CA2265727A1 - Heterocyclic compounds and their use for isolating nucleic acids - Google Patents

Heterocyclic compounds and their use for isolating nucleic acids Download PDF

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CA2265727A1
CA2265727A1 CA002265727A CA2265727A CA2265727A1 CA 2265727 A1 CA2265727 A1 CA 2265727A1 CA 002265727 A CA002265727 A CA 002265727A CA 2265727 A CA2265727 A CA 2265727A CA 2265727 A1 CA2265727 A1 CA 2265727A1
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Klaus Muhlegger
Herbert Von Der Eltz
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Roche Diagnostics GmbH
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/02—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings
    • C07D405/04—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D413/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms
    • C07D413/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings
    • C07D413/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings directly linked by a ring-member-to-ring-member bond
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic System
    • C07F9/02—Phosphorus compounds
    • C07F9/547—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom
    • C07F9/6558—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing at least two different or differently substituted hetero rings neither condensed among themselves nor condensed with a common carbocyclic ring or ring system
    • C07F9/65586—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing at least two different or differently substituted hetero rings neither condensed among themselves nor condensed with a common carbocyclic ring or ring system at least one of the hetero rings does not contain nitrogen as ring hetero atom
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/048—Pyridine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H7/00—Compounds containing non-saccharide radicals linked to saccharide radicals by a carbon-to-carbon bond
    • C07H7/06—Heterocyclic radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07J—STEROIDS
    • C07J51/00—Normal steroids with unmodified cyclopenta(a)hydrophenanthrene skeleton not provided for in groups C07J1/00 - C07J43/00

Abstract

The present invention pertains to compounds of general formula (I), where R1 to R7 have the notations given in the application, as well as preparation thereof. Compounds can be used as substrates for RNA and DNA polymerases and consequently incorporated to RNA our DNA oligonucleotides, including for the purpose of labelling and isolating nucleic acids and DNA sequencing.

Description

CA 02265727 l999-03- 10Heterocyclic compounds and their use in the detection ofnucleic acidsThe invention concerns heterocyclic compounds which canbe used to label, detect and sequence nucleic acids.Nucleic acids are of major importance in the livingworld as carriers and transmitters of geneticinformation. Since their discovery by F. Miescher theyhave aroused a wide scientific interest which has led tothe elucidation of their function, structure andmechanism of action.An important tool for explaining these connections andfor solving the problems was and is the detection ofnucleic acids and namely with regard to their specificdetection as well as with regard to their sequence i.e.their primary structure.The specific detectability of nucleic acids is based onthe property of these molecules to interact, i.e. tohybridize, with other nucleic acids to form base pairs bymeans of hydrogen bridges. Nucleic acids (probes) labelledin a suitable manner, i.e. provided with indicator groups,can thus be used to detect complementary nucleic acids(target).The determination of the primary structure (sequence),i.e. the sequence of the heterocyclic bases of a nucleicacid, is achieved by means of sequencing techniques.Knowledge of the sequence is in turn a basic requirementfor a targeted and specific