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  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6813—Hybridisation assays
  • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6869—Methods for sequencing

Definitions

• the present invention relates to a method for sequence-specific labeling and simultaneous sequencing of nucleic acids, comprising the generation of labeled nucleic acid fragments by an enzymatic labeling reaction. in which a labeled deoxyribonucleoside triphosphate is added to a nucleic acid primer molecule and the determination of the nucleic acid sequence via the label.
• DNA sequencing using the Sanger enzymatic chain termination method starting from a nucleic acid matrix, many differently long labeled nucleic acid fragments are produced by an enzymatic extension and termination reaction, in which a synthetic oligonucleotide primer using polymerase and a mixture of deoxyribonucleoside triphosphates (dNTP) and chain termination molecules, in particular dideoxyribonucleoside triphosphates (ddNTP) is extended and terminated.
• dNTP deoxyribonucleoside triphosphates
• ddNTP dideoxyribonucleoside triphosphates
• a mixture of the deoxyribonucleoside triphosphates (dNTPs) and one dideoxyribonucleoside triphosphate (ddNTP) is usually used in four batches.
• dNTPs deoxyribonucleoside triphosphates
• ddNTP dideoxyribonucleoside triphosphate
• DNA sequencing is carried out with automated systems in which a non-radioactive label, in particular a fluorescent label, is usually used (LM Smith et al., Nature 321 (1986), 674-679; W. Ansorge et al, J Biochem. Biophys. Meth. 13: 315-323 (1986).
• LM Smith et al. Nature 321 (1986), 674-679; W. Ansorge et al, J Biochem. Biophys. Meth. 13: 315-323 (1986).
• the nucleotide sequence is read directly during the separation of the labeled fragments and entered directly into a computer.
• non-radioactive labeling groups can be introduced either via labeled primer molecules, labeled chain termination molecules or as internal labeling via labeled dNTP.
• the sequencing reactions are each carried out individually in a reaction vessel, so that only a single sequence is obtained with a sequencing reaction.
• the object of the present invention was therefore to provide a method for sequence-specific labeling and sequencing of nucleic acids, in which the disadvantages of the prior art are at least partially eliminated.
• the method according to the invention is intended to enable two or more sequencing reactions to be carried out simultaneously in a single reaction vessel using at least two differently labeled dNTP and at least two, preferably unlabeled, primer molecules.
• the object of the invention is achieved by a method for the sequence-specific labeling of nucleic acids, comprising the generation of labeled nucleic acid fragments by an enzymatic labeling reaction, in which a labeled deoxyribonucleoside triphosphate is added to a nucleic acid primer molecule and the determination of the nucleic acid sequence by means of the labeling, the method being characterized thereby that the labeling reaction molecules in a single reaction vessel in the presence of one or more nucleic acid primers and labeled at least two Deoxyribonucleoside triphosphates, each containing different labeling groups and different bases, and under conditions in which only a single type of labeled deoxyribonucleoside triphosphates is added to a nucleic acid primer molecule.
• the nucleic acid primer molecule is a nucleic acid, preferably a DNA, which is sufficiently complementary to a nucleic acid in the reaction mixture to initiate a hybridization reaction under the respective reaction conditions.
• the length of the primer molecule is preferably 10-100, more preferably 12-50 and most preferably 12-30 nucleotides.
• the enzymatic labeling reaction is carried out in the process according to the invention in such a way that only one type of labeled dNTPs and preferably only one type of labeled dNTPs and preferably only one labeled dNTP are added to each nucleic acid primer molecule.
• the labeled dNTP is preferably added directly to the 3 'end of the primer (position +1).
• the base of the labeled dNTP is complementary to that base which is arranged on the nucleic acid hybridizing with the primer molecule directly on the 5 'side of the region complementary to the primer.
• the marking can also be installed at a greater distance from the 3 'end of the primer (positions +2, +3, +4 etc.).
• unlabeled dNTPs can also be present in the labeling reaction.
• sequence of one or more primer molecules can also be chosen so that when a polymerase with 3'-exonuclease activity is used, the labeled dNTPs are inserted in an exchange reaction as the terminal base of the primer (s) when the 3'-terminal base of the Primers equal the base of the labeled dNTP used.
• the conditions for carrying out the enzymatic labeling reaction are chosen such that statistically only a single type of labeled deoxyribonucleoside triphosphate can be added to the primer.
• the reaction conditions such as the concentrations of polymerase enzyme or / and dNTP, temperature, concentration of other components, etc.
• the specificity of the reaction can be increased by selecting the primer molecules as explained below.
