CA1341495C

CA1341495C - Method for detecting nucleic acid sequences

Info

Publication number: CA1341495C
Application number: CA000597529A
Authority: CA
Inventors: Peter Duck; Robert Bender
Original assignee: ID Biomedical Corp of Quebec
Current assignee: ID Biomedical Corp of Quebec
Priority date: 1988-04-29
Filing date: 1989-04-24
Publication date: 2006-02-07
Anticipated expiration: 2023-02-07
Also published as: JPH02504110A; JP2839608B2; AU3569789A; EP0365663A1; EP0365663A4; WO1989010415A1; US5011769A

Abstract

This invention provides a method for detecting a target nucleic acid molecule which comprises forming a reaction mixture which includes the target nucleic acid molecule and an amount of a complementary single-stranded nucleic acid probe which is greater than the target molecule, under conditions which allow the probe and the target nucleic acid molecule to hybridize to each other and form a double stranded target-probe complex nicking the hybridized probe at least once within a predetermined sequence so as to form at least two probe fragments hybridized to the target nucleic acid molecule, resulting in the probe fragments to become single-standed and allowing the target nucleic acid molecule to become hybridized to another probe;
and identifying probe fragments, thereby detecting the target nucleic acid molecule. This invention also provides a method for detecting a target de-oxyribonucleic acid molecule.

Description

METHOD FOR DETECTING NUCLEIC ACID SEQUENCES

This application is related to Canadian Application Serial No. 524,411 (now Canadian Patent 1,304,703).
Current DNA probe methodology basically involves attaching target DNA to a nitrocellulose filter by bringing it into contact with the filter directly or via the Southern transfer technique from an agarose gel. The DNA is then denatured and the filters baked to ensure firm attachment.
Generally, the preparation of the DNA and the running of the gels is a time consuming, costly process requiring a reasonably high technical skill level.

The next step is to prepare the probe DNA. Probe DNA
is prepared by labelling radioactively specific DNA by nick translation, polynucleotide kinase, or some other polymerase type copy reaction using nucleotides la-belled with 32P. Once prepared, the probe DNA is per-mitted to hybridize with the bound target DNA. Hybrid-ization is allowed to proceed at a suitable tempera-ture, typically for several hours. The DNA probe will associate to form hybrid duplexes with any of the bound target DNA that has complementary base sequences.
Extraneous material, including unbound probe DNA, is then washed away from the filter and the filter is then exposed to film sensitive to the radioactive label.
European Patent Application Publication No. 0 067 597, (Bender et al.) published December 22, 1982 discloses oligonucleotides and a process for their preparation which comprises incorporating ribonucleotide units at specific locations in deoxyribonucleotide chains to provide predetermined cleavage sites which allow ease of chain cleavage. Although the products from their process are said to be useful for separating mixtures of nucleotide and polynucleotide products, Bender et al. do not teach a method for detecting target nucleic acid molecules based upon the amplification of probe fragments.
International Patent Application No. WO 84/03520 (Mal-color et al.), published September 13, 1984, discloses a method of detecting nucleic acid sequences which uti-lizes tandem hybridization of a nucleic acid probe and an enzyme containing marker. The method involves con-tacting the probe with a sample containing a complemen-tart' target sequence under hybridizing conditions.
Before or after hybridization with the target sequence, the probe is attached by hybridization to an enzyme labelled marker polynucleotide which has a sequence complementary to a sequence on the probe.
U.S. Patent No. 4,358,535 (Falkow et al.) discloses radioactively labeled nucleotide probes which are com-plementary to a target nucleic acid sequence of inter-est and a method of using these probes to detect the presence of a~ pathogen from which the target nucleic acid sequence is derived. The method comprises first fixing the target nucleic acid sequence to an inert support before hybridization with the probe. Next, the fixed nucleic acid is contacted with the radioactively ~5 labeled probe under hybridizing conditions, with hy-bridization taking place on the solid support. Then, the presence of the target nucleic acid sequence is determined by detecting the presence of any label on the inert support. A disadvantage of such a system is that the probe itself cannot be immobilized. If the probe of Falkow et al. is immobilized, rather than the target nucleic acid sequence, then the label molecules of the immobilized probe will be bound to the solid support regardless of whether the probe has hybridized 25 with a target nucleic acid sequence. The result would not permit the detection of the presence of target nucleic acid.
European Patent Application Publication No. 0 117 440 (Johnson et al., published January 26, 1984) discloses non-radioactive chemically labeled polynucle-otide probes and methods of using the probes. The methods disclosed are similar to the method of Falkow et al. in that the target nucleic acid sequence is fixed to a solid support before hybridization.