use of nucleic acids formolecular biological problems and working techniques.CA 02265727 l999-03- 10The sequencing also ultimately utilizes the principle ofspecific hybridization of nucleic acids to one another.As mentioned above labelled nucleic acid fragments arealso used for this.Hence a suitable labelling of nucleic acids is anessential prerequisite for any detection method.At an early period radioactive labelling was mainly usedwith suitable isotopes such as 32P or 358. However, thedisadvantages of using radioactive reagents are obvious:such work requires special room facilities and licencesas well as a controlled and elaborate disposal of theradioactive waste. The reagents for radioactivelabelling are expensive. It is not possible to storesuch labelled probes for long periods due to the shorthalf-life of the above-mentioned nuclides.Therefore many attempts have been made in recent yearsto circumvent these serious disadvantages i.e. to getaway from using a radioactive label. However, the highsensitivity of this type of label should be retained asfar as possible.Major advances have in fact already been achieved [seee.g. Nonradioactive Labeling and Detection ofBiomolecules (Kessler, C., publ.) Springer VerlagBerlin, Heidelberg 1992].An essential requirement for any detection of a nucleicacid is the prior labelling. As indicated above it isdesirable to achieve this in a non-radioactive manner.Whereas radioactive labelling of nucleic acids isusually carried out by the enzymatically catalysedincorporation of appropriate radioactive nucleosideCA 02265727 l999-03- 10triphosphates, non—radioactive labelling has to beachieved by incorporating a suitable signal or reportergroup.Haptens (such as biotin or digoxigenin), enzymes (suchas alkaline phosphatase or peroxidase) or fluorescentdyes (such as fluorescein or rhodamine) have, amongothers, mainly proven to be suitable as non-radioactiveindicator molecules. These signal groups can be attachedto or incorporated in nucleic acids by various methods.A relatively simple procedure is for example to labelthe 5' end of an oligonucleotide provided with aterminal amino group by means of activated indicatormolecules of the above-mentioned type. However, thisonly allows the introduction of one or a few indicatormolecules into only a low molecular oligomer whereas adenser labelling of longer chain, high molecular nucleicacids with the aim of achieving a high sensitivityusually has to be accomplished by incorporatingnucleoside triphosphates provided with reporter groupsby means of polymerases as in a de novo synthesis.Such current methods are known to a person skilled inthe art as nick translation [Rigby, P.W. et al., (1977),J.Mol.Biol. 113, 237] and random primed labeling[Feinberg, A.P. & Vogelstein, B. (1984) Anal.Biochem.137, 266]. A further method is the so-called 3'-tailingreaction with the aid of the enzyme terminal transferase[e.g. Schmitz, G. et al (1991) Anal.Biochem. 192, 222].The nucleoside triphosphates which have been previouslyused in these methods are almost exclusivelyappropriately modified derivatives of the heterocyclicCA 02265727 l999-03- 10bases adenine, guanine, cytosine and thymine in thedeoxyribonucleotide series or adenine, guanine, cytosineand uracil in the ribonucleotide series. Suchderivatives are described for example by Langer et al.in Proc.Natl.Acad.Sci. USA 78, 6635 (1981), Mfihlegger etal. Biol.Chem. Hoppe—Seyler 371, 953 (1990) and in EP 0063 879. In this case the building blocks which occurnaturally in DNA and RNA are used in a labelled formi.e. provided with signal groups.The main disadvantages of these N—nucleosides is thatthe N-glycosidic bond is sensitive to acidic pHconditions and they can be degraded by nucleases.Furthermore individual C-nucleosides (see e.g. Suhadolnik,R.J. in "Nucleoside Antibiotics", Wiley-Interscience, NewYork 1970) and their use in the therapeutic (antiviral