CA2012984A1 - Process for rapid nucleic acid detection by incorporating a reporter moiety into amplified target nucleic acid followed by affinity capture - Google Patents

Abstract

TITLE
PROCESS FOR RAPID NUCLEIC ACID DETECTION
BY INCORPORATING A REPORTER MOIETY INTO
AMPLIFIED TARGET NUCLEIC ACID FOLLOWED
BY AFFINITY CAPTURE
ABSTRACT
A nucleic acid probe assay which incorporates a deoxyribonucleotide triphosphate containing a reporter moiety into a nucleic acid amplification process followed by affinity capture and detection of the reporter moiety is provided.

Description

2(~

~ITLE
PROCESS FOR RAPID NUCLEIC ACID DETECTION
BY INCORPORATING A REPORTER M~IE~Y INTO
AMPLIFIED TARGET NUCLEIC ACID ~OLLOWED
BY AFFINITY CAPTU~E
FIELD OF INVENTION

This invention relates to the detection of nucleic acid séquences and more specifically to a process of combining amplification of target nucleic acid sequences with detection of a reporter group specifically incorporated into the target sequence followed by affinity capture.
~aCKGROUND OF THE INVEN~IQN

The development of practical nucleic acid hybridization methods which can be used for detecting nucleic acid sequences of interest has been limited by several factors. These include lack of sensitivity, complexity of procedure, and the desire to convert from radiometric to nonradiometric detection methods.
A variety of methods have been investigated for the purpose of increasing the sensitivity nonradiometric procedures. In one general approach, improvements in the total assay procedure have been e~amined, with concomitant effects on the issues of cDmplexity and nonradiometric detection. In another approach, methods which increase the amount of nucleic acid to be detected by such assays have been pursued.
U.S. Patent 4,358,535, issued to ~alkow, describes a method of culturing cells to increase their number and thus the amount of nucleic acid of the organism suspected to be present, depositing the sample onto fixed support, and then contacting the sample with a labeled probe, followed by was~ing the support and detecting the label. One drawback to this 20i298~
method is that without culturing the organism first, - the assay does not have adequate sensitivity. Adding a culture step, however, is time consuming and not always successful. Maniatis et al., Molecular S Clonin~: A Laboratorv Manual, Cold Spring Harbor Laboratory, pp.390-401 (1982), describe a method in which a nucleic acid of interest is amplified by cloning it into an appropriate host system. Then, when the host organism replicates in culture, the nucleic acid of interest is also replicated. This method also suffers from the requirement to perform a culture step and thus provides for a procedure that is time consuming and complicated.
An alternative approach tG increasing the quantity of nucleic acids of organisms has been described in U.S. patents 4,683,202 and 4,683,195.
These patents disclose "a process for amplification and detection of any target nucleic acid sequence contained in a nucleic acid or mixture thereof". This process employs an in vitro cycling mechanism which doubles the nucleic acid sequence to be amplified after each cycle is complete. This is carried out by separating the complementary strands of the nucleic acid sequence to be amplified, contacting these strands with excess oligonucleotide primers and extending the primers by enzymatic treatment to form primer extension products that are complementary to the nucleic acid annealed with each primer. The process is then repeated as many times as is necessary. An advantage of this method is that it can rapidly produce large quantities of a small portion of the sequence of the nucleic acid of an organism ~f interest. A disadvantage of this method is that the detection of the nucleic acids produced, using a direct assay method, is complicated in that the 2~:2~34 amplification process can produce nucleic acid sequences which are not faithful copies of the original nucleic acid which was to be copied. These erroneous nucleic acid sequences can provide false positives in the assay which increase the background noise and thus decrease the sensitivity of the entire method.
Numerous DNA probe assays have been described in the past for the detection of nucleic acids of interest. Falkow's method (above) first renders the target nucleic acid single-stranded and then immobilizes it onto a solid support. A labeled probe which is complementary to the target nucleic acid is then brought into contact with the solid support. Any excess probe is washed away and the presence of the label in the resulting hybrid is determined. A
disadvantage of this method is that it is time consuming and cumbersome. The assay steps, i.e., hybridization and washing steps are carried out in a sealed pouch which contains the membrane (solid support) as well as the buffer solution.
Hill et al., WO 86/05815, describe a variation of the above assay format employing nitrocellulose coated magnetic particles to which the target DNA is affixed, followed by direct hybridization with a biotinylated probe and detection using a streptavidin-conjugated reporter.
Dunn et al., Cell, Vol. 12, 23-36 (1977~, describe a different hybridization format which employs a two-step sandwich assay method employing polynucleotlde probes in which the target nucleic acid is mixed with a solution containing a first or capture probe which has been affixed to a solid support.
After a period of time, the support ~s washed and a second or reporter (labeled) probe, also complementary to the target nucleic acid but not to the capture probe, is added and allowed to hybridize with the capture probe - target nucleic acid complex. After washing to remove any unhybridized reporter probe, the presence of the reporter probe, hybridized to the target nucleic acid, is detected.
Ranki et al. U.S. Patent 4,563,419, disclose ~PA 0 154 505, W086/03782, and EPA 0 200 113. It is to be recognized that all of these employ an assay procedure in which the first or capture probe is immobilized onto a solid support prior to hybridization.
A further variation has been described in German Preliminary Published Application 3,546,312 A1. This method, like that described by Ranki et al., empl~ys a capture probe and a reporter probe which hybridize to distinct portions of the target nucleic acid. The target nucleic acid is contacted in solution by the two probes. The first, or capture probe, contains a binding component, such as biotin, that is capable of binding with a receptor component, such as streptavidin, which has been affixed to a solid support. After formation of the capture probe -target nucleic acid - reporter probe complex, a streptavidin-modified solid support is added. Any unhybridized reporter probe is washed away followed by the detection of the label incorporated into the complex bound to the solid support. An advantage of this technique over that disclosed by Ranki et al. is that the hybridization, which takes place in solution, is favored kinetically. Some disadvantages are that the length of the target nucleic acid affects the overall efficiency of the reaction which decreases with increasing target nucleic acid length. Also, sandwich nucleic acid probe assays, whether 5 zo~2~84 heterogeneous two-step or one-step, or utilizing solution hybridization, are not as sensitive as the direct assay method.
pISCLOSURE OF TH~ INVENTION
S The nucleic acid assay of this invention for the detection and/or measurement of a preselected nucleic acid sequence in a sample suspected of including a nucleic acid containing said preselected sequence comprises the steps of:
(A) rendering the target nucleic acid single-stranded;
(B) amplifying at least one specific nucleic acid sequence contained within the preselected nucleic acid sequence in the presence of at least one deoxyribonucleotide triphosphate containing a reporter moiety in an amount up to the total replacement of the corresponding dNTP, by (1) treating the strands with two oligonucleotide primers, for each different specific sequence being amplified, under conditions such that for each different sequence being amplified an extension product of each primer is synthesized which is complementary to each nucleic acid strand, wherein said primers are selected so as to be sufficiently complementary to the d~fferent strands of each specific sequence to hybridize therewith such that the extension product synthesized from one primer, when it is separated from it8 complement, can serve as a template 2~3~2~34 for synthesis of the extension pro~uct of the other primer;
(2) separating the primer extension products from the templates on which they were synthesized to produce single-stranded molecules; and (3) treating the single-s~randed molecules generated from step ~2) with the primers of step ~1~ under conditions that a primer extension product is synthesized using each of the single strands produced in step ~2) as a template;

