Method for confirming positions on which probes are immobilized in nucleic acid array

The present invention provides a method for accurately and easily confirming that nucleic acid probes immobilized on a nucleic acid array are correctly arrayed on predetermined positions.

CROSS-REFERENCE TO PRIOR APPLICATION

This is a U.S. National Phase Application under 35 U.S.C. §371 of International Patent Application No. PCT/JP2006/322063 filed Oct. 30, 2006, and claims the benefit of Japanese Patent Application No. 2005-315190, filed Oct. 28, 2005, both of them are incorporated by reference herein. The International Application was published in Japanese on May 3, 2007 as WO 2007/049827 A1 under PCT Article 21(2).

FIELD OF THE INVENTION

The present invention relates to quality control of a nucleic acid array. Specifically, the present invention relates to a method for confirming types and positions of nucleic acid probes on a nucleic acid array utilizing hybridization reactions of the nucleic acid probes with nucleic acid molecules.

BACKGROUND OF THE INVENTION

A nucleic acid array consists of a carrier on which many nucleic acid probes (hereinafter sometimes referred to as “probes”) are independently immobilized at high density without being mixed. A probe immobilized on a nucleic acid array functions as a sensor for capturing a nucleic acid molecule consisting of a sequence complementary to the nucleotide sequence of the probe by means of hybridization.

Conventionally, a product consisting of a carrier made of surface-treated glass, silicone or the like on which probes are immobilized is utilized as a nucleic acid array. Recently, such carriers have been modified using other techniques such as a gel carrier.

As methods for producing a nucleic acid array, a method in which nucleic acid probes prepared in advance are immobilized on a substrate such as slide glass and silicone, and a method in which nucleic acid probes are directly synthesized on a substrate are known.

For example, according to the optical lithography method in which probes are directly synthesized on a substrate, a nucleic acid array can be prepared by using a substance having a protective group which is selectively removed by light irradiation, combining the photolithography technique with the solid-phase synthesis technique, and by selectively synthesizing (masking) DNA on a predetermined region (reaction site) of a tiny matrix (Science 251, 767-773 (1991)).

A typical example of a method for immobilizing probes prepared in advance is a spotting method (Science 270, 467-470 (1995)). According to this method, drops of a solution comprising probes prepared by PCR or artificial synthesis in advance, which have a tiny volume of several nanoliters (n1) to several picoliters (p1), are arrayed on the surface of a chip using a particular apparatus (a spotter an arrayer), and thereby the probes are immobilized on a specific region of the substrate. In addition to the above-described method, a method for producing a microarray using a hollow-fiber-arranged body has been developed. According to this method, a base having through-holes is produced using a hollow-fiber-arranged body in which a plurality of hollow fibers made of synthetic polymer are regularly arrayed in the direction of the fiber axis. One of the features of this production method is that a lot of microarray products having the same specification can be produced from the same rod by immobilizing probes in the hollow portion of each of the hollow fibers in the hollow-fiber-arranged body and by slicing the hollow-fiber-arranged body in the direction perpendicular to the direction of the fiber axis (Japanese Patent No. 3488456).

In a nucleic acid detection method utilizing a nucleic acid array, nucleic acid samples targeted for a test are sequence-specifically hybridized to probes immobilized on the nucleic acid array, and sequence-specifically formed hybrids are detected using a fluorescent substance or the like. According to this method, nucleic acid molecules comprising nucleotide sequences in the samples, which correspond to a plurality of probes, can be examined quantitatively or qualitatively. Therefore, the method is used for analyzing the expression amount of a plurality of nucleotide sequences or the sequence itself of a specific nucleotide sequence.

Usually, in the above-described nucleic acid detection, a hybridization reaction is caused under appropriate preset conditions, and nucleic acid samples and other unnecessary substances remaining on the surface of the array are removed by washing to detect nucleic acid samples forming specific hybrids with probes. A probe is often designed to be complementary or identical to a nucleotide sequence desired to be detected and used for the purpose of sequence analysis, function analysis or the like. As a probe, a nucleic acid having a relatively long chain such as cDNA or the like, a synthetic oligonucleic acid having a relatively short chain, or the like is used. In the case where a synthetic oligonucleic acid is used as the probe for detecting a nucleic acid of human, mouse or other biological organisms, for which the findings of gene information are accumulated, the nucleotide sequence information thereof is usable. Using such nucleotide sequence information, and in consideration of the homology, function and the like of each of such sequences, the sequence of a synthetic oligonucleic acid is designed. Thus, a probe can be produced.

Such nucleic acid arrays can be provided for gene analysis (gene expression, gene polymorphism and the like), can be utilized for research applications such as the discovery of the mechanism of life phenomenon, diagnosis/therapy of diseases and the like, and are further expected to be applied to industrial applications such as breed classification made by differentiating the gene type and the like. In the meantime, in order to apply such nucleic acid arrays to industrial applications, it is essential to maintain the quality thereof. Therefore, one urgent need is to establish a quality control method for guarantee of quality.

