WO2015197655A1 - Methods and products from the reaction of tetrazines with nucleic acid polymers bearing ethenyl aromatic groups - Google Patents

Methods and products from the reaction of tetrazines with nucleic acid polymers bearing ethenyl aromatic groups Download PDF

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WO2015197655A1
WO2015197655A1 PCT/EP2015/064165 EP2015064165W WO2015197655A1 WO 2015197655 A1 WO2015197655 A1 WO 2015197655A1 EP 2015064165 W EP2015064165 W EP 2015064165W WO 2015197655 A1 WO2015197655 A1 WO 2015197655A1
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formula
alkynyl
alkenyl
alkyl
nucleoside
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PCT/EP2015/064165
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French (fr)
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Nathan Luedtke
Ulrike RIEDER
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Universität Zürich
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/001—Preparation for luminescence or biological staining
    • A61K49/0013—Luminescence
    • A61K49/0017—Fluorescence in vivo
    • A61K49/005—Fluorescence in vivo characterised by the carrier molecule carrying the fluorescent agent
    • A61K49/0054—Macromolecular compounds, i.e. oligomers, polymers, dendrimers
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/56—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule
    • A61K47/59—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/001—Preparation for luminescence or biological staining
    • A61K49/0013—Luminescence
    • A61K49/0017—Fluorescence in vivo
    • A61K49/0019—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules
    • A61K49/0021—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules the fluorescent group being a small organic molecule
    • A61K49/0041—Xanthene dyes, used in vivo, e.g. administered to a mice, e.g. rhodamines, rose Bengal
    • 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
    • C07D405/14—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 three or more hetero rings
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems

Definitions

  • This invention pertains to the preparation and products of modified nucleic acids by means of enzymatic synthesis and chemical modification.
  • the invention is also directed to the products of the process; comprising nucleosides/nucleotides and nucleic acids containing one or more dihydropyridazine and/or pyridazine units located at the 5-position of pyrimidines and/or the 7-position of 7-deazapurine residues.
  • Non-native functional groups can be incorporated into nucleic acids by the addition of a synthetic nucleoside/nucleotide to whole cells, cell lysates, purified enzyme mixtures, or whole animals containing appropriate nucleotide kinases and/or polymerases that incorporate the unnatural nucleotide units into newly synthesized DNA or RNA molecules.
  • the modification and/or detection of the non-native functional groups can be accomplished by the application of an immunohistochemical or chemical reaction. This second step is most commonly used to introduce an analytical probe that is specific for the newly-synthesized nucleic acids, such as a radiolabel, fluorescent marker, and/or biotin group.
  • RNA and DNA synthesis are currently the halogenated nucleosides 5-bromouridine (BrU) (Exp. Cell Res. 260, 248-256, 2000), 5- bromo-2'-deoxyuridine (BrdU) (Brain Res Rev 53, 198-214, 2007), and their corresponding nucleotide triphosphates (NTP's).
  • PrU and BrdU NTP's are incorporated into nucleic acids by natural RNA and DNA polymerases in the presence of unmodified NTP's to give nucleic acid polymers containing one or more bromine groups.
  • Nucleic acids containing BrU or BrdU can be immunohistochemically modified by the addition of antibodies raised specifically for the brominated residues. This approach can be used for the characterization of newly synthesized DNA RNA polymers in vitro and in vivo, but is severely limited by the poor tissue permeability of antibodies (Proc. Natl. Acad. Sci. U. S. A. 108, 20404-20409, 201 1 ).
  • Bioorthogonal chemical reactions provide highly attractive alternatives for the modification of biopolymers containing non-native functional groups (Science 287, 2007-2010, 2000; J. Am. Chem. Soc. 125, 3192-3193, 2003; Chem. Commun. 49, 1 1007-1 1022, 2013).
  • a highly chemoselective reaction is used to chemically modify a biomolecule containing a non-native functional group.
  • One of the most commonly used chemoselective reactions for this purpose is the copper(l)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction (Coord. Chem. Rev. 255, 2933-2945, 201 1 ).