Recently, other detection systems have been developed, such as fluorescent tags or color change enzyme sys-tems. However, such systems have had significant prob-lems with sensitivity and background levels (noise).
U.S. Patent No. 4,362,867 (Paddock) discloses a hybrid nucleic acid construction which comprises two comple-mentary deoxynucleotide sequences which are hybridized to form a double-stranded helical structure. Situated between and covalently bonded to the two deoxynucleo-tides is a ribonucleotide sequence. The construction forms a single unit, in which none of the nucleotide sequences repeat themselves.
U.S. Patent No. 4,683,195 (Mullis, et al.) discloses a process for amplifying and detecting target nucleic acid sequences comprising treating separate complemen-tary strands of the nucleic acid with a molar excess of two olignucleotide primers. By extending the primers to form complementary primer extension products which act as templates for synthesizing the desired nucleic acid sequence, the sequence so amplified is detected.
A disadvantage of this process is the requirement of thermal cycling and the lack of constant temperature conditions.
In U.S. Patent No. 4,683,194 (Saiki et al.), a method is disclosed for detecting the presence or absence of a specific site in a nucleic acid sequence using an oligonucleotide probe that is complementary to one strand of the nucleic acid sequence spanning the re-striction site. Saiki et al. teach that their nucleic acid, i.e., oligonucleotide, probe, may be used as is or the sequence it contains can be amplified to in-crease sensitivity using the process disclosed in U.S.

-5- 13 4 1 4 9 ~
Patent No. 4,683,202. Such an amplifying process suf-fers from the disadvantages inherent in U.S. Patent No.
4,683,195, discussed above.

ZO

13 4~49~
Summary of the Invention The present invention provides a method for detecting a target nucleic acid molecule which comprises: (a) forming a reaction mixture which includes the target nucleic acid molecule and an amount of a complementary single-stranded nucleic acid probe which is greater than the target molecule, under conditions which allow the probe and the target nucleic acid molecule to hy-bridize to each other and form a double-stranded tar-get-probe complex; (b) nicking the hybridized probe at least once within a predetermined sequence so as to fona at least two probe fragments hybridized to the target nucleic acid molecule, resulting in the probe fragments to become single-stranded and allowing the target nucleic acid molecule to become hybridized to another probe; and (c) identifying probe fragments, thereby detecting the target nucleic acid molecule.
The present invention also provides a method for de-tecting a target deoxyribonucleic acid molecule which comprises: (a) forming a reaction mixture which in-cludes the target deoxyribonucleic acid molecule and a single-stranded nucleic acid probe having a ribonu-cleotide sequence complementary to the target deoxy-ribonucleic acid molecule which may be covalently bound at one or both of its termini to one or more deoxy-ribonucleotides which may or may not be complementary to the target deoxyribonucleic acid molecule under conditions which allow the probe and the target deoxy-ribonucleic acid molecule to hybridize to each other and form a double-stranded target-probe complex; (b) nicking the hybridized probe at least once within a Predetermined sequence so as to form at least two probe fragments hybridized to the target deoxyribonucleic acid molecule, resulting in the probe fragments to become single-stranded and allowing the target nucleic acid molecule to become hybridized to another probe;
and (c) identifying probe fragments, thereby detecting the target deoxyribonucleic acid molecule.

Brief Description of the Figures Figure 1 depicts the use of a nucleic acid probe as a self-amplifing and cycling construction in the method of the present invention for detecting target nucleic acid molecules. A pool of nucleic acid probes and a ribonuclease, e.g. , RNase H, are reacted with a sample which contains a target nucleic acid molecule. The single-stranded nucleic acid probe is complementary to and in an amount greater than the target nucleic acid molecule. Double-stranded target-probe complexes are formed as the result of hybridization. RNase H nicks or excises out RNA sequences in hybridized double-stranded RNA-DNA.
As a consequence of such nicking, the remaining DNA
probe fragments are "melted" off, i.e., become unhy-bridized, from the target molecule. The resulting sin-20 gle-stranded probe fragments are detectable by isotopic labelling or by the length of the probe fragment, i.e., by direct measurement. In practice, the probe frag-ments can be detected by coupling to fluorescent labels which have been initially placed on the nucleic acid 25 probes or by ATP generation using single phos-phorylated nucleotides, e.g., adenosine monophosphate, which have been formed. Additional probe molecules may react with the now free target molecules to complete the cycling sequence. RNase H does not nick or cleave unhybridized RNA. By using such a system of cycling, sensitivity of from about 10 19 to about 10 2~ mole-cules of target can be attained.