Among quality control items, the most important task is to examine whether or not probes immobilized on a nucleic acid array produced are accurately immobilized on predetermined positions. As an example of a method of the above-described examination, a method, in which a nucleic acid array is immersed in a nucleic acid staining agent such as ethidium bromide to stain a probe or a predetermined position on which a probe is immobilized, is known. According to this method, the presence or absence of the probe on/in the nucleic acid array can be known, but it cannot be examined whether or not the probe is immobilized on the predetermined position. Moreover, when utilizing the stained nucleic acid array as it is for a test or the like, the staining agent is a noise in the detection. Therefore, in order to provide nucleic acid arrays as products, it is necessary to conduct an operation, in which a stain (ethidium bromide) that stains probes or predetermined positions on which probes are immobilized must be completely washed away. This procedure must be performed on a product-by-product basis. Therefore, this is a very complicated procedure.

Moreover, in order to confirm spot positions, it is necessary to prepare labeled nucleic acids, which correspond to all probes immobilized on an array, as complementary chains of the probes, and to conduct a detection operation by means of hybridization on a probe to probe basis. When a large number of probes are immobilized, operations are more complicated and unpractical.

Thus, it is very important to easily confirm “what kind of sequence a probe has and on which position of a nucleic acid array the probe is immobilized” to guarantee the quality of the nucleic acid array.

However, presently almost no operation for confirmation is performed. That is because, as described above, since a nucleic acid array has a lot of probes immobilized on a carrier, operations for confirmation are complicated. Moreover, that is because it is difficult to easily differentiate sequences of probes themselves.

That is, in order to confirm what kind of probe is present on which position of a nucleic acid array once prepared, only the information obtained from the production process of the nucleic acid array can be relied on. It is extremely difficult to determine each position on which each probe is immobilized after the production.

If unexpected probes are immobilized on unexpected positions of a nucleic acid array, with respect to probes whose immobilized positions are wrong, wrong data may be submitted without even noticing. Moreover, particularly in the case where a nucleic acid array in which the types of probes are narrowed is prepared, the level of importance of every probe is higher compared to a nucleic acid array on which a wide variety of probes are immobilized in an all-encompassing manner. Therefore, when statistically treating and interpreting the data of every probe obtained from the entire nucleic acid array, there is a high possibility that it will lead to radically wrong conclusions.

SUMMARY OF THE INVENTION

Therefore, the problem of the present invention is to provide a method for accurately and easily confirming that probes immobilized on a nucleic acid array are correctly arrayed on predetermined positions.

In order to solve the above-described problem, the present inventors made keen examination, focusing on the advantage that, in the case of one type of arrays which can be produced from the identical rod, all the array products obtained from the rod can be confirmed by examining a certain number of the arrays. As a result, it was found that, by giving predetermined pieces of identification information to nucleic acid samples to be hybridized to an array, and by effectively combining signals obtained by hybridization with pieces of identification information obtained from individual probes to apply the combination to the test, the positions of the probes can be confirmed individually. Thus, the present invention was completed.

More specifically, the present invention is as follows:

(1) A method for confirming immobilization conditions of nucleic acid probes immobilized on a nucleic acid array, comprising the steps of:

(a) defining the number of zones to which the nucleic acid probes immobilized on the nucleic acid array belong and one or more given pieces of identification information;

(b) calculating X using the following formula:
X={log(N+1)M}+1
(wherein N represents the number of the pieces of identification information, and M represents the number of the zones to which the nucleic acid probes immobilized on the nucleic acid array belong),
defining a number of the integer portion of X as the number of nucleic acid arrays required for confirming the immobilization conditions, Xa, and allocating non-overlapping numerical values (Y), which are expressed by notation system of base N+1, and which have the same digit number as Xa, to the respective nucleic acid probes belonging to the zones;
(c) preparing complementary nucleic acid molecules comprising nucleotide sequences complementary to all or a part of nucleotide sequences of the nucleic acid probes, preparing groups of nucleic acid samples corresponding to the number of nucleic acid arrays (Xa) by mixing the complementary nucleic acid molecules based on the number of every digit of each of the allocated numerical values (Y), and preparing nucleic acid arrays (the number: Xa);
(d) contacting each of the nucleic acid arrays (the number: Xa) prepared in the step (c) with the corresponding group of the nucleic acid samples to detect signals derived from hybrids between the nucleic acid probes immobilized on the nucleic acid arrays and the complementary nucleic acid molecules; and
(e) matching patterns of expression of the signals detected to patterns of the numerical values (Y) allocated.

In the present invention, examples of the immobilization conditions of the nucleic acid probes include those related to types and/or positions of the nucleic acid probes. The identification information is, for example, at least one selected from the group consisting of: a presence or an absence of a signal; the strength of the signal; and the type of labeling. In the present invention, patterns of expression of the detected signals can be quantified by notation system of base N+1 based on the above-described identification information.

(2) A method for examining a quality of a nucleic acid array, wherein the quality of the nucleic acid array is examined based on results obtained according to the method described in item (1) above.

According to the present invention, a method for confirming types and positions of individual nucleic acid probes immobilized on the nucleic acid arrays by hybridization between the nucleic acid probes and nucleic acids comprising their complementary sequences is provided.