  • 5- ethynyluridine (EU) and 5-ethynyl-2'-deoxyuridine (EdU) can be phosphorylated and incorporated into RNA molecules (Proc. Natl. Acad. Sci. U. S. A. 105, 15779-15784, 2008) and DNA molecules (Proc. Natl. Acad. Sci. U. S. A. 105, 2415-2420, 2008) by enzymes mixtures in vitro and in vivo. Further modification of the ethynyl groups in the nucleic acid polymers can be accomplished by CuAAC reactions to furnish triazole units at the 5-positions of pyrimidine residues.
  • the objective of the present invention is to provide the materials and methods for the preparation and modification of nucleic acids, improving the above disadvantages of known methods.
  • a further object of the invention is to provide novel modified nucleic acids and the use of reagents in providing said modified nucleic acids.
  • Inverse electron demand Diels-Alder (invDA) reactions between electron-deficient tetrazines and electron-rich dienophiles are particularly attractive bioorthogonal chemical reactions since they are irreversible, do not require a catalyst, and are compatible with cell media (J. Am. Chem. Soc. 130, 13518-13519, 2008; Nat Chem 4, 298-304, 2012; Angew. Chem., Int. Ed. Engl.
  • nucleosides are known to inhibit their metabolism by enzymes (Biochem. J. 351 Pt 2, 319-326, 2000). We therefore sought the smallest possible dienophile to incorporate into nucleic acids. Since ethenyl aromatic compounds such as styrene are known to react with tetrazines, we identified 5-ethenyl pyrimidine and 7-ethenyl-7-deazapurine nucleosides or derivatives thereof as candidates for the preparation and modification of nucleic acids upon addition of a modifying reagent comprising a tetrazine group.
  • the present invention is based on our surprising finding that the nucleotide triphosphate of 5- vinyl-2'-deoxyuridine (VdU) is enzymatically incorporated into the newly synthesized DNA of living cells, yet unlike 5-ethynyl-2'-deoxyuridine (EdU), it does not cause an accumulation of tetraploid (4n) cells, arrested at G 2 /M, that stain positively for markers of DNA damage ( ⁇ 2 ⁇ ) (DNA Repair 3, 959-967, 2004). Little or no ⁇ 2 ⁇ formation or G 2 /M cell cycle arrest was observed in cells treated with VdU, correlating with its diminished cytotoxicity as compared to EdU.
  • a first aspect of the invention relates to a process for preparing at least one labelled nucleic acid, comprising steps of:
  • nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a 5-ethenyl pyrimidine moiety or a derivative thereof or a 7-ethenyl-7-deazapurine or a derivative thereof,
  • labelled nucleic acids are provided.
  • the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue is reacted with at least one reagent comprising a tetrazine moiety forming one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
  • a second aspect of the invention relates to a modified nucleic acid, in particular prepared according to the first aspect of the invention, comprising a. at least one dihydropyridazine unit of formula (IV) and/or the corresponding tautomeric forms of said formula and/or
  • At least one pyridazine unit of formula (VII) and/or the corresponding tautomeric forms of said formulas in particular from at least one unit comprising the formula (IV) and/or (VI) and/or (VII),
  • R 3 , R 5 , R 6 , R 7 , T, and L have the same meaning as discussed in the description the invention.
  • a third aspect of the invention relates to a nucleoside/nucleotide analogue comprising a. a nucleoside/nucleotide unit and a dihydropyridazine unit of formula (VIII) or (VIII * ), in particular of formula (VIII * ), and/or the corresponding tautomeric forms of said formulas:
  • a fourth aspect of the invention relates to methods for further modifying labelled nucleic acids by adding at least one tetrazines of formula (III) to at least one labelled nucleic acid, in particular a labelled nucleic acid according to the first aspect of the invention, comprising one or more ethenyl aromatic groups; such that a reaction occurs between the ethenyl aromatic group and the tetrazine group of formula (III):
  • R 6 and R 7 are selected independently from each other from
  • alkyl in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-OR b ), or thioether (-SR b ), wherein R b is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from CrC 4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
  • R 6 and R 7 are functional groups, in particular a detectable group comprising at least one detectable moiety.