• the method according to the invention enables, for example, the simultaneous sequencing of DNA fragments with two or more primer molecules, preferably unlabeled primer molecules, and several labeled dNTP in one reaction vessel.
• Several labeling reactions can be carried out simultaneously on different strands of the nucleic acid to be sequenced or at different locations on the same nucleic acid strand.
• the specificity of the method according to the invention is surprisingly so high that statistically a single type of label, in particular only a single labeled dNTP, is added to a specific primer molecule, even if several other differently labeled dNTP, primer molecules and nucleic acid template molecules are in the same Reaction vessel are present.
• the costs for carrying out the sequencing reactions can be reduced by 50-75%. Both chemical and labor costs are reduced. This is particularly important in large-scale sequencing projects, such as the "human genome” sequencing project or other genome projects.
• the most important application form is the automated DNA sequencing with fluorescent labeling groups.
• mini-sequencing in which the nucleic acid sequence is determined only within a limited range of up to three bases after the primer on the basis of a sequence-specific incorporation of the labeled dNTP.
• Another possible application is the detection of point mutations in genes, especially in human genes.
• the primer molecule is selected such that it lies immediately before a "hot spot" of the mutation. Only one primer is used together with two or more different labeled dNTPs and the labeling reaction is carried out. Only a single labeled dNTP is inserted which is complementary to the corresponding base on the nucleic acid template. The extended primer molecule can then be analyzed and the labeling group identified by its spectral characteristics. In this way, a conclusion can be drawn about the sequence of the gene in question.
• the method according to the invention is preferably carried out by
• a) binds at least one nucleic acid primer molecule to the nucleic acid to be sequenced
• one or more nucleic acid sequences are determined via the sequence-specific incorporation of the labeled deoxyribonucleoside triphosphates.
• At least two labeled deoxyribonucleoside triphosphates are used in a reaction batch, each containing different labeling groups and different bases, ie a maximum of four deoxyribonucleoside triphosphates (corresponding to bases A, T, C and G) can be used each with a different marker group.
• the labeling groups can be radioactive or non-radioactive labels and should be detectable side by side.
• Non-radioactive labeling groups, in particular fluorescent labeling groups, for example fluorescent dyes such as rhodamine, derivatives of rhodamine such as methylrhodamine, Texas red, phycoerythrin, fluorescein and derivatives thereof, CY3, CY5 are preferred.
• Other suitable non-radioactive labeling groups are, for example, metals , magnetic marker groups which can be detected by nuclear magnetic resonance or by a superconducting quantum interferometric detector (SQID) or phosphorescent dyes. Suitable excitation and / or detection systems can be used to determine the respective markings.
• fluorescence-labeled dNTP examples include fluorescein-dUTP, fluorescein-dATP (Boehringer Mannheim, Pharmacia); Texas red dCTP and dGTP (NEN-Dupont), CY5-dATP and dCTP and CY3-dATP (Pharmacia).
• fluorescent labeling groups which can be verified side by side at the same time.
• two or more different laser systems which are coupled to corresponding detection systems, can be used to excite the fluorescence groups.
• Bandpass filters can largely suppress interference between the two laser systems. The data is recorded by two detector devices, one for each laser.
• combinations of fluorescent dyes can also be used which can be excited by a single laser system and can be determined separately by different detection systems.
• the concentration of the labeled dNTPs during the labeling reaction is preferably so low that, for a given polymerase concentration, essentially only a single labeled dNTP can be added to a primer molecule.
• the labeled dNTPs are therefore preferably used in a concentration of 0.05-5 ⁇ mol / liter, particularly preferably in a concentration of 0.1-2.5 ⁇ mol / liter.
• the polymerase present in the reaction mixture can statistically add only a single molecule -dNTP to a primer.
• the polymerase concentration is preferably 1-20 U, particularly preferably 5-15 U per batch.
• the specificity of the incorporation of labeled dNTPs by the choice of the labeling molecule (e.g. fluorescein, Texas red etc.), by the choice of the dNTP (dUTP, dTTP, dATP, dCTP, dGTP etc.) or / and by the way in which the dNTP and the labeling molecule are linked (e.g. length of the spacer arm) to be influenced.
• the labeling molecule e.g. fluorescein, Texas red etc.
• a polymerase is used in the process according to the invention, preferably the Klenow fragment of E. coli DNA polymerase I, unmodified T7 DNA polymerase, modified T7 DNA polymerase (Sequenase), T. -DNA polymerase, Taq-DNA polymerase, Bst-DNA polymerase or reverse transcriptase.
• Klenow fragment of E. coli DNA polymerase I unmodified T7 DNA polymerase
• modified T7 DNA polymerase modified T7 DNA polymerase (Sequenase)
• T. -DNA polymerase T. -DNA polymerase
• Taq-DNA polymerase Taq-DNA polymerase
• Bst-DNA polymerase reverse transcriptase.
