Link:  Pharm/Biotech Resources

Title:  Method of amplifying or detecting HIV-1 RNA

United States Patent:  6,881,544

Issued:  April 19, 2005

Inventors:  Ishizuka; Tetsuya (Sagamihara, JP); Yasukawa; Kiyoshi (Kawasaki, JP); Ishiguro; Takahiko (Yokohama, JP)

Assignee:  Tosoh Corporation (Shinnanyo, JP)

Appl. No.:  126611

Filed:  April 22, 2002

Abstract

A simple, speedy and sensitive method of detecting HIV-RNA using an oligonucleotide which can bind to an intramolecularly free region of the genomic RNA of HIV-1 at relatively low and constant temperatures (at 35^oC. to 50^oC., preferably at 41^oC.) as an oligonucleotide primer for use in amplification of a nucleic acid.

Description of the Invention

The present invention relates to oligonucleotides used for amplification or detection of HIV-1 RNA in clinical tests and diagnoses.

Human immunodeficiency virus (HIV) is the pathogen of acquired immunodeficiency syndrome (AIDS). Two subtypes of HIV are known: HIV-1, which is spread worldwide, and HIV-2, which is epidemic mainly on the African West coast. The similarity between HIV-2 and simian immunodeficiency virus (SIV) in base sequence implies that HIV-2 may be zoonotic. However, clinical conditions of HIV-2 infection are less serious than those of HIV-1 infection.

HIV-1 infection induces production of antibodies against structural proteins and regulatory proteins of HIV-1. HIV-1 attacks the T cells classified as CD4+ lymphocytes as the main target immunocytes and hence abnormalizes the immune system in various ways. In the advanced stages of HIV-1 infection, B cells are stimulated to set off hypergammaglobulinemia, and autoantibodies and immunocomplexes appear with marked reduction of lymphocytes and blood platelets. Complications such as tuberculosis, Pneumocystis carinii pneumonia and other opportunistic infections at high levels of immunodeficiency induced by HIV-1 infection are diagnostic of onset of AIDS.

For diagnosis of HIV-1 infection, EIA (enzyme immunoassay) based on colorimetric detection of the reaction of an antibody against an viral antigen is available, coupled with Western blot confirmation of suspected positive serum samples by the presence of antibodies in the serum samples which react to a specific virus antigen in a blot of electrophoretically separated various virus particle antigens. However, assay methods which detect antibodies like this are not available for diagnoses of early stage infection before production of antibodies.

As discussed above, conventional assay methods can not afford diagnoses in the early stage of infection, require complicated operations and long time and can hardly detect a trace of HIV-1 in a sample in a short time. Therefore, development of a speedy and sensitive detection method is demanded. Especially, quantification of HIV-1 RNA is crucial to get information on pathological progress and the effectiveness of anti-HIV drugs. Further, development of automatic analyzers is demanded to facilitate clinical tests.

For high sensitive detection, it is preferred to amplify a specific sequence in a gene to be detected or identified or an RNA derived from such a gene before the detection. As a method of amplifying a specific sequence in RNAs like the HIV-1 genomic RNA, the reverse transcription-polymerase chain reaction (RT-PCR) is known. In this method, the reverse transcription step for synthesis of the cDNA of the target RNA is followed by repeated cycles of heat denaturation, primer-annealing and elongation reaction in the presence of a couple of primers, one of which is complementary to either end of the specific sequence and the other is homologous to the other end of the specific sequence (the antisense primer may be the same as the primer used in the reverse transcription step), and a thermostable DNA polymerase to give DNA as the amplification product of the specific sequence.

However, the necessity to conduct the operations in two steps (the reverse transcription step and the PCR step) and repeat the cumbersome operations such as rapid heating and cooling hinders automation of the RT-PCR.