  • a fifth aspect of the invention relates to a kit for preparing, in particular according to the method of the first and fourth aspect of the invention, a modified nucleic acid according to the second aspect of the invention, wherein the kit comprises at least one nucleoside/nucleotide analogue with an ethenyl aromatic moiety and/or at least one labelled nucleic acid, in particular at least one nucleoside/nucleotide analogue according to formula (I) or (II), and a reagent comprising a tetrazine moiety according to formula (III).
  • a sixth aspect of the invention relates to a use of a nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a nucleoside/nucleotide analogue according to formula (I) or (II), in preparing modified nucleic acids, in particular modified nucleic acid according to the second aspect of the invention.
  • a seventh aspect the invention relates to at least one nucleoside/nucleotide analogue and/or at least one modified nucleic acid according to the second and third aspect of the invention for use as diagnostic substance or composition.
  • the present invention provides methods and compositions useful for modifying nucleic acids in vitro and in vivo.
  • the inventive methods include the incorporation of nucleoside analogues into nucleic acids and a chemical reaction between the prior labelled nucleic acid and a reagent comprising a functional, in particular a detectable group.
  • a first aspect of the invention relates to a process for preparing at least one labelled nucleic acid, comprising steps of:
  • nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a 5-ethenyl pyrimidine moiety or a derivative thereof or a 7-ethenyl-7-deazapurine or a derivative thereof,
  • said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (l Nu ) or at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (ll Nu )
  • - R 3 is selected o in case of formula l Nu from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH 2 ) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula ll Nu hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH 2 ) and the corresponding tautomeric forms of the 7- deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine;
  • R 5 of formula ll Nu is selected from hydrogen (H), hydroxyl (OH), amino (NH 2 ), or halogen, in particular from hydrogen (H) or amino (NH 2 ), and
  • - Nu is a sugar moiety or a sugar phosphate moiety
  • - T is selected from O, S or Se, in particular T is O.
  • said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (I) or at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (II)
  • R 1 and R 2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH 2 ), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl, ether (-OR a ), or thioether (-SR a ), wherein R a is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C-
  • R 3 is selected o in case of formula I from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH 2 ) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula II hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH 2 ) and the corresponding tautomeric forms of the 7- deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine;
  • R 4 is selected from hydroxyl (OH), phosphate (OP0 3 2" ), diphosphate (OP0 3 P0 3 3” ), triphosphate (OP0 3 P0 3 P0 3 4" ), phosphate diester (OP0 2 R p O " ), phosphate triester (-
  • R p is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, CrC 4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, or aryl; and - R 5 of formula II is selected from hydrogen (H), hydroxyl (OH), amino (NH 2 ), or halogen, in particular from hydrogen (H) or amino (NH 2 ), and
  • - T is selected from O, S or Se, in particular T is O.
  • said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (I) or ( ), in particular of formula (I * )
  • R 1 and R 2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH 2 ), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl, ether (-OR a ), or thioether (-SR a ), wherein R a is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C-
  • R 3 is selected from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH 2 ) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and
  • R 4 is selected from hydroxyl (OH), phosphate (OP0 3 2" ), diphosphate (OP0 3 P0 3 3” ), triphosphate (OP0 3 P0 3 P0 3 4" ), phosphate diester (OP0 2 R p O " ), phosphate triester (-OP0 3 (R p ) 2 ) or their derivatives in forms of acids, esters, bases and salts thereof, wherein R p is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C 2 -C 4 alkenyl, C2-C4 alkynyl, or aryl, and
  • T is selected from O, S or Se, in particular T is O.
  • An example for corresponding amino tautomeric forms of the pyrimidine moiety is given below.
  • R 3 is OH
  • a lactim compound of a formula l ta is provided and the corresponding lactam tautomeric form is shown in formula l tb .
  • said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (II)
  • R 1 and R 2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH 2 ), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl, ether (-OR a ), or thioether (-SR a ), wherein R a is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C-
  • - R 3 is selected from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH 2 ) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine;
  • - R 4 is selected from hydroxyl (OH), phosphate (OP0 3 2" ), diphosphate (OP0 3 P0 3 3" ), triphosphate (OP0 3 P0 3 P0 3 4" ), phosphate diester (OP0 2 R p O " ), phosphate triester (- OP0 3 (R p ) 2 ) or their derivatives in forms of acids, esters, bases and salts thereof, wherein R p is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an al
  • R 5 is selected from hydrogen (H), hydroxyl (OH), amino (NH 2 ), or halogen, in particular from hydrogen (H) or amino (NH 2 ).