Detailed Description of the Invention The present invention provides a method for detecting a target nucleic acid molecule which comprises: (a) forming a reaction mixture which includes the target nucleic acid molecule and an amount of a complementary single-stranded nucleic acid probe which is greater than the target molecule, under conditions which allow the probe and the target nucleic acid molecule to hy-bridize to each other and form a double-stranded tar-get-probe complex; (b) nicking the hybridized probe at least once within a predetermined sequence so as to form at least two probe fragments hybridized to the ~5 target nucleic acid molecule, resulting in the probe fragments to become single-stranded and allowing the target nucleic acid molecule to become hybridized to another probe: and (c) identifying probe fragments, thereby detecting the target nucleic acid molecule.
In one embodiment, the invention further provides a method for detecting a target nucleic acid molecule which comprises repeating the above-described steps of (a), (b), and (c). In repeating these steps, the com-Plementary single-stranded nucleic acid probe, which is in an amount greater, i.e., in molar excess, than the target molecule, is allowed to recycle, i.e., hybrid-ize to the target molecule with other nucleic acid probes included in the reaction mixture.
The nucleic acid probe which is useful in the practice of this invention comprises the structure:
[NAl---R---NA2ln _io_ 13 4 '~ 4 9 5 wherein NA1 and NA2 are nucleic acid sequences, wherein R is an RNA sequence; and wherein n is an integer from about 1 to about l0.
In one embodiment of this invention, NAl and NA2, in the nucleic acid probe independently comprise from about 0 to about 20 nucleotides, R comprises from about 1 ~to about 100 ribonucleotides, or more, and n is an integer from about 1 to about 10.
In another embodiment of this invention, NAl and NA2 in the nucleic acid probe are DNA sequences. In a further embodiment, NAl and NA2 in the nucleic acid probe are RNA sequences. In still yet another embodiment, the nucleic acid probe comprises a structure wherein NAl is either an RNA or DNA sequence, and NA2 is either an RNA
or DNA sequence.
In one embodiment, nicking the hybridized probe at predetermined RNA sequences is carried out with a dou ble-stranded ribonuclease. Such ribonucleases nick or excise ribonucleic acid sequences from double-stranded DNA-RNA hybridized strands. An example of a ribonu clease useful in the practice of this invention is RNase H. Other ribonucleases and enzymes may be suit-able to nick or excise RNA from RNA-DNA strands, such as Exo III and reverse transcriptase.
The molecules of the present~invention may have a de-tectable marker attached to one or more of the nucleic acid sequences, NAl or NA2. This marker is contemplat-ed to be any molecule or reagent which is capable of being detected. Examples of such detectable molecules are radioisotopes, radiolabelled molecules, fluorescent molecules, fluorescent antibodies, enzymes, or chemiluminescent catalysts. Another suitable marker is a ligand capable of binding to specific proteins which have been tagged with an enzyme, fluorescent molecule or other detectable molecule. One example of a suit-able ligand is biotin, which will bind to avidin or streptavidin.
In one embodiment of this invention, the nucleic acid probe is immobilized on a solid support. In another, the nucleic acid probe is labelled with a detectable marker.
When the nucleic acid sequences, NA1 and NA2 are DNA, the R portion described above may also be properly termed a scissile linkage in language consistent with usage in Canadian Application Serial No. 524,411 (now Canadian Patent 1,304,703). Such linkage is capable of being cleaved or disrupted without cleaving or disrupting any nucleic acid sequence of the molecule itself or of the target nucleic acid molecule. As used herein, such a scissile linkage, i.e., R, is any connecting chemical structure which joins two nucleic acid sequences and which is capable of being selectively cleaved without cleavage of the nucleic acid sequences to which it is joined. The scissile linkage may be a single bond or a multiple unit sequence. As used herein, R denotes a ribonucleic acid (RNA) sequence.
In molecules useful as probes in the present invention in which n is greater than one, the unit NAB ---R---NA2 repeats. It is contemplated that the unit may be the same within each repeat or it may vary randomly or in a defined pattern. The unit may vary in that NAB or NA2 or both may vary within each repeat. NAB or NAZ may vary in that they have different nucleic acid sequences from one repeat unit to the next. This variation may occur randomly such that in every repeat unit, NA1 and NA2, may also vary in that the number of bases of each may vary, either greater or less, from one repeat to the next. This variation may also occur randomly or in a pattern. An example of a random variation where n=3 and both NA1 and NA2 vary is:
NA1--'R___NA2___Nprl~___R___NA2~___NAln___R___Np~2~~
An example of a patterned variation where n=4 and both NA1 and NA2 vary is:
NA1___R___NA2___NA1~___R___NA2~___Np~l___R___Np~2___ NA '---R---NA ' In both of the above examples, the solid lines joining each unit are chemical bonds which may be either hydro-gen bonds or covalent bonds.
The repeat unit may also vary by variations in the scissile linkage, i.e., R, such that the sequence of ribonucleotides in R, the scissile linkage, will vary.
The variation in the sequence of ribonucleotides in R, the scissile linkage, may also be in a random or pat terned fashion as discussed above. Also, the repeat units may vary by any combination of the above-men tioned differences in NA1, NA2 or the scissile linkage, i.e., R, and the variations may be random or patterned.
Those skilled in this art will readily appreciate that best results may be achieved with the use of nucleic acid probes whose lengths are relatively short, and therefore, highly specific to the target nucleic acid molecule. By limiting rather than increasing the total number of nucleotides in the complementary nucleic acid probe, high gain - low noise detection of target nucleic acid molecules can be achieved. -Those skilled in this art will readily appreciate that the total length of the nucleic acid probe may vary according to a number of factors including the nature of the target nucleic acid molecule to be detected, the construction of the nucleic acid probe, i.e., whether the probe is a DNA-RNA hybrid or is constructed of RNA
sequences alone, and so forth. When the probe is con-structed of DNA and RNA sequences, it is important that the R portion or scissile linkage be accessible to nicking or excision in order that a DNA probe fragment remain hybridized to the target nucleic acid molecule.
In this regard it is advantageous though not required that the R portion or scissile linkage be located be-tween DNA sequences of from about 8 to about 10 nucleotides in order to allow the probe fragments to become single-stranded in accordance with the method provided by this invention.
When the probe is constructed entirely of RNA sequenc-es, the nicking is facilitated especially when carried out with a double-stranded ribonuclease, such as RNase H or Exo III. Straight RNA probes constructed entirely of RNA sequences are particularly useful because first, they can be more easily produced enzymatically, and 3p second, they have more cleavage sites which are ac-cesible to nicking or cleaving by a nicking agent, such as the aforementioned ribonucleases. Thus, the straight RNA probes do not rely on a scissile linkage as in the DNA-RNA hybrid probes.