orcancerostatic) field has also been known for a long time.In addition fluorescent C-nucleoside derivatives and theirincorporation into DNA and RNA oligonucleotides has beendescribed (WO 93/16094). The so-called intrinsicfluorescence of these nucleosides is, however, many timeslower with regard to quantum yield than that of thespecial fluorophores such as fluorescein or correspondingrhodamine derivatives. A further disadvantage of the self-fluorescent C-nucleosides is their comparatively lowexcitation and emission wavelengths. As a result detectionsystems which are based on such derivatives only have alow sensitivity of detection and on the other handinfluences of the measuring environment which interferespectrally (such as biological material, autofluorescenceof gel matrices etc.) have a very major effect.Hence the known nucleosides and nucleoside derivativeshave a series of disadvantages which especially have anadverse effect on the detection of nucleic acids. HenceCA 02265727 l999-03- 10the object of the invention is to provide nucleosidederivatives modified with signal groups for the detectionof nucleic acids which do not have the afore—mentioneddisadvantages i.e. in particular are more stable and atthe same time capable of being processed enzymatically andare suitable for the detection of nucleic acids at apracticable wavelength.The object is achieved by heterocyclic compounds of thegeneral formula IR1N/ x),.IO '/’z\\“§%L/Hin whichR1 and R2 can be the same or different and representhydrogen, oxygen, halogen, hydroxy, thio or substitutedthio, amino or substituted amino, carboxy, lower alkyl,lower alkenyl, lower alkinyl, aryl, lower alkyloxy,aryloxy, aralkyl, aralkyloxy or a reporter group,R3 and R4 each represent hydrogen, hydroxy, thio orsubstituted thio, amino or substituted amino, loweralkyloxy,_lower alkenoxy, lower alkinoxy, a protectinggroup or a reporter group,CA 02265727 l999-03- 10R5 represents hydrogen, hydroxy, thio or substitutedthio, amino or a substituted amino group, a reactivetrivalent or pentavalent phosphorus group such as e.g. aphosphoramidite or H—phosphonate group, an ester oramide residue that can be cleaved in a suitable manneror a reporter group,R4 and R5 together form a further bond between C-2' andC-3' or an acetal group,R6 represents hydrogen or a hydroxy, thio or substitutedthio, amino or substituted amino group,R7 represents hydrogen, a monophosphate, diphosphate ortriphosphate group or the alpha, beta or gammathiophosphate analogue of this phosphoric acid ester ora protective groupas well as possible tautomers and salts thereof.X denotes methylene or methine substituted with halogen,hydroxy, thio or substituted thio, amino or substitutedamino, carboxy, lower alkyl, lower alkenyl, loweralkinyl, aryl, lower alkyloxy, aryloxy, aralkyl,aralkyloxy or a reporter group, or oxygen and n=0 or 1,Z denotes nitrogen or carbon provided that if Z denotesnitrogen, m is zero (0) and if X represents methylene,substituted methylene or substituted methine, Z cannotbe carbon and if X denotes oxygen, Z cannot be nitrogen.All detectable groups come into consideration as areporter group such as in particular haptens, afluorophore, a metal-chelating group, a lumiphore, aprotein or an intercalator.Those compounds of the general formula I are preferredin which the acetal group of the residues R4 and R5 issubstituted with a reporter group. The reporter groupCA 02265727 l999-03- 10can be bound directly or indirectly i.e. via a linkergroup.In addition those compounds of the general formula Ihave proven to be particularly suitable in which R1 canrepresent oxygen, R2 can represent hydrogen or areporter group, R3 and R4 can represent hydrogen, R5 canrepresent hydroxy, hydrogen, a reactive trivalent orpentavalent phosphorus group, R5 can represent hydrogenand R7 can represent hydrogen, monophosphate,diphosphate or triphosphate groups.Compounds of the general