To confirm whether or not individual probes on a nucleic acid array are arrayed on predetermined positions is the most important examination item in terms of the quality control of DNA microarrays. According to the present invention, the positions on which the probes are arrayed can be accurately and easily examined. Therefore, conventionally-used complicated examination steps are no longer required.

EXPLANATIONS OF LETTERS OR NUMERALS

DETAILED DESCRIPTION OF THE INVENTION

Hereinafter, the present invention will be described in detail. The documents, laid-open publications, patents and other patent documents cited in this specification are incorporated herein by reference.

The present invention relates to a method for confirming immobilization conditions of nucleic acid probes immobilized on a nucleic acid array, comprising the steps of:

(a) defining the number of zones to which the nucleic acid probes immobilized on the nucleic acid array belong and one or more given pieces of identification information;

(b) calculating X using the following formula:
X={log(N+1)M}+1
(wherein N represents the number of the pieces of identification information, and M represents the number of the zones to which the nucleic acid probes immobilized on the nucleic acid array belong),
defining a number of the integer portion of X as the number of nucleic acid arrays required for confirming the immobilization conditions, Xa, and allocating non-overlapping numerical values (Y), which are expressed by notation system of base N+1, and which have the same digit number as Xa, to the respective nucleic acid probes belonging to the zones;
(c) preparing complementary nucleic acid molecules comprising nucleotide sequences complementary to all or a part of nucleotide sequences of the nucleic acid probes, preparing groups of nucleic acid samples corresponding to the number of nucleic acid arrays (Xa) by mixing the complementary nucleic acid molecules based on the number of every digit of each of the allocated numerical values (Y), and preparing nucleic acid arrays (the number: Xa);
(d) contacting each of the nucleic acid arrays (the number: Xa) prepared in the step (c) with the corresponding group of the nucleic acid samples to detect signals derived from hybrids between the nucleic acid probes immobilized on the nucleic acid arrays and the complementary nucleic acid molecules; and
(e) matching patterns of expression of the signals detected to patterns of the numerical values (Y) allocated.
1. Method for Confirming Types and Positions of Nucleic Acid Probes

In a general method of using a nucleic acid array, firstly, a sample whose sequence is unknown is hybridized to a nucleic acid probe having a predetermined sequence. If a nucleic acid molecule having a nucleotide sequence complementary to the nucleotide sequence of the nucleic acid probe is present in the sample, a hybrid is formed between the nucleic acid probe and the nucleic acid molecule.

Next, by quantifying or qualifying the hybrid formation using a signal derived from a substance by which the sample is labeled in advance (e.g., fluorescence, chemiluminescence, radioisotope, etc.), the presence of the complementary nucleic acid molecule corresponding to the pertinent nucleic acid probe can be confirmed.

Further, by utilizing the above-described method, the arrangement of a probe immobilized on a nucleic acid array can also be examined. By using a nucleic acid molecule complementary to the probe as a sample, the position of the probe to be present on the nucleic acid array can be identified by means of hybridization.

As described above, in order to confirm on which portion of a nucleic acid array a specific nucleic acid probe is immobilized, a sample comprising a nucleic acid molecule having a nucleotide sequence complementary to the nucleic acid probe (complementary nucleic acid molecule) is hybridized to the nucleic acid array, and a hybrid formed between the nucleic acid probe and the complementary nucleic acid molecule is detected by a signal sent from a labeling substance (e.g., a fluorescent substance, an enzyme, etc.) by which the complementary nucleic acid molecule is labeled. For example, in the case of a nucleic acid array in which nucleic acid probes with 5 different nucleotide sequences are independently immobilized on a substrate, in order to examine the presence or absence of the 5 nucleic acid probes and the positions on which they are present, each of nucleic acid molecules complementary to the respective nucleic acid probes (complementary nucleic acid molecules) is hybridized to each of nucleic acid arrays, and signals derived from hybridization are read, and thereby the relative positions of the nucleic acid probes and nucleotide sequences of the nucleic acid probes immobilized on the positions can be identified.

In this case, the required number of the nucleic acid arrays to be used is 5, corresponding to the number of the nucleic acid probes. Further, if signals, by which 5 types of complementary nucleic acid molecules corresponding to 5 types of nucleic acid probes can be recognized independently (e.g., 5 types of fluorescent substances having different wavelength), can be read, by hybridizing 5 types of the complementary nucleic acid molecules to one nucleic acid array, the relative positions of the nucleic acid probes immobilized and the nucleotide sequences of the nucleic acid probes immobilized on the positions can be confirmed independently.

However, many types of probes are immobilized on a nucleic acid array. At least several tens to several hundreds of types of nucleic acid probes are immobilized. In such a case, it is extremely complicated to confirm the position of each of the nucleic acid probes immobilized by preparing complementary nucleic acid molecules whose number corresponds to the number of the nucleic acid probes and using nucleic acid arrays whose number is the same as that of the immobilized probes. Moreover, such a process cannot be substantially practiced since the number of nucleic acid arrays to be used is excessive. Under present circumstances, it is difficult to provide signal molecules, by which several tens to several hundreds of types of probes can be independently recognized, to respective complementary nucleic acid molecules.