The present invention also provides a method for de-tecting a target deoxyribonucleic acid molecule which comprises: (a) forming a reaction mixture which in-s cludes the target deoxyribonucleic acid molecule and a single-stranded nucleic acid probe having a ribo-nucleotide sequence complementary to the target deoxy-ribonucleic acid molecule which may be covalently bound at one or both of its termini to one or more deoxy-ribonucleotides which may or may not be complementary to the target deoxyribonucleic acid molecule under conditions which allow the probe and the target deoxy-ribonucleic acid molecule to hybridize to each other and form a double-stranded target-probe complex; (b) nicking the hybridized probe at least once within a predetermined sequence so as to form at least two probe fragments hybridized to the target deoxyribonucleic acid molecule, resulting in the probe fragments to become single-stranded and allowing the target nucleic acid molecule to become hybridized to another probe:
and (c) identifying probe fragments, thereby detecting the target deoxyribonucleic acid molecule.
In one embodiment, the invention provides a method for 25 detecting a target deoxyribonucleic acid molecule which comprises repeating the above-described steps of (a), (b), and (c).
The single stranded nucleic acid probe useful in method of this invention for detecting a target deoxyribo-nucleic acid comprises from about 10 to about 2000 ribonucleotides. Those skilled in the art will readi-ly appreciate that the number of ribonucleotides in such a nucleic acid probe may vary widely according to 35 the target deoxyribonucleic acid, the degree of sensi-tivity required, and so forth. In forming the reaction - 13 41+95 mixture in step (a) the target deoxyribonucleic acid molecule may have been converted to DNA sequences using methods well-known to those skilled in the art.
In a further embodiment of this invention, nicking the hybridized probe in step (b) is carried out with a double-stranded ribonuclease. In still yet a further embodiment such a ribonucleases may be RNase H. There are other enzymes having RNase H-like activity, such as Exo III and reverse transcriptase and so forth. These enzymes and others may be suitable, with or without modification to the methods described herein.
~5 In forming the reaction mixture in step (a) above, the target nucleic acid molecule and an amount of a comple-mentary single-stranded nucleic acid probe which is greater, i.e., in molar excess, than the target mole-cule, are mixed together under hybridizing conditions 2p which allow the probe and the target to hybridize to each other and form a double-stranded target-probe complex.
Nicking the hybridized probe in step (b) above can be 25 carried out enzymatically, for example, by contacting the hybridized probe with an agent capable of nicking, i.e., excising out, predetermined sequences in the hy-bridized probe. Such predetermined sequences in the practice of this invention include the scissile link-3p ages, i.e., R, or RNA sequences.
Typically the target nucleic acid molecule and the labelled complementary single-stranded nucleic acid probe, which is in excess to the target molecule, are 35 combined in a reaction mixture with an appropriate buffer. The reaction mixture so formed is incubated at a temperature, of from about 30' to about 45'C, opti-mally at about 37'C for from about 5 to about 30 min-utes, up to about 60 minutes or how ever long a period of time is required to effect annealing.
The reaction mixture which includes the hybridized target and probe is next combined with a nicking agent also at a temperature of from about 30 to 45'C, opti-mally at about 37'C for an additional amount of time.
The additional amount of time may vary from about 5 to about 60 minutes although 30 minutes is sufficient in most eases. The cycling reaction which involves re-peating the steps of hybridizing, nicking and causing single-stranded probe fragments to form takes place in a short period of time, e.g., on the order of millisec-onds.
By nicking the hybridized double-stranded target-probe complex at least once within a predetermined sequence, e.g., in R or the scissile linkage, so as to form at least two probe fragments hybridized to the target nucleic acid molecule, the remaining hybridized probe fragments will become single-stranded as the result of 25 the change in size of the hybridized probe sequences in the target-probe complex. For example, a 20 mer (mono-mer) double-stranded DNA sequence will remain annealed or hybridized at 37'C. After nicking, assuming that an intervening 4-ribonucleotide (RNA) base sequence be-tween two 8-deoxyribonucleotide (DNA) base sequences is excised by a ribonuclease, e.g., RNase H or Exo III, the remaining two B-mer hybridized probe fragments will aelt or fall off the target-probe complex. These sin-gle-stranded probe fragments may then be identified 35 using well-known aethods, thereby detecting the target nucleic acid molecule.