(4) repeating steps ~) and ~3) to produce sufficient primer extension product for detection and/or measurement:;
~C) contacting the product of step ~B) with a solid affinity support matrix;
~D) removing any unincorporated reporter moiety; and ~E) detecting and/or measuring the reporter moiety immobilized on the affinity support.
~AILED ~E~RIPTION OF THE INVENTION
The nucleic acid assay of this invention comprises the following overall process for the detection of target nucleic acids of a preselected sequence:
a) Using the polymerase chain reaction ~PCR) nucleic acid amplification method described in U.S.
4,683,202, incorporated herein by reference, specific nucleic acid sequences are amplified by annealing the denatured target nucleic acid present in the sample with primers specific for the target and forming extension products. In this process, a deoxyribonucleotide triphosphate containing a reporter group ~moiety), dNTP-R, is used to replace some or all 20~.2~84 of at least one of the corresponding deoxyribonucleotide triphosphates employed. Each extension product formed is complementary to a portion of the preselected nucleic acid sequence contained within the target nucleic acid and becomes a template for further primer binding. This process ls then repeated as necessary in order to produce the desired amount of primer extension product for detection and/or measurement.
b) The resulting nucleic acid is brought in contact with an affinity support and allowed to bind to the affinity support for a period of from 1 to 30 minutes. The affinity support is then rinsed with an appropriate buffer in order to remove non-incorporated reporter group modified deoxyribonucleotide triphosphate.
The term "PCR" as used herein in referring to the process of amplifying target nucleic acid sequences employing primer oligonucleotides to produce by enzymatic means a greatly increased number of copies of a small portion of the target nucleic acid is described in U.S. patent 4,683,202.
The PCR target amplification reaction requires approximately 20 to 30 repeat cycles in order to produce a sufficient quantity of the amplified target nucleic acid for further hybridization. Denaturation of the amplified nucleic acid can be accomplished by treatment with alkali, acid, chaotropic agents, or heat, although the preferred method is to place the amplified target nucleic acid in a boiling water bath for at least 10 minutes followed by a chilled water bath ~4C) for at least two mlnutes.
A variety of affinity supports can be utilized.
Among these are known affinity membranes 9uch as Gene Screen~ hybridization transfer membrane ~a registered 8 20~,2984 trademark of E.I. du Pont de Nemours and Company; a nylon-based membrane), nitrocellulose, and Gene Screen Plus~M, a positively charged and supported nylon 66 membrane. The method of transferring nucleic acids is described in U.S. Patent 4,455,370 which is hereby incorporated by reference.
A variety of known detection methods can be utilized in the assay of this invention, depending upon the reporter group incorporated into the amplified product. When the reporter group is a chromophor or fluorophor, then the incorporated reporter group can be detected by known spectroscopic techniques.
In an alternative detection method, a labeled antibody to the reporter group incorporated during the amplification process is employed. It is brought into contact with the amplified product before or subsequent to capture of the amplified product. The label on the antibody can then be used to detect the presence of the amplified product.
The Example below exemplifies the invention.
~XAMPLE
Detection of HIV I
A. Amplification of Target Nucleic 25Acid by PCR
The procedure as described in U.S. Patent 4,683,202 and in a product bulletin for GeneAmp DNA
Amplification Reagent ~it (~N801-0043) can be followed utilizing the following specific conditions and reagents. A 103-nucleotide base sequence located within the GAG pl7 region of HIV I, incorporated lnto a plasmid (the plasmid incorporating most of the HIV I
genome is designated pBH10-R3), can be amplified using primers A and ~ as shown below:

9 ~n~ss4 5'-TGGGCAAGCAGGGAGCTAGG
Primer A
5'-TCTGAAGGGATGGTTGTAGC
Primer B
Aliquots of serial dilutions (lx10+7, lx10+6, lx10+5, lx10+4, lx10+3, lx10+2, lxlO+1, and zero copies) of plasmid p~HlO-R3 can be amplified using PCR. Each aliquot can be combined with a buffer 200 ~M in each of dATP, dTTP, dCTP, and dGTP, and 10 ~M in succinyl-fluorescein dTTP, 1.0 ~M in each of Primer A
and Primer B, and containing l ~g of human placental DNA/reaction and 2.5 units of a DNA polymerase enzyme, in a total reaction volume of 100 ~l.
Each reaction mixture can then be temperature cycled as described in the product bulletin thirty (30) times.
This process is expected to result in the estimated increase in the number of target molecules by lx10+5 to lx10+6.
B. Capture The product of Step A car. be adsorbed onto a microtiter plate having a bottom composed of Gene Screen Plus for 30 minutes at 25C. The microtiter plate wells can then be washed three times for 5 minutes at 25C by adding 200 ~l of wash buffer containing lX SSC, pH 7.0, and 0.17% Triton X-100, and aspirating between washes.
C. p~tection Detection can be accomplished by adding 200 ~l of 10 mM Tris, pH 7.00 to each sample and detecting the amplified nucleic acid product detected by reflectance fluorescence visualization.

Claims (5)

1. A nucleic acid assay for the detection and/or measurement of a preselected nucleic acid sequence in a sample suspected of including a nucleic acid containing said preselected sequence comprises the steps of:
(A) rendering the target nucleic acid single-stranded;
(B) amplifying at least one specific nucleic acid sequence contained within the preselected nucleic acid sequence in the presence of at least one deoxyribonucleotide triphosphate containing a reporter moiety in an amount up to the total replacement of the corresponding dNTP, by (1) treating the strands with two oligonucleotide primers, for each different specific sequence being amplified, under conditions such that for each different sequence being amplified an extension product of each primer is synthesized which is complementary to each nucleic acid strand, wherein said primers are selected so as to be sufficiently complementary to the different strands of each specific sequence to hybridize therewith such that the extension product synthesized from one primer, when it is separated from its complement can serve as a template for synthesis of the extension product of the other primer;

(2) separating the primer extension products from the templates on which they were synthesized to produce single-stranded molecules;
(3) treating the single-stranded molecules generated from step (2) with the primers of step (1) under conditions that a primer extension product is synthesized using each of the single strands produced in step (2) as a template; and (4) repeating steps (2) and (3) to produce sufficient primer extension product for detection and/or measurement;
(C) contacting the product of step (B) with a solid affinity support matrix;
(D) removing any unincorporated reporter moiety; and (E) detecting and/or measuring the reporter moiety immobilized on the affinity support.

2. The assay of claim 1 wherein said preselected nucleic acid sequence is HIV I DNA.

3. The assay of claim 1 wherein said reporter moiety is a fluorescent moiety.

4. The assay of claim 1 wherein said reporter moiety is an antigenic moiety.

5. The assay of claim 1 wherein said affinity support matrix comprises nylon.