  • R 1 of formula I, I* or II is selected from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH 2 ), C1-C4 alkyl, in particular methyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, ether (-OR a ), or thioether (-SR a ), wherein R a is selected from C-
  • R 1 of formula I, I* or II is selected from hydrogen (H), hydroxyl (OH), fluoride (F) or methyl.
  • R 2 of formula I, I * or II is selected from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH 2 ), C1-C4 alkyl, in particular methyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, ether (-OR a ), or thioether (-SR a ), wherein R a is selected from C1-C4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl.
  • R 2 of formula I, I * or II is selected from hydrogen (H), hydroxyl (OH), fluoride (F) or methyl.
  • R 3 of formula I, I * is selected from hydroxyl (OH), halogen, methyl, or amino (NH 2 ) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine. In some embodiments, R 3 of formula I, I * is selected from hydroxyl (OH), halogen, or amino (NH 2 ) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine.
  • R 3 of formula II is selected from hydroxyl (OH), halogen, methyl, or amino group (NH 2 ) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine.
  • R 3 of formula II is selected from hydroxyl (OH), halogen, or amino (NH 2 ) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7- deazaadenine and 7-deazaguanine.
  • R 4 of formula I, I * or II is selected from phosphate diester (OP0 2 R p O " ), phosphate triester (-OP0 3 (R p ) 2 ) or their derivatives in forms of acids, esters, bases and salts thereof, wherein R p is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, or aryl.
  • R p is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 al
  • R 4 of formula I or II is selected from hydroxyl (OH).
  • R 5 of formula II is selected from hydrogen (H), hydroxyl (OH), amino (NH 2 ), or halogen.
  • R 5 of formula II is selected from hydrogen (H), amino (NH 2 ), or halogen.
  • R 5 of formula II is selected from hydrogen (H) or amino (NH 2 ).
  • T of formula I is O.
  • R 1 and R 2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH 2 ), C1-C4 alkyl, in particular methyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, ether (-0R a ), or thioether (-SR a ), wherein R a is selected from Ci-C 4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl; and
  • R 3 is selected a. in case of formula I, I * from hydroxyl (OH), halogen, methyl, or amino (NH 2 ) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and b.
  • R 4 is selected from phosphate diester (OP0 2 R p O " ), phosphate triester (-OP0 3 (R p ) 2 ) or their derivatives in forms of acids, esters, bases and salts thereof, wherein R p is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C-
  • - R 1 and R 2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), fluoride (F) or methyl; and - R 3 is selected a. in case of formula I, I * from hydroxyl (OH), halogen, or amino (NH 2 ) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and b. in case of formula II hydroxyl (OH), halogen, or amino (NH 2 ) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7- deazaadenine and 7-deazaguanine; and
  • R 4 is selected from hydroxyl (OH).
  • R 5 of formula II is selected from hydrogen (H) or amino (NH 2 ), and
  • said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (I), wherein T is O, and i. R 1 is H, R 2 is H, R 3 is OH, R 4 is OH; or ii. R 1 is F, R 2 is H, R 3 is OH, R 4 is OH; or iii. R 1 is H, R 2 is H, R 3 is OH, R 4 is triphosphate, or iv. R 1 is H, R 2 is OH, R 3 is OH, R 4 is OH, or v.
  • R 1 is H, R 2 is OH, R 3 is OH, R 4 is triphosphate; or vi.
  • R 1 is H, R 2 is H, R 3 is NH 2 , R 4 is OH, or vii.
  • R 1 is H, R 2 is H, R 3 is NH 2 , R 4 is triphosphate; or viii.
  • R 1 is H, R 2 is OH, R 3 is NH 2 and R 4 is OH, or ix.
  • R 1 is H, R 2 is OH, R 3 is NH 2 , R 4 is triphosphate.
  • said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (II), wherein i. R 1 is H, R 2 is H, R 3 is OH, R 4 is OH, R 5 is NH 2 ; or ii. R 1 is H, R 2 is H, R 3 is OH, R 4 is triphosphate, R 5 is NH 2 ; or iii. R 1 is H, R 2 is OH, R 3 is OH, R 4 is OH, R 5 is NH 2 ; or iv.