A=T and G=C base-pairs exhibit Tms of approximately 2'/base-pair and 4'/base pair, for short olgomers re-spectively. On the average, assuming equal ratios of A-T and G-C base pairs in a hybridized target-probe complex, each paired nucleotide exhibits a melting point temperature of approximately 3°/base-pair.
Identifying the probe fragments and thereby detecting the target nucleic acid molecule in step (c) may be performed using a number of methods. The method of identification and detection in step (c) will depend on the type of labelling or detectable marker which has been placed on the nucleic acid probe or which is gen-erated in step (b) above. For example, detection of the target nucleic acid molecule may be performed by coupling to a fluorescent label or by ATP generation.
Where, for example, a probe is constructed entirely of ribonucleic acid (RNA) sequences, the probe fragments which result from the nicking step (b) may range from mononucleotides to short olignucleotides. Such frag-ments will possess unique 5' phosphate groups which may be advantageously used in their detection. Among such fragments are 5' adenosine monophosphate (5'-AMP) which 25 may be fed into an enzymatic ATP generating system and subsequently linked to a luciferin-luciferase photomet-ric read out system. As an alternative method of de-tection, the generated probe fragments may be detected directly using, for example, high performance liquid chromatography (HPLC).
Those skilled in the art will further appreciate that the methods of the present invention may be employed to obtain a high gain-low noise amplification system for 35 detecting target nucleic acid molecules. The single-stranded nucleic acid probe, whether constructed of ~~ 41495 deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) sequences, or ribonucleic acid (RNA) sequences alone, is completely stable to the action of certain double-s stranded ribonucleases, e.g., RNase H. When such a probe is hybridized to a target nucleic acid molecule, the RNA link, which may or may not be a scissile link-age, becomes susceptible to digestion by the ribo-nuclease, e.g., RNAse H.
Taking as an example for illustrative purposes only, a probe of an overall length of 20 nucleotides of which the first eight and last eight nucleotides are deoxy-ribonucleotides and the intervening four nucleotides are ribonucleotides, the amplifying aspect of the methods of this invention may be explained. A 20 mer, (monomer) probe will form stable hybrids with a com-plementary target whereas an 8 mer (monomer) probe or probe fragment is easily melted off, i.e., becomes unhybridized, under the same conditions. Consequent-ly, the 20 mer probe after hybridization to the target nucleic acid molecule, becomes cleavable and is cleaved by the ribonuclease, e.g., RNase H, resulting in pieces which readily melt off under the identical conditions of the primary hybridization in which the single-stranded nucleic acid probe became hybridized to the target molecule to form the double-stranded target-probe complex.
If hybridization is carried out with a customary excess of probe and in the presence of a suitable ribonu-clease, e.g. , RNase H, the system described above will cycle (see Figure 1) and generate cleaved probe frag-ments, which may be detected using a number of well-~o~ methods, e.g., chemiluminescence, radio-isotopes.
The primary amplifier, i.e., the probe, is nucleic acid 19 1~ 41495 specific and will operate under constant conditions.
High gain-first stage detection of 10 20 moles of target with a radio-isotope label may be obtained.
In a situation where a straight RNA probe made entirely of ribonucleic acid sequences has been constructed, the resulting products after RNase H cycling will range from mononucleosides upwards to oligonucleotides de-pending on the size of the original probe. Each prod-uct, however, will have a 3'-OH terminus. These tenai-ni can be tailed with a suitable polymerise such as polynucleotide phosphorylase or poly A polymerise.
A useful adjunct to this approach is to have a biotin on the 5' terminus of the probe and a chain terminating ~5 nucleotide on the 3' terminus e.g., dideoxy. If the probe was designed so as to have a "U" at the 5' termi-nus and a "U" at the 3' terminus but with no other "U"s contained within the central region and if this probe was made by the action of T7 RNA polymerise on a suit-20 able termplate, the following situation would hold:
No ACG
Probe transcript _5' U(N N N N N N N N)X U 3' 3' T7 Polymerise ANN N N N N N N) A .5' 25 ~i ding ite Restriction Site For Run Off Transcription (optional) 30 If the nucleoside triphosphate precursors for the T7 transcript (probe) polymerization are in the ratio of 35 100 Dideoxy UTP