According to the present invention, in order to efficiently identify the positions of nucleic acid probes immobilized, (groups of) complementary nucleic acid samples prepared following definite laws are hybridized to a nucleic acid array, and signals obtained therefrom are matched to the presence or absence of complementary nucleic acid molecules in the nucleic acid samples or the type of labeling.

In this regard, the term “complementary nucleic acid sample” (also referred to as “nucleic acid sample”) refers to a sample which comprises a molecule comprising a nucleotide sequence complementary to at least a part of a nucleotide sequence of a nucleic acid probe (complementary nucleic acid molecule) following definite laws. The population of a plurality of complementary nucleic acid samples is referred to as “the group of complementary nucleic acid samples” (also referred to as “the group of nucleic acid samples”). It is preferred to prepare nucleic acid samples as many as nucleic acid arrays to be used for confirmation. The phrase “prepared following definite laws” means that a nucleic acid sample included in a complementary nucleic acid sample is prepared so that respective probes show different patterns at the time of hybridization detection depending on the type of labeling or the presence or absence of the nucleic acid sample. The detailed method will be exemplified below.

(1) Definition of the Number of Zones to which Nucleic Acid Probes Immobilized on a Nucleic Acid Array Belong and One or More Given Pieces of Identification Information

Nucleic acid probes immobilized on a nucleic acid array are positioned within certain zones. Therefore, the number of zones on which nucleic acid probes are immobilized means the number of the nucleic acid probes (the number of the types of probes). In the present invention, the above-described number of zones is defined as the number of probes. However, the number of zones on which probes are not immobilized can be included in the number of probes, for example, as negative control. “The number of probes” does not mean the number of respective probes included in zones, but refers to the number of populations of probes in zones.

When preparing (groups of) complementary nucleic acid samples, sequence information, concentration, the type of labeling and the like of complementary nucleic acid molecules constituting the (groups of) samples are recorded in advance. These pieces of information are used as pieces of “identification information” for evaluating conditions of hybrids formed between probes and complementary nucleic acid molecules after hybridization. Further, complementary nucleic acid molecules, nucleic acid samples and groups of nucleic acid samples are identified (defined) by number allocation or the like. For example, the presence or absence of a certain nucleic acid sample in a group of nucleic acid samples is represented by a piece of identification information, “the presence or absence of hybridization signal”, at the time of detection after hybridization. Further, when using a group of nucleic acid samples including nucleic acid samples labeled with different types of labels (for example, Cy3 and Cy5), “the type of hybridization signal” is utilized as a piece of identification information in the sense that the difference between labels can be distinguished. Moreover, change in the concentration of nucleic acid sample can also be employed as identification information from the viewpoint of “the strength of hybridization signal”. Thus, pieces of identification information are used as parameters indicating differences in information obtained after hybridization and causes thereof.

Specifically, when a probe A is immobilized on a nucleic acid array, at the time of putting its complementary chain A′ into respective complementary nucleic acid samples of a group of complementary nucleic acid samples, already-known pieces of information such as “whether or not A′ is put”, “the type of label applied to A′” and “the amount of A′ put” can be identified by pieces of information obtained after hybridization such as “whether or not signal was obtained”, “the type of fluorescence obtained” and “the degree of signal obtained”. Therefore, conditions of input of the complementary nucleic acid molecule A′ into respective complementary nucleic acid samples can be easily judged based on results of hybridization.

The number of arrays required for confirming immobilized nucleic acid probes is determined by the number of types of nucleic acid probes and the number of pieces of identification information. When confirming positions of nucleic acid probes immobilized on a nucleic acid array, the more pieces of identification information, the smaller the number of complementary nucleic acid samples to be prepared. Therefore, the number of nucleic acid arrays to be used can be reduced, and as a result, confirmation can be efficiently made.

(2) Calculation of the Number of Nucleic Acid Arrays Required for Confirmation of Immobilization Conditions and Allocation of Numerical Values to Nucleic Acid Probes

When confirming positions of all nucleic acid probes immobilized on a nucleic acid array, the number of pieces of identification information required, the number of arrays to be used and the number of complementary nucleic acid samples are represented by conditions satisfying the following formula:
M≦(N+1)x−1

M: the number of types of nucleic acid probes;

N: the number of pieces of identification information; and

X: the number of arrays to be used.

The equality portion of the above-described formula can be represented by the following formula:
X={log(N+1)M}+1
(wherein N represents the number of the pieces of identification information, and M represents the number of the zones to which the nucleic acid probes immobilized on the nucleic acid array belong), and X can be calculated using this formula. The calculated X is represented by a number of the integer portion and a number of the fractional portion. In the present invention, the number of the integer portion of X is defined as the number of nucleic acid arrays required for confirmation of immobilization conditions (Xa).

For example, when judging a nucleic acid array, wherein the number of probes (M) is 250 and the number of pieces of identification information is 1 (the presence or absence of signal), since the number of pieces of identification information by which hybridization can be confirmed is 1 (N=1), X=log2250+1=8.9657 . . . . Since the integer portion of X is “8”, the number of arrays required for confirmation (Xa) is 8. By using 8 arrays (Xa=8), the relative positions of all the probes immobilized on the array can be confirmed.