• polymerases without 3 'exonuclease activity are preferred, e.g. modified T7 polymerase.
• polymerases with 3 'exonuclease activity e.g. unmodified T7 polymerase may be preferred, for example if the labeled deoxyribonucleoside triphosphate is inserted as the last base of the primer molecule (position -1) by sequential exonuclease and polymerase activities in an exchange reaction.
• An advantage of the method according to the invention is its simplicity, since no labeled primer molecules are required. This is particularly important for large scale sequencing projects such as sequencing the human genome or other genome projects.
• labeled primers in order to obtain additional information about the nucleic acid sequence, if necessary.
• the sequencing reaction can also be carried out using a combination of unlabeled and labeled (fluorescent dyes or otherwise, for example digoxigenin, biotin, metals, etc.) primers, the choice of the primers preferably being carried out in such a way that the inner labeling is only carried out on unlabeled primers is added.
• the labeled primers preferably carry other labeling groups than the labeled dNTPs.
• the choice of the primer molecules is important. For example, the primers must be followed by different nucleotides, which are incorporated as the next base when the primer is extended by the polymerase. In this way, only one type of marker group is added to each type of primer molecule in the labeling reaction. The choice of the reaction conditions in the labeling reaction prevents the incorporation of other labeling groups.
• a preferred embodiment of the present invention relates to a method in which at least two primer molecules are used which bind to different regions of the nucleic acid to be sequenced, the primer molecules being selected such that the base to be added next to their 3 'end in each case is different, and a labeled deoxyribonucleoside triphosphate with a corresponding base is used for each primer molecule, so that only a single different labeled deoxyribonucleoside triphosphate is added to each primer molecule.
• the base at the 3 'end of a primer molecule is referred to as "position -1" in the present application.
• the base to be added next to the 3 'end of the primer molecule by the polymerase is referred to as "position +1" and the base to be added as the next but one as "position +2".
• primer molecules To increase the specificity of the labeling reaction, additional criteria should preferably be taken into account when designing the primer molecules. For example, only those primer molecules are used in one approach in which the base to be added next to the 3 'end of the primer (position +1) is not immediately the same as the base to be added to the 3' end of another primer as the next but one (Position +2). This reduces the likelihood that a primer molecule will be labeled with two different labeling groups.
• primer molecules in which the base at the 3 'end of one primer molecule (position - 1) is not the same as the base to be added next to the 3' end of another primer molecule (position +1) is. In this way, possible double labeling due to a 3 'exonuclease activity of the polymerase enzyme used can be avoided.
• this selection criterion does not necessarily have to be considered.
• two or more nucleic acid sequences can be determined simultaneously by the method according to the invention.
• the sequencing reaction of the method according to the invention is usually carried out in two steps.
• a labeling reaction a single type of labeled dNTPs is added to the 3 'end of the primer.
• a primer is preferably selected such that the labeled dNTP is added directly to its 3 'end (position +1). It is further preferred that only labeled dNTPs are present in the labeling reaction, since in this way the likelihood of the incorporation of labeled dNTPs is reduced in the event of an undesired binding of the primer to secondary binding sites on the template.
• the next step is an extension reaction up to the incorporation of a chain termination molecule, through which the Polymerization is terminated.
• This extension reaction is preferably carried out in separate batches in the presence of the oligonucleotide primers specifically labeled by the labeling reaction, the polymerase, the nucleic acid to be sequenced as a template, the four unlabeled deoxyribonucleoside triphosphates and in each case one chain termination molecule.
• the extension of a primer produces a nucleic acid strand which bears a labeling group specific for the respective primer and is terminated by the incorporation of a chain termination molecule.
• the nucleic acid sequence is therefore preferably determined by the method according to the invention by
• the four unlabeled dNTP are in a large excess compared to the labeled dNTP used in the labeling reaction, so that no further incorporation of labeled dNTP takes place during the extension reaction.
• the unlabeled deoxyribonucleoside triphosphates are preferably present in an at least 100-fold excess, particularly preferably in an at least 1000-fold excess with respect to the labeled deoxyribonucleoside triphosphates.
• the concentration of the unlabelled dNTP is therefore preferably 0.05-5 mmol / liter and particularly preferred 0.1-2.5 mmol / liter in the extension batch.
• Deoxyribonucleoside triphosphates which are modified at the 3 'position of the deoxyribose in such a way that they have no free OH group, but are nevertheless accepted as a substrate by the polymerase, are expediently used as chain termination molecules.