- 13.41495 1 Biotinylated UTP
then virtually every probe transcript will begin with biotinylated U and end with dideoxy U. Polymerization will fail if a dideoxy U is selected for the first base. Thus a start with biotinylated UTP is mandatory.
Because, with excess template, almost all the biotiny-lated U will be used for starting and because the dideoxy U is 100 times in excess over the biotinylated U, the 3' U will almost always be a dideoxy U. Hence, detection goals may be obtained via an enzymatic syn-thesis. The resulting probe cannot be tailed unless .cut by RNase H because of the 3' dideoxy U and the biotin can be used to separate the probe, which is now ~5 tailed with a fluorescent base or other detectable moiety, from non-biotinylated reactants.
When the nucleic acid probe is constructed entirely of RNA sequences complementary to the target molecule and, 2p therefore, not dependent on the scissile link, various modifications in the probe may be made which are fully contemplated by the invention described herein.
For example, a ribonucleic acid probe, i.e., construct-25 ed entirely of RNA sequences, may be synthesized and its 3' hydroxyl end optionally blocked. Blocking may be effected by enzymatically producing a "tail" to the ribonucleic acid probe by attachment to a ligand, such as biotin, periodate oxidized ribonucleoside or an affinity tail, e.g., poly A (polymerise A) tailing. The "tail" to the probe may be used for affinity isolation and for signal generation. The 5' end of the RNA probe may likewise be optionally modified. For example, the 5' end may be extended with non-homologous RNA/DNA
35 sequences which, in turn, may be attached to a ligand, as described above, e.g., biotin, periodate oxidized ribonucleoside or an affinity tail. In this particular embodiment, the 5' end could instead be linked to a signal generator such as a fluorescent base. This arrangment is shown below:
~ or ~y3-5' RNA robe Non-homologous 3'enzymatically RNA/DNA produced RNA tail (optional) (optional) ~ - atttachment ligand, e.g., biotin, periodate oxi-dized ribonucleoside, or affinity tail.
~ - signal generator such as a fluorescent base The nonhomologous 5' tail in such an arrangment allows the ribonuclease, e.g. , RNase H, to nick, i.e. , excise or chew up, the homologous region of the RNA probe which has paired with the target. Thus the 5' tail arrangement leaves a fragment available for poly-nucleoside phosphate (PNP) or polymerase A (poly A) tailing. Such a tail may be used as an affinity tail to pull the signal out of solution or as a further fragment to enhance detection. This arrangement is depicted below:

Non-homologous 5'sequence X ~ 3' block one or target more detectable elements RNase H
PNP
PNP tails target In another feature of this invention, the cycling nucleic acid probe may be used in immunoassays to de tect antibodies or antigens. In this situation, a nucleic acid sequence, which could be a homopolymer, may be attached to either an antibody or antigen in competing or non-competing immunoassays:
Antibody ucleic Acid for Cycling Probe Target or Antigen Nucleic Acid for Cycling Probe Target An example of a competing immunoassay is the enzyme linked immunoassay (ELISA) This invention is illustrated in the examples which follow. These examples are set forth to aid in the understanding of the invention but are not intended to, and should not be construed to, limit in any way the invention as set forth in the claims which follow thereafter.

CONSTRUCTION OF SCISSILE LINK PROBES
Probe molecules useful in the detection methods of this invention have been constructed on a solid support ~5 medium (either silica gel or controlled pore glass) using either a hydrolysable linkage or a permanent (non-hydrolysable) linkage. Published chemical meth-ods were used for this synthesis. (Alvarado-Urbina, G. , G.M. Sathe, W. C. Liu, M. F. Gillan, P. D. Duck, R.
Bender, and K.K. Ogilvie (1981), Automated Synthesis of Gene Fragments, Science 214: 270-274: Roberts, D.M., R.-Crea, M. Malecha, G. Alvarado-Urbina, R.H. Chiarello, and D.M. Watterson (1985), Chemical Synthesis and Ex-pression of a Calmodulin gene designed for a Site-Spe-25 cific Mutagenesis, Biochemistry, in press: Van Boom, J.H., and C.T. Wreesman (1984), Chemical Synthesis of Small Oligoribonucleotides in Solution, In Oligonucleotide Synthesis--A Practical Approach, pp.
153-183, Ed. M. J. Gait, IRL Press). Standard protect-30 ed deoxynucleoside monomers were obtained from commer-cial sources whereas protected deoxyuridine and the ribonucleoside whereas protected deoxyuridine. and the ribonucleoside monomers were prepared using published procedures. (Ti, G.S., B.L. Gaffney, and R.A. Jones 35 (1982), Transient Protection: Efficient One Flask Syn-thesis of Protected Nucleosides, J. AM. Chem. Soc. 104:

-24- ~ 3 4 1 4 9 5 1316). Synthesis was performed with a BIOLOGICALS
automated synthesizer using a cycle time of 10 minutes for each DNA condensation and 12 minutes for each RNA
condensation.
The following probe constructions were used in various test systems.
SCISSILE LINK PROBES
P. L. - Permanent Linkage to Solid Support H. L. - Hydrolysable Linkage to Solid Support 1. MRC046:

5'd(TTTTTTTTTT)r(UUUUUU)d(TTTTTTTTTTT)3' - P.L.