NASBA or 3SR is known as a technique for amplifying a specific RNA sequence by the cooperative action of a reverse transcriptase and an RNA polymerase. This technique activates the chain reaction comprising synthesis of a double-stranded DNA having a promoter sequence from the target RNA by using a primer having a promoter sequence, a reverse transcriptase and ribonuclease H, and formation, by an RNA polymerase, of an RNA having the specific base sequence, which is then used as the template for synthesis of the above-mentioned double-stranded DNA having the promoter sequence, along the double-stranded DNA as the template. NASBA or 3SR allows relatively isothermal amplification of nucleic acid and is considered suitable for automation.

However, since the reactions involved in this amplification technique are carried out at relatively low temperatures (for example, at 41^oC.), it is possible that the formation of an intramolecular structure of the target RNA lowers the reaction efficiency by hindering binding of the primers. Therefore, an operation of destroying the intramolecular structure of the target RNA such as heat denaturation of the target RNA is necessary before the amplification reaction to increase the binding efficiency of the primers.

The object of the present invention is to provide a simple, speedy and sensitive method of amplifying or detecting HIV-RNA through provision of an oligonucleotide which can bind to an intramolecularly free region of the genomic RNA of HIV-1 at relatively low and constant temperatures (at 35^oC. to 50^oC., preferably at 41^oC.) as an oligonucleotide primer for use in amplification of a nucleic acid.

The present invention has been accomplished to attain the above-mentioned objects. The invention defined in a first embodiment of the present application provides a step of amplifying an RNA derived from HIV-1, which comprises synthesizing a cDNA by the action of an RNA-dependent DNA polymerase by using a specific sequence in an RNA derived from HIV-1 anticipated in a sample as a template, a first primer containing a sequence complementary to the specific sequence and a second primer containing a sequence homologous to the specific sequence (either of which additionally has a promoter sequence for the RNA polymerase at the 5' end), denuding the cDNA to a single-stranded DNA through degradation of the RNA in the resulting RNA-DNA double strand by ribonuclease H, forming a double-stranded DNA having a promoter sequence which can be transcribed into an RNA consisting of the specific base sequence or a sequence complementary to the specific base sequence by using the single-stranded DNA as a template by the action of a DNA-dependent DNA polymerase, and then transcribing the double-stranded DNA into an RNA transcript, which acts as a template in the subsequent cDNA synthesis by the RNA-dependent DNA polymerase, in the presence of the RNA polymerase, wherein the first primer is an oligonucleotide of any one of SEQ ID NOS: 1 to 7, and the second primer is an oligonucleotide of any one of SEQ ID NOS: 8 to 20.

The invention defined in a second embodiment of the present application provides the step according to the first embodiment, which further comprises adding a third oligonucleotide which is complementary to a region of the RNA derived from HIV-1 which flanks the 5' end of the specific sequence with an overlap (of from 1 to 10 bases) with the specific sequence to form a template used in the initial stage of the amplification by cutting the RNA derived from HIV-1 at the 5' end of the specific sequence (by the action of the rebonuclease H), wherein the first primer is an oligonucleotide of any one of SEQ ID NOS: 1 to 7, and

(1) the second primer is an oligonucleotide of SEQ ID NO: 8, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 21 and 22,

(2) the second primer is an oligonucleotide of SEQ ID NO: 9, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 22 to 26,

(3) the second primer is an oligonucleotide of SEQ ID NO: 10, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 22 to 28,

(4) the second primer is an oligonucleotide of SEQ ID NO: 11, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 22 to 29,

(5) the second primer is an oligonucleotide of SEQ ID NO: 12, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 22 to 29,

(6) the second primer is an oligonucleotide of SEQ ID NO: 13, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 23 to 30,

(7) the second primer is an oligonucleotide of SEQ ID NO: 14, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 23 to 30,

(8) the second primer is an oligonucleotide of SEQ ID NO: 15, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 24 to 30,

(9) the second primer is an oligonucleotide of SEQ ID NO: 16, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 25 to 30,

(10) the second primer is an oligonucleotide of SEQ ID NO: 17, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 27 to 31,

(11) the second primer is an oligonucleotide of SEQ ID NO: 18, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 31 and 32,

(12) the second primer is an oligonucleotide of SEQ ID NO: 19, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS: 32 and 33, or

(13) the second primer is an oligonucleotide of SEQ ID NO: 20, and the third oligonucleotide is an oligonucleotide of SEQ ID NO: 33.

