and/or C is consecutively located in the number of 8 or more;

(iv) when the tagging portion forms a homodimer, exclusion of a sequence in which the ratio of nucleotides involved in the formation of the homodimer is 70% or more based on a total nucleotide number of the tagging portion;

(v) when the tagging portion forms a homodimer, exclusion of a sequence in which the ratio of consecutive nucleotides involved in the formation of the homodimer is 65% or more based on a total nucleotide number of the tagging portion;

(vi) when the tagging portion forms the tagging oligonucleotide together with the targeting portion, exclusion of a sequence rendering Δ

G value for a hairpin structure of the tagging oligonucleotide to become −

8.0 kcal/mol or less;

(vii) when there is a complementary nucleotide in the first tagging part, exclusion of a sequence in which the complementary nucleotide is located at a position of 0-1 nucleotide apart from a nucleotide of the first tagging part immediately adjacent to the targeting portion;

(viii) inclusion of a sequence in which a nucleotide of the first tagging part immediately adjacent to the targeting portion is A or T;

(ix) when the tagging portion forms a heterodimer with a primer for amplification of the target nucleic acid sequence, exclusion of a sequence in which the ratio of nucleotides involved in the formation of the heterodimer is 40% or more based on a total nucleotide number of the tagging portion; and

(x) when the tagging portion forms a heterodimer with a primer for amplification of the target nucleic acid sequence, exclusion of a sequence in which the ratio of consecutive nucleotides involved in the formation of the heterodimer is 40% or more based on a total nucleotide number of the tagging portion.

14. The method according to claim 1, wherein the nucleotide sequence of the targeting portion is selected from sequences that satisfy one or more of the following criteria:

(i) inclusion of a sequence with 30-80% GC content;

(ii) inclusion of a sequence having a Tm value of 35°

C. to 85°

C.;

(iii) when the tagging oligonucleotide is a probe used with a primer for amplifying the target nucleic acid sequence, inclusion of a sequence having a T_m value being 5°

C. to 20°

C. higher than a T_m value of the primer; and

(iv) when the tagging oligonucleotide is used in a cleavage reaction by 5′

nuclease activity, inclusion of a sequence of which 5′

-end or 5′

-penultimate nucleotide is G or C.

15. The method according to claim 1, wherein the tagging oligonucleotide prepared is selected from oligonucleotides that satisfy one or more of the following criteria:

(i) exclusion of a tagging oligonucleotide in which Δ

G value for a hairpin structure is −

8.0 kcal/mol or less;

(ii) when the tagging oligonucleotide forms a homodimer, exclusion of a tagging oligonucleotide in which the ratio of nucleotides involved in the formation of the homodimer is 70% or more;

(iii) when the tagging oligonucleotide forms a homodimer, exclusion of a tagging oligonucleotide in which the ratio of consecutive nucleotides involved in the formation of the homodimer is 65% or more;

(iv) when the tagging oligonucleotide forms a heterodimer with another oligonucleotide, exclusion of a tagging oligonucleotide in which the ratio of nucleotides involved in the formation of the heterodimer is 70% or more; and

(v) when the tagging oligonucleotide forms a heterodimer with another oligonucleotide, exclusion of a tagging oligonucleotide in which the ratio of consecutive nucleotides involved in the formation of the heterodimer is 65% or more.

18. The method according to claim 1, wherein the non-hybridizable-non-complementary nucleotide sequence of the tagging portion is selected such that a non-complementarity level of an entire sequence of the tagging portion satisfies a predetermined threshold value criterion.

19. The method according to claim 7, wherein the unfavorability is a weighted unfavorability in which weighting values are assigned to the tagging portion in a successively increasing manner from a location of the second tagging part most distant from the targeting portion to a location of the first tagging part most adjacent to the targeting portion.

20. The method according to claim 1, wherein the hybridizable-complementary nucleotide sequence of the targeting portion is first selected and then as the tagging portion selected is the non-hybridizable-non-complementary nucleotide sequence to a sequence of the target nucleic acid sequence adjacent to a sequence with which the targeting portion is hybridized.

