Multiplex amplification and detection

• US 9,284,607 B2
• Filed: 10/25/2011
• Issued: 03/15/2016
• Est. Priority Date: 10/25/2010
• Status: Active Grant

• Current Assignee: Oxitec Limited (Precigen, Inc.)
• Original Assignee: Oxitec Limited (Precigen, Inc.)
• Inventors: Fu, Guoliang
• Primary Examiner(s): Woolwine, Samuel
• Assistant Examiner(s): Zhang, Kaijiang
• Application Number:
  US13/822,129
• Publication Number:
  US 20130267434A1
• Time in Patent Office: 1,603 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• 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 2527/107 Temperature of melting, i.e. Tm
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2537/162 Helper probe
• CPC Class Codes: C12Q 2565/107 Alteration in the property of hybridised versus free label oligonucleotides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

The invention relates to the field of multiplex amplification. In particular, the invention relates to methods for assaying a sample for one or more nucleic acid targets in a single reaction based on the distinct melting temperatures or melting profiles of primers and/or probes. The invention also provides probes and kits for use in such methods.

Claims

1. A method for assaying a sample for one or more target nucleic acids, said method comprising:

(a) contacting a sample comprising one or more target nucleic acids with a polymerase chain reaction mixture comprising;

(i) one or more pairs of forward/reverse oligonucleotide primers, wherein the primer pairs are capable of amplifying one or more target nucleic acids, if present in the sample,

(ii) a set of two or more probes, wherein at least one probe in the set comprises a double-stranded portion,

wherein at least one probe comprises two oligonucleotides;

first oligonucleotide, which is also referred to as a target-hybridising oligonucleotide (THO) and second oligonucleotide, which is also referred to as a partially complementary oligonucleotide (PCO), THO and PCO are capable of hybridising to each other, forming a partially double-stranded probe,

wherein each probe in the set comprises a detectable label or detectable combination of labels which is/are capable of producing a changeable signal which is characteristic for each probe,

wherein said two or more probes comprise the same detectable label or different detectable labels with undistinguishable emission spectra and wherein the melting characteristics of each of such probes are different, each probe with double-stranded portion has a signature melting temperature, whereas single-stranded probes having no double stranded portion do not have a signature melting temperature;

and wherein said set of two or more probes comprises mixed plus probes and minus probes;

(b) performing a polymerase chain reaction on the sample/reaction mixture under amplification conditions, wherein, when a target nucleic acid is present, THO which are substantially complementary to part of that target nucleic acid are hybridised with the target nucleic acid, therefore being consumed, wherein the consumption of probes causes changes of detectable signal in the labels, and the consumed probes are no longer able to form a double stranded portion if the original probe has a double-stranded portion; and

(c) measuring, at least once, the melting profile of the unconsumed probes in the reaction mixture by detecting the signal(s) from the labels in those probes as a function of temperature, wherein the presence or absence of melting characteristics of any probes in the melting profile analysis is an indication of unconsumption or consumption of that probe, which further provides an indication of whether or not at least one target nucleic acid is present in said sample,

wherein THO is complementary to a target sequence, and is labeled with a fluorophore and a quencher,

wherein PCO, which is partially complementary to THO, contains modified the 3′

end to prevent its extension,

wherein, if the 3′

end of PCO is attached with a label which is not quencher, fluorescence emission is increased by hybridisation of THO and PCO, this type of probe is termed plus probe (+THO;

PCO),

wherein, if the 3′

end of PCO is attached with a quencher, fluorescence emission is decreased by hybridisation of THO and PCO, this type of probe is termed minus probe (−

THO;

PCO).

2. A method according to claim 1, wherein said melting profile is measured before reaction/amplification takes place (pre-amplification melting profile), and/or is measured after completion of reaction/amplification (post-amplification melting profile), and/or is measured during reaction/amplification at each cycle or selected cycles (mid-amplification melting profile),

wherein said method additionally comprises step (d)

(i) comparing at least two melting profiles obtained in (c) and/or

(ii) comparing a melting profile obtained in step (c)

with a previously-obtained melting profile of the same probes or

with a melting profile of the same probes obtained in parallel at the same time in control reactions, or

with a theoretical melting profile of the same probes

wherein a change in the melting profile provides an indication of whether or not at least one target nucleic acid is present in said sample/reaction mixture.

3. A method according to claim 2, wherein said pre-amplification melting profile is measured in the same reaction vessel before the start of reaction/amplification, or is measured in a separate reaction vessel where no amplification takes place due to that reaction mixture lacking one or more ingredients necessary for the reaction/amplification,

wherein in step (d) the post-amplification or mid-amplification melting profile is compared with the pre-amplification melting profile of the duplex of probes to determine whether a particular probe is consumed, this being indicative of the presence of the corresponding target in the sample.

4. A method according to claim 1, wherein said consumption of probes is achieved through hybridisation of the THO to the target sequence, which is followed by the incorporation of the THO into the amplified product, or wherein when the THO can be incorporated into the amplified product, the THO is an extendable primer or one of the pair of forward/reverse oligonucleotide primers.

5. A method according to claim 1, wherein said consumption of probes is achieved through hybridisation of the THO to the target sequence, which is followed by degradation of the THO, wherein when the THO is degraded during the reaction, the reaction mixture comprises an enzyme with nuclease activity.

6. A method according to claim 1, wherein said set of two or more probes comprises at least two probes having double-stranded portions,

wherein a first probe has a melting temperature T_m1 in terms of its double-stranded portion,

wherein a second probe has a melting temperature T_m2 in terms of its double-stranded portion,

wherein T_m1>

T_m2,

wherein the same labels are independently attached to the first and second probes,

wherein a reduction of any melting peak at T_m1 and/or T_m2 provides indication of consumption of the first and/or second probe(s).

7. A method according to claim 1, wherein said amplification reaction mixture comprises two related THO (probes) for assaying single nucleotide polymorphism (SNP), one THO is for one allele, second THO is for second allele.

8. A method according to claim 7, wherein said two related THOs for assaying single nucleotide polymorphism (SNP) are capable of hybridising the same PCO to form partially double stranded probes.

9. A method according to claim 7, wherein said two related THOs are attached with the same label(s).

10. A method according to claim 1, wherein the second oligonucleotides of the probes is physically separated from the main reaction mix containing first oligonucleotides of the probe, primers, reaction buffer, enzyme and other ingredients necessary for a reaction during the amplification, but is mixed with the main reaction mix after the completion of the amplification process to measure the melting profile, wherein the second oligonucleotides are added to the main reaction vessel after the reaction completion.