Further, in another embodiment of the present invention, when judgment is made using the following pieces of identification information: 2 types of fluorescence (Cy3 and Cy5); and 2 concentrations of complementary nucleic acid molecule, the number of pieces of identification information by which hybridization can be confirmed is 4 (N=4). Therefore, by using 4 arrays (Xa=4), the relative positions of all the probes immobilized on the array can be confirmed.

Hereinafter, an embodiment of the present invention in which a nucleic acid array on which 24 types of nucleic acid probes are immobilized is examined by the presence or absence of fluorescence signal will be considered.

Since the presence or absence of fluorescence signal can be confirmed by one fluorescent label, the number of pieces of identification information (N) is 1. When this number and the number of the probes (M) are applied to the above-described formula, the number of arrays required for confirmation is 5.

Complementary nucleic acid samples, which are to be hybridized to 5 arrays, respectively, are designated as Sample A, Sample B, Sample C, Sample D and Sample E, respectively. Non-overlapping numerical values (Y), which are represented by notation system of base N+1, and which have the same digit number as Xa(Samples A to E=5 types of samples, that is, 5-digit), are allocated to the respective nucleic acid probes belonging to the aforementioned zones. In the above-described example, Xa=5, and N+1=2, and therefore, numerical values (Y), which are allocated to probes 1 to 24 in Table 1, can be represented by 5-digit numbers in binary notation, using “1” and “0” as shown in columns A-E therein. In columns of samples A-E, “1” indicates that a fluorescently-labeled complementary nucleic acid is included, and “0” indicates that no complementary nucleic acid is included.

As shown in Table 1, the numerical value allocated to probe 1 (designated as Y1) is “10000”, and the numerical value allocated to probe 2 (designated as Y2) is “10001”. Numerical values allocated to probes 1-24 do not overlap each other and are different.

(3) Preparation of Groups of Complementary Nucleic Acid Samples and Preparation of Arrays for Hybridization

In this step: complementary nucleic acid molecules comprising a nucleotide sequence complementary to all or a part of nucleotide sequences of the aforementioned nucleic acid probes are prepared; complementary nucleic acid molecules are mixed based on each numerical value in 5 digits of the allocated numerical values (Y) to prepare groups of nucleic acid samples whose number corresponds to the number of nucleic acid arrays (Xa); and the nucleic acid arrays (the number thereof: Xa) are prepared.

After allocating the above-described numerical values (Y), groups of complementary nucleic acid samples to be independently hybridized to 5 arrays are prepared and designated as samples A, B, C, D and E (Table 1). Nucleic acids can be synthesized using a chemical synthesis apparatus based on sequence information of probes.

Each sample is a mixture obtained by mixing complementary chains of probes, to which the numerical value “1” is allocated. For example, sample A includes complementary chains corresponding to probes 1-16, and sample B includes complementary chains corresponding to probes 9-24. “Complementary chains” are not required to be complementary to all nucleic acid probes, and may be complementary to a part of them.

When complementary nucleic acid molecules are labeled to give identification information, such complementary nucleic acid molecules are confirmed with single labeling, or they are independently detected with single labeling, and it is required that differences can be confirmed simultaneously or with time intervals at the time of detection. That is, regarding labeling, there is a case where single labeling is conducted and confirmation is made by one detection, and there is a case where single labeling is conducted but complementary nucleic acid molecules are independently confirmed by a plurality of detections. Specifically, the following cases are included:

(i) the case where difference in labels is confirmed simultaneously at the time of detection (e.g., combination of Cy3 and Cy5, etc.); and

(ii) the case where difference in labels is confirmed with time intervals at the time of detection (e.g., the case where using an identical labeling substance, detection is performed with direct labeling, and thereafter detection is performed with indirect labeling).

In the case of item (2) above, detection can be performed using the combination of Cy5 direct labeling and biotin direct labeling-streptavidin-Cy5 indirect labeling.

The above-described method of “labeling” is not particularly limited as long as hybridization of nucleic acid can be detected. Examples of labeling substances to be used for labeling include: fluorescent substances such as Cy3, Cy5, Alexa Fluor® and the like; enzymes or proteins for utilizing chemiluminescence associated with substrate degradation using alkaline phosphatase, horseradish peroxidase or the like; and radioisotopes such as γ-32P, α-32P, etc. From the viewpoint of convenience, use of fluorescent substances is preferable.

When these labeling substances are introduced into complementary nucleic acid molecules, any method (associated with direct, indirect, physical, or chemical binding) can be used as long as it is stable and does not inhibit specific hybridization to probe nucleic acids. Examples of methods of chemical modification include a method, in which an analog base modified by biotin or an aminoaryl group is introduced at the time of reaction, and a labeling substance is introduced via the modified analog base. Moreover, a method for intercalating a labeling substance into a complementary nucleic acid molecule using SYBR® Green, acridine orange, SYBR® Gold or the like, a method for binding a labeling substance such as ULYSIS to a complementary nucleic acid molecule via platinum and the like can also be employed.