The invention defined in a third embodiment of the present application provides a step of detecting HIV-1, which comprises conducting the step as defined in the first or second embodiment in the presence of an oligonucleotide probe (having a sequence different from those of the first primer and the second primer) which can specifically bind to the RNA transcript resulting from the amplification and is labeled with an fluorescent intercalative dye, and measuring the change in the fluorescence from the reaction solution.

The invention defined in a fourth embodiment of the present application provides the step according to the third embodiment, wherein the oligonucleotide probe is designed to hybridize with at least part of the RNA transcript and alters its fluorescence upon hybridization.

The invention defined in a fifth embodiment of the present application provides the step according to the fourth embodiment, wherein the oligonucleotide probe has a sequence consisting of or complementary to at least 10 consecutive bases in SEQ ID NO: 34.

The present invention provides a nucleic acid amplification step for amplification of HIV-RNA in a sample, and a method of detecting the RNA transcript formed by the nucleic acid amplification step. The amplification step of the present invention covers any amplification methods such as PCR, NASBA or 3SR. However, isothermal nucleic acid amplification such as NASBA or 3SR by the cooperative action of a reverse transcriptase and an RNA polymerase (under such conditions that the reverse transcriptase and the RNA polymerase act cooperatively) is preferred for amplifying a specific RNA sequence in HIV-1.

For example, NASBA amplification of an RNA comprises synthesizing a cDNA by the action of an RNA-dependent DNA polymerase by using a specific sequence in HIV-1 RNA in a sample as the template, denuding the cDNA to a single-stranded DNA through degradation of the RNA in the resulting RNA-DNA double strand by ribonuclease H, forming a double-stranded DNA having a promoter sequence which can be transcribed into an RNA consisting of the specific base sequence or a sequence complementary to the specific base sequence by using the single-stranded DNA as the template by the action of a DNA-dependent DNA polymerase, and then transcribing the double-stranded DNA into an RNA transcript, which acts as a template in the subsequent cDNA synthesis by the RNA-dependent DNA polymerase, in the presence of an RNA polymerase. The present invention is characterized by the use of an oligonucleotide primer of any one of SEQ ID NOS:1 to 7 as a first primer, which can bind to a specific site of the HIV-1 RNA and an oligonucleotide of any one of SEQ ID NOS:8 to 20 as a second primer, which is homologous to part of the HIV-1 RNA to be amplified (either of which additionally has a promoter sequence for the RNA polymerase at the 5' end).

One embodiment of the present invention is the above-mentioned amplification step wherein the first primer is an oligonucleotide of any one of SEQ ID NOS:1 to 7, and the second primer is an oligonucleotide of any one of SEQ ID NOS:8 to 20 (provided that either the first primer or the second primer additionally has a promoter sequence for the RNA polymerase at the 5' end). The RNA-dependent DNA polymerase, the DNA-dependent DNA polymerase and the ribonuclease H are not particularly limited, but AMV reverse transcriptase is preferable because it has the activities of all of them. As the RNA polymerase, T7 phage RNA polymerase or SP6 phage RNA polymerase is preferred, though there is no particular restriction.

In the above-mentioned amplification step, even if the specific sequence is not present at the 5' end, HIV-1 RNA can be amplified by adding an oligonucleotide complementary to a region of HIV-1 RNA which flanks the 5' end of the specific sequence with an overlap (of from 1 to 10 bases) with the specific sequence to cleave HIV-1 RNA at the 5' end (by the action of a ribonuclease H) before it is used as the template in the initial stage of the nucleic acid amplification. As the scissor oligonucleotide, an oligonucleotide of any of SEQ ID NOS:21 to 33 may be used. The scissor oligonucleotide is preferred to have a chemically modified hydroxyl group (for example, an aminated hydroxyl group) at the 3' end not to elongate from the 3' end.