formula I are also preferred inwhich the reporter group is bound to the heterocyclic ortetrahydrofuran ring by means of a so—called linkergroup. Suitable linker groups are known to a personskilled in the art (see e.g. Mfihlegger, K. et al. (1990)Biol.Chem. Hoppe-Seyler 371, 953-965 or Livak, K.J. etal. (1992) Nucl.Acids Res. 20, 4831-4837).Compounds of the general formula I are additionallypreferred in which R1 represents hydrogen, hydroxy, anamino group, an optionally substituted amino group or areporter group, R2 represents an optionally substitutedamino group or a reporter group, R3 represents hydrogen,R4 represents hydrogen, hydroxy, amino or substitutedamino, lower alkyloxy, lower alkenoxy, lower alkinoxy,R5 represents hydrogen, hydroxy, thio, an optionallysubstituted amino group, a phosphoramidite or a reportergroup, R4 and R5 together represent an acetal group, R5represents hydrogen and R7 represents a triphosphategroup.Compounds of formula I are also preferred in which XCA 02265727 l999-03- 10denotes oxygen and at the same time Z represents carbonsubstituted with R2 or Z denotes nitrogen and at thesame time X represents methylene or methine substitutedwith amino or substituted amino, carboxy or with areporter group.A further preferred embodiment is compounds according toformula I in which X = 0 and Z represents methinesubstituted with amino or substituted amino, carboxy orwith a reporter group.The compounds according to the invention can besynthesized in various ways. In some cases one can startwith naturally occurring precursors such as for example3-(3,4-dihydroxy-5-hydroxymethyl-tetrahydrofuran-2—yl)-pyrrol-2,5—dione or 3—(3,4—dihydroxy—5—hydroxy—methyl—tetrahydrofuran-2-yl)-oxazine—2,6-dione. The important3-(3-deoxy—4-hydroxy-5-hydroxymethyl-tetrahydrofuran-2-yl) derivatives are synthesized from these precursors bydeoxygenation preferably according to Barton (Barton,D.H.R & Motherwell, W.B. (1981) Pure Appl.Chem. 53, 15).In addition the chemical synthesis of the newheterocyclic compounds can for example be carried out asfor example described in detail by K.A. Watanabe in"Chemistry of Nucleosides and Nucleotides" 3, 421-535(L.B. Townsend, publ.) Plenum Press, New York andLondon, 1994.Other syntheses of the said starting compounds have forexample been described by Hosmane, R.s. et al. inBioorg. & Med.Chem.Lett. 3, 2847 (1993) and by Townsend,L.B. et al. in Tetrahedron Lett. 36, 8363 (1995).CA 02265727 l999-03- 10The use of the compounds according to the invention tolabel nucleic acids with diverse, defined signal groupsand hence to detect and sequence nucleic acids hasproven to be particularly advantageous.The substances according to the invention of the generalformula I have a number of advantages especiallycompared to the classical nucleosides and nucleotidessuch as adenosine, guanosine, cytidine, thymidine,uridine etc. and their corresponding phosphoric acidesters.One advantage is chemical stability i.e. towards acidicpH conditions. A further major advantage is thestability of these compounds towards enzymaticdegradation by endonucleases and exonucleases. Theseenzymes are present in biological material and canseverely interfere with the nucleic acid detection. Onthe other hand it is known that DNA and RNA polymerasesare critical with regard to the acceptance of more orless modified nucleoside 5'—triphosphates i.e. withregard to the recognition and incorporation of suchnucleotides as substrates in de novo synthesis.Experience has shown that the attachment of signalgroups to nucleotides influences in particular theirincorporation and incorporation rate.The fact that the derivatives according to the inventioncan be incorporated by suitable polymerase into nucleicacids in a very efficient manner such as e.g. by theaforementioned methods of nick translation or of randomprimed labelling cannot be inferred from the prior artand must therefore be regarded as