• chain termination molecules are about 3'-fluoro, 3'-0-alkyl and 3 '-H-modified deoxyribonucleosides.
• 3'-H-modified deoxyribonucleotides, i.e. Dideoxyribonucleoside triphosphates (ddNTP) are used.
• the process according to the invention is preferably carried out with unlabelled chain termination molecules, but it is also possible to use labeled chain termination molecules as are known to the person skilled in the art.
• the determination of the nucleic acid sequence via the label is usually carried out by separating the labeled nucleic acid fragments according to their length. This separation can be carried out by all methods known in the art, e.g. by various electrophoretic (e.g. polyacrylamide gel electrophoresis) or chromatographic (e.g. HPLC) methods, with gel electrophoretic separation being preferred. Furthermore, the separation of the labeled nucleic acids can be carried out in any way, i.e. manually, semi-automatically or automatically, but the use of an automated sequencer is generally preferred.
• electrophoretic e.g. polyacrylamide gel electrophoresis
• chromatographic e.g. HPLC
• the labeled nucleic acids can be separated in ultra-thin plate gels of 20-500 ⁇ m, preferably 100 ⁇ m thick (see, for example, Stegemann et al, Methods in Mol. And Cell. Biol. 2 (1991), 182-184) or capillaries become.
• the sequence determination can also take place in non-automated devices, e.g. by a blotting process.
• Nucleic acid is available, an amplification step can also be carried out.
• One way of amplification is to carry out one or more cycles of a polymerase chain reaction (PCR) using two primers before the actual sequencing.
• the PCR is usually carried out without labeled dNTP.
• the nucleic acid to be sequenced can thus be amplified before the actual sequencing procedure is carried out.
• the amplification step can also be carried out with the aid of a "thermocycling" reaction.
• the thermocycling reaction corresponds to a "normal” sequencing reaction which, however, like a PCR, is carried out in several cycles.
• the reaction mixture contains the nucleic acid template, the primer molecules, the dNTP and the corresponding chain termination molecules as well as the preferably thermostable polymerase. In this way, a certain amount of the labeled nucleic acid fragments is always synthesized per cycle, it being possible to generate large amounts of labeled fragments in several cycles.
• the nucleic acid to be sequenced can be in both single-stranded and double-stranded form. Good results are obtained if the nucleic acid to be sequenced is located on a double-stranded DNA sector - e.g. a plasmid, cosmid, bacteriophage (lambda or PI), a viral vector or an artificial chromosome.
• a double-stranded DNA sector e.g. a plasmid, cosmid, bacteriophage (lambda or PI), a viral vector or an artificial chromosome.
• Another object of the invention is a reagent kit for the selective introduction of a single labeling group into a nucleic acid, which contains at least two labeled deoxyribonucleoside triphosphates in addition to other components required for labeling or sequencing, each containing different labeling groups and different bases.
• the reagents can be present, for example, in the form of a solution, a suspension or a lyophilisate.
• This reagent kit can be used in particular for the sequencing of Small acids are used and contain additional reagents (e.g. enzyme, primer, buffer solutions, unlabeled dNTPs, terminators).
• FIG. 1 schematically shows the sequencing procedure according to the invention
• FIG. 2 shows the result of plasmid sequencing using two unlabeled primers in the presence of fluorescein-15-dATP and Texas red-5-dCTP,
• FIG. 3 shows the result of an investigation into the repeated incorporation of labeled dNTP
• FIG. 4 shows the result of an investigation regarding the incorporation of a label into the primer itself.
• cDNA molecules derived from a human keratinocyte cDNA library were cloned into a Bluescript vector (Stratagene, LaJolla, California, USA) using standard methods.
• the plasmid DNAs were purified using Quiagen (Hilden, Germany) or Nucleobond AX ion exchange columns (Machery-Nagel, Düren, Germany).
• primers were developed using the computer programs GeneSkipper (EMBL, Heidelberg, Germany) or Oligo TM, 4.1 (Medprobe, Norway). Primer pairs were selected which did not tend to form dimers and which had no further binding sites on the template or no tendency to form a hairpin structure. One of the primers was selected so that an "A” is added to the 3 'end as the next base. The second primer was chosen so that a "C” was added as the next base. The primers were synthesized on the EMBL multiple segment DNA synthesizer (Ansorge et al, Electrophoresis 13 (1992) 616-619).
• extension buffer (304 mmol / liter sodium citrate, 40 mmol / liter MnCl 2 , 324 mmol / liter dithiothreitol) was added to the mixture and mixed.