All When the third oligonucleotide complementary to a region which flanks the 5' end of the specific sequence with a (1 to 10-base) overlap with the specific sequence as mentioned above is added to cleave HIV-1 RNA at the 5' end (by the action of a ribonuclease H) before it is used as the template in the initial stage of the nucleic acid amplification, it is preferred that the first primer is an oligonucleotide of any one of SEQ ID NOS:1 to 7, and

(1) the second primer is an oligonucleotide of SEQ ID NO:8, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:21 and 22,

(2) the second primer is an oligonucleotide of SEQ ID NO:9, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:22 to 26,

(3) the second primer is an oligonucleotide of SEQ ID NO:10, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:22 to 28,

(4) the second primer is an oligonucleotide of SEQ ID NO:11, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:22 to 29,

(5) the second primer is an oligonucleotide of SEQ ID NO:12, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:22 to 29,

(6) the second primer is an oligonucleotide of SEQ ID NO:13, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:23 to 30,

(7) the second primer is an oligonucleotide of SEQ ID NO:14, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:23 to 30,

(8) the second primer is an oligonucleotide of SEQ ID NO:15, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:24 to 30,

(9) the second primer is an oligonucleotide of SEQ ID NO:16, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:25 to 30,

(10) the second primer is an oligonucleotide of SEQ ID NO:17, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:27 to 31,

(11) the second primer is an oligonucleotide of SEQ ID NO:18, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:31 and 32,

(12) the second primer is an oligonucleotide of SEQ ID NO:19, and the third oligonucleotide is an oligonucleotide of any one of SEQ ID NOS:32 and 33, or

(13) the second primer is an oligonucleotide of SEQ ID NO:20, and the third oligonucleotide is an oligonucleotide of SEQ ID NO:33.

In this case, the third oligonucleotide (the scissor oligonucleotide) is preferred to have a chemically modified hydroxyl group (for example, an aminated hydroxyl group) at the 3' end not to elongate from the 3' end, too.

Detection of the amplification product obtained in the nucleic acid amplification step is preferably carried out by measuring the change in the fluorescence of the reaction solution during the amplification step in the presence of an oligonucleotide probe labeled with a fluorescent intercalative dye, though it can be detected by conventional methods for detection of nucleic acid. The oligonucleotide probe may be, for example, an oligonucleotide having a fluorescent intercalative dye linked to a phosphorus atom via a linker. Such a preferable probe alters its fluorescence upon formation of a double strand with the target nucleic acid (a complementary nucleic acid) through intercalation of the intercalator moiety to the double strand (Ishiguro, T. et al., (1996) Nucleic Acids Res. 24 (24) 4992-4997).

The sequence of the probe is not particularly limited as long as it contains a sequence complementary to at least part of the RNA transcript. For example, when the combination of a first primer of any one of SEQ ID NOS:1 to 7 and a second primer of any one of SEQ ID NOS:8 to 20, is used in the RNA amplification step, a sequence consisting of or complementary to at least 10 consecutive bases in SEQ ID NO:34 is preferred. In this case, it is also preferred to chemically modify the hydroxyl group at the 3' end of the probe (for example, by adding glycolic acid) to prevent elongation reaction using the probe as a primer.

By carrying out the amplification step in the presence of the above-mentioned probe, amplification and detection of HIV-1 RNA can be carried out at constant temperature in one tube in one step and can be automated easily.

Claim 1 of 13 Claims

What is claimed is:

1. A method for amplifying HIV-1 RNA in a sample comprising: contacting a sample containing HIV-1 RNA with a set of primers under conditions suitable for transcription and amplification of HIV-1 nucleic acid,

wherein said set of primers comprises SEQ ID NO: 2 and SEQ ID NO: 13.

____________________________________________
If you want to learn more about this patent, please go directly to the U.S. Patent and Trademark Office Web site to access the full patent.