surprising for aperson skilled in the art.CA 02265727 l999-03- l0_l0..The said methods are used quite generally in nucleicacid detection e.g. for quantitative detection usingblotting techniques on membranes or also in microtitreplates.In sequencing, i.e. detecting the sequence of a nucleicacid, a complementary opposite strand is newlysynthesized on the nucleic acid to be sequenced with theaid of a short (start)oligonucleotide (primer) and theaddition of labelled nucleoside triphosphates and apolymerase, subsequently so-called termination reactionsare carried out and the nucleic acid fragments that aregenerated in this process are separated by gelchromatography.In principle the same occurs in the cell in the in situhybridization to detect certain genes or genome sectionsi.e. the specific incorporation of labelled nucleotides.The above-mentioned primers i.e. short—chainoligonucleotides should form stable base pairs with thetemplate strand as well as not be attacked by endogenousnucleases in order to ensure an optimal function.This is fulfilled by oligonucleotides which contain thecompounds according to the invention as building blocksinstead of the classical nucleosides.The same applies to longer chain polynucleotides andnucleic acids which contain such building blocks. Theseare also a subject matter of the present invention.CA 02265727 l999-03- 10_11..Corresponding oligonucleotides and their preparativeprecursors in the form of so—called phosphoramidites andH-phosphonates are therefore also a subject matter ofthe invention.oligonucleotides are nowadays usually produced by knownmethods in automated DNA/RNA synthesizers by solid phasesynthesis.Such methods of synthesis are based essentially on thestepwise reaction of the aforementioned phosphoramiditesor H-phosphonates and hence the continuous linkage ofthese monomeric building blocks to form oligomers (seee.g. T. Brown & D. J.S.Brown in oligonucleotides andAnalogues-A Practical Approach, (1991) (Eckstein,F.,publ. IRL Press at Oxford University Press, Oxford,New York, Tokyo).LegendFigure 1:I and II denote pBR 328-DNA labelled by DIG-dUTPincorporation (standard) and III denotes pBR 328-DNAlabelled by the compound 3-(4—hydroxy-5-triphosphoryl-tetrahydrofuran—2-yl)-4-(digoxigeninyl-3-O—succinyl-aminocaproylamino—pentyl)-amino-pyrrol-2,5-dionesynthesized according to example 6. They are applied tothe gel at concentrations of 10 to 0.01 pg.The invention is further elucidated by the followingexamples:CA 02265727 l999-03- 10-12..Example 1:3-(4-Hydroxy-5-hydroxy-methyl—tetrahydrofuran-2-yl)-pyrrole-2,5-dioneThe compound was prepared in a de novo synthesisaccording to Hosmane, R.S. et al. Bioorg. &Med.Chem.Lett. 3, 2847 (1993).Alternatively it can be obtained by Barton deoxygenation[Barton, D.H.R. & Motherwell, W.B. (1981) PureApp1.Chem. 53, 15] from the 3,4-dihydroxy derivative(showdomycin) obtained by fermentation.Example 2:3-(4—Hydroxy-5-hydroxymethyl—tetrahydrofuran-2-yl)-4-bromo-pyrro1e—2,5-dione213 mg (1 mmol) 3-(4-hydroxy-5-hydroxymethyl-tetrahydrofuran-2-yl)-pyrrol—2,5-dione obtainedaccording to example 1 is dissolved in 25 ml watersaturated at RT with bromine and stirred for 3 hours atroom temperature. Afterwards only a small amount ofstarting material is observed in the TLC. The solutionis freed of excess bromine in a vacuum, adjusted to pH 7and evaporated to an oil. It is taken up in a smallamount of methanol and separated on a silica gel columnwith a mixture of chloroform/methanol 8:2. Afterevaporating the fractions, 140 mg (48 %) of a paleyellow oil is obtained.Elemental analysis: for CgfiONO5Br (MW292.2): Cca£36.9;Hca1c3.4; NCalc4.8; BrCa1C27.4; Cfound37¢35; Hf°und3o6;Nfmmd4.5; Brfmmd27.8.CA 02265727 l999-03- 10-13-Example 3:3-(4-Hydroxy-5-hydroxymethyl-tetrahydrofuran-2—yl)-4-(1,5—diaminopentyl)-pyrrole-2,5-dione140 mg (ca. 0.5 mmol) of the bromine compound fromexample 2 is dissolved in 50 ml ethanol, admixed