2. MRC059:

5'd(TTTTTTTTTT)r(WW)d(TTTTTTTTTTTT)3' H.L.
-3. MRC060:

5'd(TTTTTTTTTTTT)R(WW)D(TTTTTTTTTT)3' H.L.
-4. MRC064:

5' d ( TTTTTTTTTTTT ) d ( U~iTUUW W ) 3 ' - H
d ( TTTTTTTTTT ) . L .

5. MRC068:

5' d ( TTTTTTTTTZ"rTTT ) d ( U'W~JW'W
) d ( TTTTTTTTTT ) 3 ' - H . L .

6. MRC069:

5'd(GGGTAACGCCAG)r(GGWW)d(CCCAGTCAC)3' - H.L.

7. MRC070:

5'd(GGGTAACGCCAG)r(GGWW)d(CCCAGTCAC)3' - P.L.

8. MRC071:

5' d ( TTZ"rTTTTTTTTTTT ) r ( W ) d ( - H . L
TTTTTTTTTT ) 3 ' .

Probe molecules 1-3 and 5-8 were shown to be cleavable at the ribonucleotides by a number of RNases including pancreatic RNase as well as by basic conditions (e. g., 0.5 M NaOH). Most general methods for cleavage by RNases and other routine procedures can be found in Maniatis et al. (Maniatis, T., E. F. Fritsch, and J.
Sambrook, (1982), Molecular Cloning, A Laboratory Manu-al, Cold Spring Harbor Laboratory).
cwavnT ~
The following probe constructions* were used in accordance with the methods provided by this invention:

X261 (9)5' G G T T a c c c A G C A C G
C G a T 3' C
A

X268 (10)5' A GC C A G G T T T T C c a g T
C G C C A

C G A C ' #271 (il)5' C GG G T T a a a c a C A C G
A g G A C
T

3' X276 (12)5' T CA A A C A c c c C A A A T T G
A c T 3' #284 (13)5' T GA C T T T c a a C T C T G G T
A g T 3' X286 (14)5' a aa a c a c c c c a a a a a 3' c c a X287 (15)5' C AG g g a T T C c c a G C A 3' C T T

X293 (16)Biotin -5'C a a c C A G
C c T C
A
G
G
G
T
T

A C G 3' X296 ( 5' T TT T T T g g g T T T T T T 3' 17 T g T
) X300 (18)5' T TT T T T c c c T T T T T T 3' T c T

X308 (19)5' T GC T T a a a a T T C G T 3' A a A

#311 (20)5' C GT G C a a a a A G T G G
A c C

#313 (21)5' G CT G C a c c a A G T G A
A a C

#316 (22)5' G TT A A A g c a g C C C A G A 3' T a A

* Upper letters are Lowe r c ase letters case DNA. are RNA. Some above sequences were M-13phage com-of the pleme ntsbut all had synthetic DNA t arget complements const ructed for them.

Kination and Cycling with RNase H.
2~g of the electropurified probes (9-22) were placed in a mixture containing the following:

~.~"

2 ~g probe 2 ~1 4 uM ATP 4 ~1 lOX KB (Kinase buffer) 5 ~1 dA2 0 32 ~1 P3Z ATP 2 ~1 = 20 uCi Polynucleotide Kinase 5 ~1 = 5 units The mixture was incubated at 37°C for 40 minutes and then heat inactivated* The mixture was then passed through a Sephadex G-50 column using deionized water as an eluent. (Use Sanco transfer pipettes 15 mm X 7.5 mm as disposable columns. Plug with siliconized glass wool and pack with G-50 up to 12 mm.) 500 ~1 fractions were collected into 1.5 ml Eppendorf tubes and the first peak was selected (usually tubes 3-5). The selected fractions were dried in a speed vac concentrator. The tubes were pooled together to give a final concentration of 0.1 ~g/~lin sterile water.
Dilution for Cycling Reaction Target: 2 ~g are diluted in 20 ~1 to give a concentra tion of 0.1 ~g/~1. This initial concentration is seri ally diluted 1:10 (10 ~1 in 90 ~1 distilled water) to the desired concentrations. For the cycling reaction, 10 ~1 (100 ng) were used for each reaction.
Labelled Probe: 2~ are diluted in 20 ~1 (0.1 ~g/~1). This initial concentration is diluted 1:10 (10 ~1 in 90 ~1 distilled water) to .O1 ~g/~l. 10 ~1 (100 ng) were used for each reaction.
Cycling Reaction For the cycling reaction, each of the probes(9-22) were separately placed in the following reaction mixture:
* Trademark -27- 1 ~ 4 1 4 9 5 ~l (100 ng) of probe in distilled water(sterile) 3 ~1 lOX RNAse H buffer 7 ~1 distilled water 5 10 ~1 target DNA (1 ~g to .O1 fg) The 30 ~1 reaction mixture was incubated at 65°C for 10 minutes and at 37°C for 30 minutes. From each 30 ~1 reaction mixture, the following were taken:
C1 (RNAse H) control - 5 ~1 = 16.7 ng probe C2 (30 min. time) control -~5 ~1 = 16.7 ng probe To the remaining 20 ~l of reaction mixture, the follow-ing were added with Control C1 above:
1 ~1 RNase H at 0 minutes time ~5 1 ~1 RNase H at 10 minutes time 1 ~l RNase H at 20 minutes time.
The reaction mixture was incubated for 30 minutes.
Each reaction was loaded with the same amount of probe as the control plus an equal amount of formamide dye on 2p a 0.8 mm 20% acrylamide/7 M urea gel at 800 volts with a heating plate.