  • R 1 is H, R 2 is OH, R 3 is OH, R 4 is triphosphate, R 5 is NH 2 ; or v.
  • R 1 is H, R 2 is H, R 3 is NH 2 , R 4 is OH, R 5 is H; or vi.
  • R 1 is H, R 2 is H, R 3 is NH 2 , R 4 is triphosphate, R 5 is H, or vii.
  • R 1 is H, R 2 is OH, R 3 is NH 2 , R 4 is OH, R 5 is H, or viii.
  • R 1 is H, R 2 is OH, R 3 is NH 2 , R 4 is triphosphate, R 5 is H.
  • the nucleic acid source is selected from a.
  • nucleic acid template in particular a polynucleotide template; b. cells; or c. organisms; or d. cell extracts; or and/or wherein the enzymatic synthesis is conducted with a. a purified enzyme; or b. a purified enzyme mixture.
  • the previous discussed embodiments of the present invention provide methods for labelling nucleic acids by enzymatic synthesis.
  • the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue is reacted with at least one reagent comprising a tetrazine moiety forming one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
  • the at least one tetrazine is selected from a tetrazine of formula (I I I):
  • R 6 and R 7 are selected independently from each other from
  • alkyl in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-OR b ), or thioether (-SR b ), wherein R b is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C1-C4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
  • R 6 and R 7 are functional groups, in particular a detectable group comprising at least one detectable moiety.
  • the at least one tetrazine is selected from a tetrazine of formula (I I I):
  • R 6 and R 7 are selected independently from each other from
  • heteroaryl group in particular 2-pyridine and 2-pyrimidine, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
  • R 6 and R 7 are functional groups, in particular a detectable group comprising at least one detectable moiety.
  • the detectable group comprises at least one detectable moiety that is attached to the tetrazine moiety via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle. In some embodiments, the detectable group comprises a directly or indirectly detectable moiety.
  • the detectable group comprises a detectable moiety selected from a. a luminescent agent, in particular a fluorescent agent; or b. a biotin; or c. a hapten; or
  • the labelled nucleic acid which comprises the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue, provided by step c, is reacted directly after the step c with the at least one reagent comprising a tetrazine moiety forming one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
  • the labelled nucleic acid which comprises the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue, provided by step c, is separated, in particular purified, prior to the reaction with the at least one reagent comprising a tetrazine moiety forming one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
  • the process of preparing the modified nucleic acid comprises two steps; first, the addition of one or more 5-ethenyl pyrimidine and/or 7-ethenyl-7-deazapurine derivatives to enzyme mixtures that incorporate the ethenyl nucleotides into the nucleic acids providing the labelled nucleic acids; second, the addition of a tetrazine reagent that undergoes a [4+2] Diels-Alder cycloaddition with the ethenyl aromatic groups providing the modified nucleic acid.
  • inventive methods comprise steps of: contacting cell lysates, enzyme mixtures, cells or organisms with an effective amount of nucleoside analogues of formula I, and II, wherein R 1 , R 2 , R 3 , R 4 , R 5 and T have the meaning indicated above, such that one or more nucleoside analogues are incorporated into nucleic acids
  • a reagent comprising a tetrazine of formula III, wherein R 6 and R 7 have the meaning indicated above, such that Diels-Alder cycloaddition reaction occurs between the incorporated nucleoside analogue and the reagent.
  • the invention relates to a modified nucleic acid, in particular prepared according to the first of the invention, comprising at least one dihydropyridazine unit formula (IV) or (IV * ), in particular of formula (IV * ) and/or the corresponding tautomeric forms of said formulas:
  • the modified nucleic acid comprises at least one unit comprising the formula (IV) and/or (VI) and/or (VII), wherein - R 3 is selected o in case of formula IV, IV * , V and V * from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH 2 ) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula VI and VII hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH 2 ) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7- deazaguanine; and
  • R 5 denotes a hydrogen (H), hydroxyl (OH), amino (NH 2 ), or halogen, in particular from hydrogen (H) or amino (NH 2 );
  • R 6 and R 7 are selected independently from each other from o hydrogen (H), halogen, trifluoromethyl (CF 3 ), trichloromethyl (CCI 3 ), cyano (CN), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-OR b ), or thioether (-SR b ), wherein R b is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C 1 -C4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, o wherein at least one of R 6 and R 7 is a functional group, in particular a detectable group comprising at least one detectable moiety, and
  • - T is selected from O, S or Se, in particular from O, and
  • - L is a sugar-phosphate linkage to a nucleic acid.