with1.75 g (ca 10 mmol) diaminopentane dihydrochloride andheated to reflux for 5 hours. Afterwards the conversionis almost quantitative (compared to the lower spot ofthe bromine compound, ninhydrin positive) according toTLC (silica gel, chloroform/methanol 8:2). The reactionmixture is evaporated in a vacuum and used in example 4without further purification.Example 4:3-(4-Hydroxy-5-hydroxymethyl-tetrahydrofuran-2—yl)-4-(N-trifluoroacetamidopentyl)-amino—pyrrole-2,5-dioneThe oily residue from example 3 (ca. 2 g) is dissolvedin 50 ml anhydrous pyridine, undissolved material isremoved by suction filtration and the filtrate isevaporated to dryness in a vacuum. It is taken up in50 ml absolute pyridine and 0.75 ml (ca. 5 mmol)trifluoroacetic anhydride is added. After standing for5 hours at RT the acylation is complete according toTLC. Subsequently the reaction solution is evaporated ina vacuum and coevaporated three times with methanol. Itis taken up in ca. 20 ml ethanol, filtered andchromatographed on silica gel with a mixture ofchloroform/methanol (9:1). The combined fractions areevaporated, the residue is taken up in dioxane andlyophilized. 110 mg (53 % of theory) of the desiredCA 02265727 l999-03- 10-14..compound is obtained.Elemental analysis for C1gfiBN3O6F3 (MW 410.4): Caflc46.8;HcalC5.6; NcalC10.2; Fcalc13.9; Cfound47o35; HfOund5.9;Nfound10.5; Ffound13o8oExample 5:3-(4-Hydroxy—5-triphosphoryl-tetrahydrofuran-2-yl)—4-(N-trifluoroacetamidopentyl)-amino-pyrrole-2,5-dione40 mg (0.1 mmol) of the protected nucleoside fromexample 4 is converted by phosphorylation with POCI3into the 5'-monophosphate according to the method ofYoshikawa et al. [Tetrahedron Lett. 50, 5065 (1967)];the desired triphosphate is obtained from this in ayield of 30 mg (46 %) according to the method of Hoard &Ott [J.Am.Chem.Soc. 87, (1965)] after activation withcarbonyldiimidazole and reaction with pyrophosphoricacid and subsequent ion exchange chromatography on DEAESephadex.31P-NMR (0.1 M EDTA/D20/Eth3N): -5.2(d,P-y); —10.3(d,P-ot); -21.0 (t,P-B).Example 6:3-(4—Hydroxy-5—triphosphoryl-tetrahydrofuran-2-yl)-4-(N-fluoresceinyl-carboxamido-pentyl)-amino-pyrrole-2,5-dione25 mg (0.038 mmol) of the trifluoracetyl—protectedcompound from example 5 is allowed to stand for 1 h atCA 02265727 l999-03- 10-15-RT in 5 ml concentrated ammonia solution andsubsequently evaporated in a vacuum. The residue istaken up in 5 ml 0.1 M borate buffer, pH 8.5 and admixedwith a solution of 25 mg (0.05 mmol) 5(6)-carboxy-fluorescein-N-hydroxy-succinimide ester in 5 ml amine-free dimethyl formamide. It is allowed to standovernight at room temperature. The reaction mixture isapplied to a DEAE Sephadex column (30 X 1 cm) and elutedwith a linear LiCl gradient (200 ml H20 to 0.4 M LiCl).After combining the appropriate fractions, evaporating,precipitating the concentrate in acetone/ ethanol (2:1)and drying, 25 mg (ca. 50 %) of the title substance isobtained.Spectral data (0.1 M phosphate buffer, pH 9.0:excitationmax [nm]: 495;emissionmax: [nm]: 521The 3-(4-hydroxy—5-triphosphoryl—tetrahydrofuran-2-yl)—4-(digoxigeninyl—3-0-succinyl—aminocaproylamino—pentyl)—amino-pyrrole-2,5-dione was prepared in a correspondingmanner by reacting the compound from example 5 withdigoxigenin—3-O-succinyl-aminocaproic acid-N-hydroxy—succinimide ester.Example 7:3-(4-Hydroxy-5—hydroxymethy1-tetrahydrofuran-2—yl)-1,3-oxazine-2,6-dioneThe compound was obtained by Barton deoxygenation[Barton, D.H.R. & Motherwell, W.B. (1981) PureAppl.Chem. 53, 15] from the 3,4-dihydroxy derivative(oxazinomycin) obtained by fermentation.CA 02265727 l999-03- 10-16-Example 8:3-(4—Hydroxy-5-hydroxymethyl-tetrahydrofuran-2-yl)-4-bromo—l,3—oxazine-2,6-dioneThe derivative was obtained by brominating the startingcompound from example 7 as described in example 2.Example 9:3-(4-Hydroxy-5-hydroxymethyl-tetrahydrofuran-2—yl)-4-(1,5-diaminopentyl)-1,3—oxazine-2,6—dione150 mg (0.5 mmol) of the bromine compound from example 8was converted into the title compound according to themethod of example 3. This was finally reacted withfluorescein-labelled triphosphate without furtherpurification according to the methods of examples 4, 5and 6.Example 10:3-(4—Hydoxy-5-hydroxymethyl-tetrahydrofuran-2-yl)—2,6-diamino-5-chloro-pyrazineThe derivative was synthesized according to Townsend,L.B. et al. Tetrahedron Lett. 36, 8363 (1995).Example 11:3-(4—hydroxy-5-hydroxymethyl—tetrahydrofuran—2—yl)-2,6-diamino-5-chloro-pyrazine264 mg (1 mmol) 3-(4-Hydroxy-5-hydroxymethyl-tetrahydrofuran-2-yl)-2,6-dihydroxy-5-chloro-pyrazinefrom example 10 was subjected to a deamination reactionCA 02265727 l999-03- 10-17-in a mixture of 50 ml 80 % acetic acid and 700 mg(10 mmol) NaNO2. After standing for 5 hours at RT, thereaction was almost complete according to TLC. 2 g ureawas added to the reaction mixture to destroy excessnitrite and stirred for a further three hours at RT.Afterwards the solution was applied to an activatedcarbon column (Carboraffin C, ca. 50 ml volume),adequately washed and the desired product was eluted withethanol/water/ammonium. 230 mg (ca. 87 %) of a viscousoil resulted after evaporation which was used in the nextstage without further purification.Example 12:3-(4-Hydroxy-5-hydroxy—methyl-tetrahydrofuran-2—yl)—2,6-dihydroxy-5-(1,8-diamino—3,6-dioxa-octyl)—pyrazine200 mg (0.75 mmol) of the oil from example 11 wasdissolved in 30 ml ethanol, 555 mg (3.75 mmol) 1,8~diamino-3,6-dioxa-octane was added and it was heated for3 hours to ca. 60°C.Subsequently the solvent and amine were removed in anoil pump vacuum and the residue was further reactedwithout further purification by reaction withtrifluoroacetic anhydride in pyridine as described inexample 4.Example 13:3-(4-Hydroxy-5-triphosphoryl-tetrahydrofuran-2-yl)-2,6-dihydroxy—5-[N-trifluoro-acetamido-(3,6-dioxa)-octyl]-amino-pyrazineCA 02265727 l999-03- 10-18-150 mg of the trifluoracetylated derivative from example12 was converted into the title compound according toYoshikawa and Hoard & Ott as described in example 5. Thedesired triphosphate was obtained in a yield of 120 mg(40 %) after ion exchange chromatography on DEAESephadex.31P-NMR (0.1 M EDTA/D20/Eth3N):—5.1(d,P-7); -10.6 (d,P-d);-20.8 (t,P-B).Example 14:3-(4-Hydroxy-5—triphosphory1-tetrahydrofuran-2—y1)-2,6-dihydroxy—5—[N-tetramethyl-rhodaminyl-5,6—carboxamido-(3,6-dioxa)-octyl]-amino—pyrazine20 mg of the triphosphate from example 13 were reacted -after cleavage of the trifluoroacetyl protective groupwith ammonia solution (as described in example 6) - with20 mg tetramethylrhodamine—5(6)-carboxylic acid-N-hydroxy-succinimide ester in 0.1 M sodium borate buffer,pH 8.5/DMF as described in example 6 and purified.12 mg of the TMR—labelled product was obtained.Spectral data (0.1 M Na—borate buffer, pH 8.5):excitationmax [nm]: 551;emissionmaxz [nm]: 575Example 15:Non—radioactive DNA labelling and detection byincorporation of 3-(4-hydroxy-5-triphosphory1-tetrahydrofuran-2-yl)-4-(digoxigeninyl—3—O-succinyl-aminocaproylamino-pentyl)-amino—pyrrole-2,5-dioneThe DNA labelling and the DNA detection were carried outusing the commercially available kit from the BoehringerCA 02265727 l999-03- 10-19.-Mannheim Company (order No. 1093 657). All essentialprocess steps are described in the working instructions.For the labelling reaction the DIG-dUTP in the dNTPmixture in the kit was substituted by a 3-(4-hydroxy-5-triphosphoryl-tetrahydrofuran—2—yl)-4-(digoxigeninyl-3-O—succinyl—aminocaproylamino-pentyl)—amino-pyrrole—2,5-dione (synthesized as described in example 6).The immunological detection reaction showed thatincorporation of the inventive compound of example 6resulted in a detection sensitivity of the labelled DNAwhich is similar to the use of DIG-dUTP.The result which demonstrates the detection and theachieved sensitivity of the system is shown in Figure 1.