Claims

1. A method for detecting a single-stranded target nucleic acid which comprises:
(a) obtaining a population of single strand nucleic acid molecules which may contain a single-stranded target nucleic acid;
(b) forming a reaction mixture which includes the target nucleic acid and a complementary single-stranded nucleic acid probe under conditions which allow the target nucleic acid and the probe to hybridize to each other and form a double-stranded, target probe complex, the probe being from 10 to 2,000 nucleotides in length, present in molar excess relative to the target and comprising the structure:

-[-NA1-R-NA2-]n-wherein NA1 and NA2 are nucleic acid sequences, wherein R is a scissile nucleic acid linkage and wherein n is an integer from 1 to 10;
(c) treating the double-stranded, target probe complex from step (b) so as to cleave the probe within a predetermined sequence of the scissile linkage and thereby form at least one intact DNA-containing oligonucleotide fragment from the probe, such fragment being, or being treated so as to be, no longer capable of remaining hybridized to the target nucleic acid;
(d) repeating steps (b) and (c); and (e) detecting the intact DNA-containing fragments so formed and thereby detecting the single-stranded target nucleic acid.

2. The method of claim 1 wherein the oligonucleotide fragment in step (c) is labelled with a detectable marker and labelled fragments are detected in step (e).

3. The method of claim 1 wherein the oligonucleotide fragment in step (c) is unlabelled, but capable of being labelled with a detectable marker, the fragment is so labelled prior to step (d) or (e) , and labelled fragments are detected in step (e).

4. The method of claim 1 wherein the scissile nucleic acid linkage is an RNA sequence.

5. The method of claim 1 wherein NA1 and NA2 are DNA
sequences.

6. The method of claim 1 wherein NA1 and NA2 are RNA
sequences.

7. The method of claim 1 wherein NA1 is either an RNA or DNA sequence, and NA2 is either an RNA or DNA sequence.

8. The method of claim 1 wherein the treating in step (c) comprises contacting the double-stranded target-probe complex with a double-stranded-specific ribonuclease.

9. A method of claim 8, wherein the ribonuclease is RNase H.

10. A method of claim 8, wherein the ribonuclease is Exo III.

11. A method of claim 1, wherein the nucleic acid probe is labelled with a detectable marker.

12. A method of claim 1, wherein the nucleic acid probe is immobilized on a solid support.

13: A method for detecting a single-stranded nucleic acid target sequence which comprises:
(a) obtaining a population of single-stranded nucleic acid molecules which may contain a nucleic acid target sequence;
(b) forming a reaction mixture which includes said population and a single-stranded nucleic acid probe complementary to said target sequence, under conditions which allow said target sequence and said probe to hybridize to each other and form a double-stranded probe-target complex, where said probe is present in molar excess relative to any target sequence in said population and where said probe contains a predetermined sequence which is enzymatically cleavable when said probe is hybridized to said target sequence;
(c) treading said reaction mixture so as to cleave said probe within said predetermined sequence in any probe-target complex present, under conditions where probe fragments resulting from cleavage of said probe no longer remain hybridized to said target sequence;
(d) repeating steps (b) and (c);
(e) detecting any probe fragments, where the presence of fragments indicates the presence of target sequence in said population.

14. A method for detecting a target nucleic acid sequence which comprises:
(a) obtaining a population of single-stranded nucleic acid molecules which may contain a target nucleic acid sequence;
(b) forming a reaction mixture which includes said population and a single stranded nucleic acid probe, under conditions which allow said target sequence and said probe to hybridize to each other to provide a probe: target duplex;
(c) cleaving the probe within the probe:target duplex to release the target sequence intact;
(d) recycling of the target sequence repeatedly through the reaction pathway; and (e) detecting the extent of cleavage of said probe.