However, preparation of many complementary nucleic acid molecules labeled with a labeling molecule may lead to high costs. In order to avoid this, aside from a portion of each complementary nucleic acid molecule complementary to a corresponding nucleic acid probe, a common nucleotide sequence (tag) is added to the 3′- or 5′-terminus of each complementary nucleic acid molecule, and then, a labeled nucleic acid molecule complementary to the tag sequence can be used. In this case, any labeling method can be employed as long as signals can be independently detected. Moreover, a plurality of types of tag sequences themselves can also be used.

(4) Hybridization and Signal Detection

In this step, each of the nucleic acid arrays (the number thereof: Xa) prepared as described above is contacted with the aforementioned corresponding group of the nucleic acid samples, and signals derived from hybrids between the nucleic acid probes immobilized on the nucleic acid array and the aforementioned complementary nucleic acid molecules are detected.

When contact of probes with complementary nucleic acids (hybridization) is performed by adding the samples A-E to the nucleic acid arrays A-E, respectively, in the case of the nucleic acid array A, fluorescence signal is detected with respect to the probes 1-16, and in the case of the nucleic acid array B, fluorescence signal is detected with respect to the probes 9-24. Similarly, in the cases of the nucleic acid arrays C-E, fluorescence signal is detected with respect to probes to which the numerical value “1” is allocated.

(5) Matching of Expression Patterns of Detected Signals to Patterns of Allocated Numerical Values (Y)

According to the above-described method, by matching the combination of complementary nucleic acid molecules included in the complementary nucleic acid sample, position information of probes at each position of the nucleic acid array and signals actually obtained by hybridization to identification information, it can be confirmed to which position on the nucleic acid array each nucleic acid probe corresponding to each complementary nucleic acid sample is spotted.

When detection results of each nucleic acid array are examined with respect to each complementary nucleic acid, for example, in the case of the complementary nucleic acid corresponding to probe 1 in Table 1, since it is included only in nucleic acid sample A, the combination of pieces of identification information among nucleic acid samples A-E (the numerical value Y1) is “10000”. Further, in the case of the complementary nucleic acid corresponding to probe 16, since it is included in all the nucleic acid samples A-E, the combination of pieces of identification information among nucleic acid samples A-E is “11111”. Each complementary nucleic acid has a different combination of pieces of identification information. Therefore, when the pattern of numerical value allocated to each of the probes is matched to the pattern of detection result, and the obtained detection result corresponds to the combination, i.e., the pattern of value Y, it can be judged that the type and the position of the nucleic acid probe immobilized on the nucleic acid array are correct.

For example, when the presence of signal is represented by “+” and the absence of signal is represented by “−”, and given that the results “+, −, −, −, −” were obtained in the order of samples A-E as detection results of probe 1, the detection results correspond to Y1=“10000”. The above-described detection results (“+” and “−”) can be represented by numerical values. When the detection results are represented by “1” and “0” (binary notation), the detection results correspond to the allocated numerical value Y1(“10000”). Therefore, it can be judged that the nucleic acid is immobilized on the correct position.

Next, an embodiment, in which a nucleic acid array on which 24 types of nucleic acid probes are immobilized is examined with 3 types of fluorescence signals, will be considered. Since 3 types of fluorescent labels are used, the number of pieces of identification information (N) is 3. When this number and the number of the probes (M) are applied to the above-described formula, the number of arrays required for confirmation (Xa) is 3.

Complementary nucleic acid samples, which are to be hybridized to 3 arrays, respectively, are prepared and designated as Sample A, Sample B and Sample C, respectively (Table 2). As pieces of identification information, “0” represents a green fluorescent label, “1” represents a yellow fluorescent label, and “2” represents a red fluorescent label. “0”, “1” or “2” is applied to column of Samples A-C in Table 2.

In this case, since Xa=3 and N+1=3, numerical values (Y), which are allocated to probes 1 to 24 in Table 2, can be represented by 3-digit numbers in ternary notation, using “0”, “1” and “0” as shown in columns A-C therein.

When detection results of each nucleic acid array are examined with respect to each complementary nucleic acid, for example, in the case of the complementary nucleic acid corresponding to probe 1, since all the nucleic acid samples A-C are labeled with the green fluorescent label, the combination of pieces of identification information among the nucleic acid samples A-C is “000”. In the case of the complementary nucleic acid corresponding to probe 6, the combination of pieces of identification information among the nucleic acid samples A-C is “012”. Each complementary nucleic acid has a different combination of pieces of identification information. Therefore, if detection results associated with the pieces of identification information corresponded to the combination, it can be judged that the type and the position of the nucleic acid probe immobilized on the nucleic acid array are correct.

2. Method for Examining Quality of Nucleic Acid Array

Based on the above-described method, one rod of the nucleic acid array is examined before shipment of the nucleic acid array, and it can be utilized as one of the quality control standard thereof.