Claims (16)

Claims
1. Compounds of the general formula in which R1 and R2 can be the same or different and represent hydrogen, oxygen, halogen, hydroxy, thio or substituted thio, amino or substituted amino, carboxy, lower alkyl, lower alkenyl, lower alkinyl, aryl, lower alkyloxy, aryloxy, aralkyl, aralkyloxy or a reporter group, R3 and R4 each represent hydrogen, hydroxy, thio or substituted thio, amino or substituted amino, lower alkyloxy, lower alkenoxy, lower alkinoxy, a protecting group or a reporter group, R5 represents hydrogen, hydroxy, thio or substituted thio, amino or a substituted amino group, a reactive trivalent or pentavalent phosphorus group such as e.g. a phosphoramidite or H-phosphonate group, an ester or amide residue that can be cleaved in a suitable manner or a reporter group, R4 and R5 together form a further bond between C-2' and C-3' or an acetal group, R6 represents hydrogen or a hydroxy, thio or substituted thio, amino or substituted amino group, R7 represents hydrogen, a monophosphate, diphosphate or triphosphate group or the alpha, beta or gamma thiophosphate analogue of this phosphoric acid ester or a protective group as well as possible tautomers and salts thereof, X denotes methylene or methine substituted with halogen, hydroxy, thio or substituted thio, amino or substituted amino, carboxy, lower alkyl, lower alkenyl, lower alkinyl, aryl, lower alkyloxy, aryloxy, aralkyl, aralkyloxy or a reporter group, or oxygen and n=0 or 1, Z denotes nitrogen or carbon provided that if Z
denotes nitrogen, m is zero (0) and if X represents methylene, substituted methylene or substituted methine, Z cannot be carbon and if X denotes oxygen, Z cannot be nitrogen and if Z denotes carbon R2 cannot be hydrogene.
2. Compounds as claimed in claim 1, in which R1 can represent oxygen, R2 can represent hydrogen or a reporter group, R3 and R4 can represent hydrogen, R5 can represent hydroxy, hydrogen, a reactive trivalent or pentavalent phosphorus group, R6 can represent hydrogen and R7 can represent hydrogen, mono-, di-, or triphosphate groups.
3. Compounds as claimed in claim 1 wherein R1 represents hydrogen, hydroxy, an amino group, an optionally substituted amino group or a reporter group, R2 represents an optionally substituted amino group or a reporter group, R3 represents hydrogen, R4 represents hydrogen, hydroxy, amino or substituted amino, lower alkyloxy, lower alkenoxy, lower alkinoxy, R5 represents hydrogen, hydroxy, thio, an optionally substituted amino group, a phosphoramidite or a reporter group, R4 and R5 together represent an acetal group, R6 represents hydrogen and R7 represents a triphosphate group.
4. Compounds of formula I are also preferred in which X denotes oxygen and at the same time Z represents carbon substituted with R2 or Z denotes nitrogen and at the same time X represents methylene or methine substituted with amino or substituted amino, with carboxy or with a reporter group.
5. Compounds according to formula I in which X = 0 and Z represents methine substituted with amino or substituted amino, with carboxy or with a reporter group are a further preferred embodiment.
6. Compounds as claimed in claim 1, wherein the acetal group of the residues R4 and R5 is substituted with a reporter group.
7. Compounds as claimed in one of the claims 1 to 6, wherein the reporter group denotes a hapten, a fluorophore, a metal-chelating group, a luminophore, a protein or an intercalator.
8. Compounds as claimed in one of the claims 1 to 7, in which the reporter group is linked via a linker group.
9. Use of compounds as claimed in one of the claims 1 to 8 as substrates for DNA and RNA polymerases.
10. Use of compounds as claimed in claims 1 to 8 for labelling nucleic acids.
11. Use of compounds as claimed in claims 1 to 8 for the detection of nucleic acids.
12. Use of compounds as claimed in one of the claims 1 to 8 in DNA sequencing.
13. Use of compounds as claimed in one of the claims 1 to 8 in in situ hybridization.
14. Use of compounds as claimed in claims 1 - 8, in which R7 represents a phosphoramidite or a H-phosphonate for the chemical synthesis of oligonucleotides.
15. Oligonucleotides which contain one or several of the compounds mentioned in claims 1 to 8.
16. Nucleic acids which contain one or several of the compounds mentioned in claims 1 to 8.
CA002265727A 1996-09-12 1997-09-11 Heterocyclic compounds and their use for isolating nucleic acids Abandoned CA2265727A1 (en)

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