• the solution was then divided into aliquots and 4 separate extension / termination mixtures were added, which consist of 3 ⁇ l of the respective termination solutions (40 mmol / liter Tris / HCl pH 7.4, 50 mmol / liter NaCl, 5 ⁇ mol / liter of the respective ddNTP, in each case 1 mmol / liter dATP, dCTP, C 7 -dGTP and dTTP) and 1 ul DMSO passed.
• the reaction was carried out for 5 min. incubated for a long time at 37 ° C. and stopped by adding 4 ⁇ l stop solution (6 mg / ml dextran blue and 20 mmol / liter EDTA, pH 7.3 in deionized formamide). Then the samples were 4 min. denatured at 85 ° C for a long time and placed on a sequence gel.
• the structure of the modified DNA sequencing device is described in detail in Wiemann et al (Anal. Biochem. 224 (1995), 117-121.
• a helium-neon laser was also used in the sequencing device
• the Ar laser excites the fluorescein-labeled samples, while the HeNe laser is used to excite Texas red-labeled DNA fragments, both of which are guided into the gel using a single light coupling plate that is between two spacers
• the spatial distance of 0.7 cm between the lasers and the combination of two different laser, detector and filter systems with corresponding fluorophores ensures that no cross-over detection of the sequence signals occurs.
• FIG. 1 shows schematically the principle of simultaneous sequencing of nucleic acids. After denaturation, two primers bind to the complementary regions of the nucleic acid template to be sequenced.
• the matrices can originate from the same strand of a single- or double-stranded DNA or from different strands of the same double-stranded DNA or from different DNA's.
• Two differently labeled dNTP are used in the sequencing reaction. Only the two labeled nucleotides fluorescein-15-dATP and Texas red-5-dCTP are present in the labeling step of the sequencing reaction.
• a selective labeling of specific products with only one dye is achieved by incorporating the respective nucleotide as the first base directly downstream of the primer molecule.
• This response is comparable to Minise sequencing (Syvänen et al, Genomics 8 (1990), 684-692) of point mutations, where the base added directly to the primer is the distinguishing factor as to whether a labeled dNTP is incorporated or not .
• the primers are selected such that the bases to be added directly to the primer are different, e.g. an "A”. and a "C”. In this labeling step, only the correct nucleotide is ever incorporated into each primer.
• the polymerase After incorporation of the first labeled dNTP, the polymerase could take a break because the labeled dNTP is only present in a low concentration. The polymerase could also fall off the template and be available for the extension of further primer molecules up to the incorporation of the labeled dNTPs (e.g. in cycle sequencing).
• FIG. 2 shows sequence data obtained in a simultaneous sequencing on both strands of a plasmid DNA. Two unlabeled walking primers were used.
• FIG. 2a shows the sequence generated with fluorescein-15-dATP and
• FIG. 2b shows the sequence generated with Texas red 5-dCTP.
• FIG. 3 shows the result of a test for multiple incorporation of labeled dNTP. Sequencing primers were selected in which a "C” and then an "A” or first an "A” and then a “C” were inserted at positions +1 and +2. The sequencing reactions were carried out with native T7 DNA polymerase.
• Figure 3a shows the Texas Red signals from a primer with a "C” at position +1 and an "A” at position +2.
• Figure 3b shows the fluorescein signals from the same primer.
• Figure 3c shows Texas Red signals from a primer with "A” at position +1 and “C” at position +2.
• FIG. 3d shows fluorescein signals with the primer from FIG. 3c.
• FIG. 3 shows that there was little incorporation of Texas red 5 dCTP at position +2. Since the marking in position +2 is significantly weaker than the marking in position +1, the sequence data obtained with the second primer are also clear.
• Figure 4 shows the results of a test for the incorporation of a label within the primer.
• Sequencing primers are selected which contain an "A" as the 3 '-terminal base (position -1) and which are to be incorporated with a "C” as the next base (position +1), and primers with the reverse base sequence.
• the sequencing reactions were carried out with either native T7 DNA polymerase (n-T7) or Sequenase (Seq).
• 4a shows Texas red signals from sequencing with Sequenase and one Primer with "A" as 3 'terminal base and a "C” at position +1.
• FIG. 4b shows fluorescein signals from a sequencing with Sequenase and with the primer from FIG. 4a.
• Figure 4c shows Texas Red signals from sequencing with native T7 polymerase and the primer of Figure 4a.
• FIG. 4d shows fluorescein signals from sequencing with native T7 DNA polymerase and the primer from FIG. 4a.
• 4e shows fluorescein signals from sequencing with Sequenase and a primer, with "C” as the 3 'terminal base and an "A" at position +1.
• Figure 4f shows Texas Red signals from sequencing with Sequenase and the primer of Figure 4e.

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