Nucleic acid arrays to be used for quality examination for confirmation of positions of probes immobilized are desirably prepared from nucleic acid arrays mass-produced from the same rod. In the present method, any nucleic acid array is applicable, but a nucleic acid microarray, which can be produced in a manner in which respective probe spot positions are not physically mixed, is preferred. Such a nucleic acid microarray can be obtained by immobilizing probes to hollow fibers or the like, bundling them together and slicing the bundle. Immobilization of probes to hollow fibers can be evenly performed. Therefore, when determining immobilization positions of nucleic acid probes using microarrays obtained by slicing as described above, examination of the microarrays from the same rod can be conducted with high accuracy and without variation of quality.

Further, when a plurality of nucleic acid arrays cannot be used for confirmation of immobilization positions of probes, a nucleic acid array, which was used for hybridization once, can be reutilized. Specifically, after hybridization, hybrids between nucleic acid probes and complementary nucleic acid samples are dissociated from each other. Hybrids can be dissociated by immersing the nucleic acid array in water or the like and heating it to a given temperature or higher. The dissociated nucleic acid array can be reutilized depending on the immobilization conditions of probes or conditions of remaining signals. In the case of nucleic acid arrays prepared on a dried substrate, reutilization is often not recommended. However, in the case of nucleic acid arrays utilized in the state of constant moistness, since hybrids can be easily dissociated and it is more difficult to remove immobilized probes compared to the case of dried substrates, there is no particular false recognition with respect to, for example, just a piece of identification information regarding the presence or absence of signals.

EXAMPLES

Hereinafter, the present invention will be described in more detail with reference to working examples. The present invention, however, is not limited to the examples described below.

Preparation of Nucleic Acid Array

Synthesis of Nucleic Acid Probes

In order to prepare a nucleic acid array, oligo DNAs set forth in SEQ ID NOs: 1-192 in Table 3 below were synthesized.

A hollow-fiber bundle was produced utilizing an arrangement fixing tool shown inFIG. 1. InFIG. 1, x, y and z are axes which are at right angles to one another and constitute three-dimensional coordinate. The direction of axis x corresponds to the longitudinal direction of fibers.

Firstly, 2 porous plates (21) having the thickness of 0.1 mm, in which 228 pores (11) (12 vertical rows×19 horizontal rows) having the diameter of 0.32 mm were provided with the center-to-center spacing of the pores of 0.42 mm, were prepared. These porous plates were overlapped with each other, and through each of the pores, one hollow fiber (31) made of polycarbonate (manufactured by Mitsubishi Engineering-Plastics Corporation; 1% by mass of carbon black was added) was passed.

The positions of 2 porous plates were moved under the conditions where 0.1 N of tensile force was applied to each fiber in the direction of axis X, and the porous plates were fixed to the positions at 20 mm and 100 mm from one end portion of the hollow fibers, respectively. That is, the distance between the porous plates was 80 mm.

Next, three faces surrounding the open space between the porous plates were surrounded by plate-like bodies (41). Thus, a container with only the upper side thereof being open was obtained.

Next, a resign material was poured into the container from the upper side thereof. The resin used was prepared by adding 2.5% by mass of carbon black to the total weight of polyurethane resin adhesive (Nippon Polyurethane Industry, Co., Ltd., NIPPOLAN 4276, CORONATE 4403). The resin was cured by being allowed to stand at 25° C. for one week. After that, the porous plates and the plate-like bodies were removed to obtain a hollow-fiber bundle.

Next, gel precursor polymerizable solutions comprising a monomer and an initiator mixed in the mass ratio shown in Table 4 were prepared for respective nucleic acid probes to be immobilized on the array.

Next, containers containing the gel precursor polymerizable solutions and the hollow-fiber bundle prepared above were placed in a desiccator in order to fill hollow portions of the hollow fibers of the bundle corresponding to the positions shown inFIG. 2with the respective gel precursor polymerizable solutions comprising the respective nucleic acid probes as prepared above. After the pressure in the desiccator was reduced, the end portion of the hollow-fiber bundle in which each fiber is not sealed was immersed in the predetermined gel precursor polymerizable solutions in the containers. The desiccator was filled with nitrogen gas, and the gel precursor polymerizable solutions comprising capture probes were introduced into the hollow portions of the hollow fibers. Next, the container was heated to 70° C. to perform polymerization reaction for 3 hours.

In this way, the hollow-fiber bundle, in which the nucleic acid probes were held in the hollow portions of the hollow fibers via the gel-like material, was obtained.

Next, the obtained hollow-fiber bundle was sliced in the direction perpendicular to the longitudinal direction of the fibers using a microtome to obtain 300 thin sheets (nucleic acid arrays) having the thickness of 0.25 mm.

The nucleic acid arrays were prepared to have probe positions shown inFIG. 2. InFIG. 2, the numbers represent SEQ ID NOs of probes, and probes having nucleotide sequences set forth in respective SEQ ID NOs are arrayed on the nucleic acid arrays. B represents a spot where no nucleic acid probe is present.

Preparation of Groups of Nucleic Acid Samples for Identification of Immobilization Positions of Nucleic Acid Probes

Nucleic acid samples (oligo DNAs) for identification of probe positions on the nucleic acid array prepared above were prepared as follows. These nucleic acid samples comprise a portion complementary to a part of 3′ terminal side of each corresponding probe, and 5′ terminal side of the nucleic acid samples comprises a nucleotide sequence consisting of the GT repeat sequence, which is complementary to SEQ ID NO: 385. SEQ ID NO: 385 was prepared with oligo DNA whose 5′ terminal side is Cy5-labeled in the concentration of 100 pmol/μl.