2. A method for preparing a tagging oligonucleotide comprising a targeting portion comprising a hybridizable-complementary nucleotide sequence to a target nucleic acid sequence and a tagging portion comprising a non-hybridizable-non-complementary nucleotide sequence to the target nucleic acid sequence, comprising:

(a) providing a nucleotide sequence for the tagging portion;

wherein the tagging portion comprises a first tagging part adjacent to the targeting portion and a second tagging part adjacent to the first tagging part;

(b) selecting in the target nucleic acid sequence one or more non-hybridizable-non-complementary regions to the nucleotide sequence for the tagging portion by (i) selecting at least one region in the target nucleic acid sequence and (ii) evaluating a non-complementarity level of the selected at least one region to the nucleotide sequence for the tagging portion;

(c) selecting a nucleotide sequence for the targeting portion by (i) selecting a nucleotide sequence with a predetermined length in the target nucleic acid sequence that is adjacent to the non-hybridizable-non-complementary region to the nucleotide sequence of the tagging portion and (ii) selecting a hybridizable-complementary nucleotide sequence to the selected nucleotide sequence in the target nucleic acid as the nucleotide sequence for the targeting portion; and

(d) preparing the tagging oligonucleotide comprising the nucleotide sequence of the tagging portion provided in the step (a) and the nucleotide sequence of the targeting portion selected in the step (c).

5. The method according to claim 2, wherein the evaluation of the non-complementarity level of the selected at least one region in the target nucleic acid sequence in the step (b) is performed by evaluating the non-complementarity level to an entire sequence of the nucleotide sequence for the tagging portion.

6. The method according to claim 2, wherein the evaluation of the non-complementarity level of the selected at least one region in the target nucleic acid sequence in the step (b) is performed by evaluating the non-complementarity level to the first tagging part of the nucleotide sequence for the tagging portion in an independent manner.

9. The method according to claim 2, wherein the one or more non-hybridizable-non-complementary regions in the target nucleic acid sequence is selected in the step (b) such that they comprise no nucleotides involved in Watson-Crick base pairing with the first tagging part.

10. The method according to claim 2, wherein the one or more non-hybridizable-non-complementary regions in the target nucleic acid sequence are selected in the step (b) such that they are Watson-Crick base paired with 80% or less of nucleotides of the second tagging part based on the total nucleotides number of the second tagging part.

13. The method according to claim 2, wherein the predetermined length of the nucleotide sequence in the target nucleic acid sequence in the step (c) is 6-50 nucleotides.

4. (canceled)

11. (canceled)

16-17. -17. (canceled)

21. (canceled)

22. A computer readable storage medium containing instructions to configure a processor to perform a method for preparing a tagging oligonucleotide comprising a targeting portion comprising a hybridizable-complementary nucleotide sequence to a target nucleic acid sequence and a tagging portion comprising a non-hybridizable-non-complementary nucleotide sequence to the target nucleic acid sequence, the method comprising:

(a) selecting the hybridizable-complementary nucleotide sequence to the target nucleic acid sequence for the targeting portion and the non-hybridizable-non-complementary nucleotide sequence to the target nucleic acid sequence for the tagging portion;

wherein the tagging portion comprises a first tagging part of 3-8 nucleotides in length adjacent to the targeting portion and a second tagging part of 4-40 nucleotides in length adjacent to the first tagging part;

the non-hybridizable-non-complementary nucleotide sequence for the tagging portion is selected not to be hybridized with the target nucleic acid sequence;

wherein a non-hybridizable-non-complementary nucleotide sequence of the first tagging part is selected by an independent non-complementarity level such that a sequence with a non-complementarity level satisfying a predetermined threshold value criterion is selected as the non-hybridizable-non-complementary nucleotide sequence of the first tagging part; and

(b) preparing the tagging oligonucleotide comprising (i) the targeting portion comprising the selected hybridizable-complementary nucleotide sequence and (ii) the tagging portion comprising the selected non-hybridizable-non-complementary nucleotide sequence.

23. A computer readable storage medium containing instructions to configure a processor to perform a method for preparing a tagging oligonucleotide comprising a targeting portion comprising a hybridizable-complementary nucleotide sequence to a target nucleic acid sequence and a tagging portion comprising a non-hybridizable-non-complementary nucleotide sequence to the target nucleic acid sequence, the method comprising:

(a) providing a nucleotide sequence for the tagging portion;

wherein the tagging portion comprises a first tagging part adjacent to the targeting portion and a second tagging part adjacent to the first tagging part;

(b) selecting in the target nucleic acid sequence one or more non-hybridizable-non-complementary regions to the nucleotide sequence for the tagging portion by (i) selecting at least one region in the target nucleic acid sequence and (ii) evaluating a non-complementarity level of the selected at least one region to the nucleotide sequence for the tagging portion;

(c) selecting a nucleotide sequence for the targeting portion by (i) selecting a nucleotide sequence with a predetermined length in the target nucleic acid sequence that is adjacent to the non-hybridizable-non-complementary region to the nucleotide sequence of the tagging portion and (ii) selecting a hybridizable-complementary nucleotide sequence to the selected nucleotide sequence in the target nucleic acid as the nucleotide sequence for the targeting portion; and

(d) preparing the tagging oligonucleotide comprising the nucleotide sequence of the tagging portion provided in the step (a) and the nucleotide sequence of the targeting portion selected in the step (c).