Regarding the correspondence relationship between the probe sequences and the sequences of the nucleic acid samples for confirmation of probe immobilization positions comprising complementary chains thereof, SEQ ID NOs: 1, 2, . . . and 192 correspond to SEQ ID NOs: 193, 194, . . . and 384, respectively (Tables 3 and 5). A part of each sequence in the table of probes above is complementary to a part of each corresponding sequence in Table 5. Each analyte has a sequence which forms a double strand with a corresponding sequence of a probe. For example, a sequence represented by small letters in the nucleotide sequence of SEQ ID NO: 193 in Table 5 is complementary to the underlined part of the nucleotide sequence set forth in SEQ ID NO: 1 in Table 3 (positions 33-65 of the sequence), and can form a double strand therewith.

These nucleic acid samples were mixed according to Table 6 to prepare 8 samples for identification of probe positions.

In Table 6, “1” means that a complementary nucleic acid having a nucleotide sequence represented by SEQ ID NO: described in the leftmost column in Table 6 is included in a sample. “0” means that a complementary nucleic acid having a nucleotide sequence represented by SEQ ID NO: described in the leftmost column in Table 6 is not included in a sample. Samples 1-8 were prepared by mixing each model analyte indicated by SEQ ID NO: shown as “1” in an amount of 500 pmol/5 μl, and adding pure water so that the final liquid volume was adjusted to 500 μl. That is, Samples 1-8 were prepared so that the concentration of each of the model analytes contained was adjusted to 1 pmol/μl. Further, patterns of the presence/absence of input of all the analytes represented by SEQ ID NOs: 193-384 in Samples 1-8 were different from each other.

0.2 μl (20 pmol) of Cy5-labeled analyte represented by SEQ ID NO: 385 was added to 0.2 μl of each of 8 samples prepared according to the above table (0.2 pmol each), and hybridization was performed under the following conditions. One hybridization reaction was performed for each nucleic acid array, i.e., a hybridization was performed 8 times.

The nucleic acid samples prepared above were contacted with the nucleic acid arrays prepared above, and hybridization was conducted in a temperature-controlled bath at 65° C. for 1 hour.

After hybridization, washing was conducted using a mixed solution of 2×SSC and 0.2% SDS and 2×SSC, and subsequently detection was conducted. In the detection operation: a cooled CCD camera-type automatic detection apparatus for nucleic acid array was used; arrays were immersed in 2×SSC; a cover glass was applied thereto; and subsequently the fluorescence signal strength of labeled nucleic acid sample molecules was measured.

Results

Images of detection of Samples 1-8 are shown inFIG. 3. In the case where the types and immobilization positions of the nucleic acid probes are confirmed based on the results inFIG. 3, for example, ON/OFF of signal from the position identified by column (R)=1 and row (C)=2 (SEQ ID NO: 96) inFIG. 2is expressed as “OFF, ON, ON, OFF, OFF, OFF, OFF, OFF” in the order of Samples 1-8. In Table 6, only SEQ ID NO: 288, which is an analyte corresponding to SEQ ID NO: 96, has this combination of ON and OFF. Therefore, it was confirmed that on the position identified by R=1 and C=2, a nucleic acid probe, which has a sequence complementary to SEQ ID NO: 288, i.e., a nucleic acid probe set forth in SEQ ID NO: 96, is surely immobilized. Similarly, ONs/OFFs of signals from the positions of respective nucleic acid probes obtained this time were compared and the results are described in Table 7. In Table 7, “Presence or absence of analyte input (predetermined)” is expressed by numerical values allocated to probes set forth in respective SEQ ID NOs. “0” means that a complementary nucleic acid with respect to a corresponding probe is not included, and “1” means that a complementary nucleic acid with respect to a corresponding probe is included. Regarding ON/OFF of signal, when the ratio of S/N is 5 or higher, it is defined as ON, and when the ratio is less than 5, it is defined as OFF. “ON” and “OFF” in Table 7 can be replaced by “1” and “0” in binary notation, respectively.

Patterns of signals for all the nucleic acid probes immobilized on the array are different from each other. Further, patterns of signals expected from the complementary nucleic acid molecules included in Samples 1-8 corresponded to the actual patterns of signals. Accordingly, it was confirmed that these nucleic acid probes are present on predetermined positions. It became clear that immobilization positions of nucleic acid probes can be confirmed by using this technique.

Sequence Listing Free Text

SEQ ID NOs: 1-385: synthetic DNA

INDUSTRIAL APPLICABILITY

According to the present invention, a method for confirming the types and positions of respective nucleic acid probes immobilized on a nucleic acid array by means of hybridization between the nucleic acid probes and nucleic acids comprising a complementary sequence thereof is provided.

To confirm whether or not individual probes on a nucleic acid array are arrayed on predetermined positions is the most important examination item in terms of the quality control of DNA microarrays. According to the present invention, the positions on which the probes are arrayed can be accurately and easily examined.