  • sugar-phosphate linkage L is part of the nucleic acid backbone.
  • L is a sugar-phosphate linkage to a nucleic acid derived from a reaction of the sugar moiety L * of the compound according to formula I or II
  • R 1 , R 2 , and R 4 having the same meaning as defined previously, and a corresponding sugar/sugar-phosphate moiety of the nucleic acid.
  • the compound according to formula I or II is connected to a preceding or subsequent monomer or building block in the nucleic acid via a covalent bond, particularly via a phosphodiester bond.
  • the invention also includes the Diels-Alder cycloaddition products comprised of one or more dihydropyridazine and/or pyridazine units that are formed between the ethenyl aromatic groups and the tetrazine reagent within the nucleic acid.
  • the invention relates to a nucleoside/nucleotide analogue comprising
  • R 1 and R 2 have the same meaning as discussed previously, in particular in the first aspect of the invention,
  • R 3 is selected o in case of formula VIII and VIII * from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH 2 ) and the corresponding amino and amido tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and o in case of formula IX and IX * from halogen, methyl, thiol (SH), seleno (SeH), or amino (NH 2 ) and the corresponding amino and amido tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and o in case of formula X, X * , XI and XI * hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH 2 ) and the corresponding amino and amido tautomeric forms of the 7-deazapurine nucleobase including 7-deazaa
  • R 4 is selected from hydroxyl (OH), phosphate diester (OP0 2 R p O " ) or phosphate triester (-OP0 3 (R p ) 2 ) or their derivatives in forms of acids, esters, bases and salts thereof, wherein R p is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, or aryl;
  • R 5 denotes a hydrogen (H), amino (NH 2 ), or halogen group
  • R 6 and R 7 are selected independently from each other from o hydrogen (H), halogen, methyl, trifluoromethyl (CF 3 ), trichloromethyl (CCI 3 ), cyano (CN), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (- OR b ), or thioether (-SR b ), wherein R b is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C C 4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, o wherein at least one of R 6 and R 7 is a functional group, in particular a detectable group comprising at least one detectable moiety;
  • - Nu is a sugar moiety or a sugar phosphate moiety
  • nucleoside/nucleotide analogue of the third aspect of the invention is selected from O, S or Se, in particular from O.
  • the present invention provides methods for modifying labelled nucleic acids by adding at least one tetrazines of formula (III) to at least one labelled nucleic acid, in particular a labelled nucleic acid according to the first aspect of the invention, comprising one or more ethenyl aromatic groups; such that a reaction occurs between the ethenyl aromatic group and the tetrazine group of formula (III):
  • R 6 and R 7 are selected independently from each other from - hydrogen (H), halogen, methyl, trifluoromethyl (CF 3 ), trichloromethyl (CCI 3 ), cyano
  • R b is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C1-C4 alkyl, C 2 -C 4 alkenyl, C 2 -C 4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety,
  • R 6 and R 7 are functional groups, in particular a detectable group comprising at least one detectable moiety.
  • the at least one tetrazine is selected from a tetrazine of formula (I I I):
  • R 6 and R 7 are selected independently from each other from
  • heteroaryl group in particular 2-pyridine and 2-pyrimidine, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
  • R 6 and R 7 are functional groups, in particular a detectable group comprising at least one detectable moiety.
  • the invention relates to a kit for preparing, in particular according to the method of the first and fourth aspect of the invention, a modified nucleic acid according to the second aspect of the invention, wherein the kit comprises at least one nucleoside/nucleotide analogue with an ethenyl aromatic moiety and/or at least one labelled nucleic acid, in particular at least one nucleoside/nucleotide analogue according to formula (I) or (I I), and a reagent comprising a tetrazine moiety according to formula (I I I).
  • the kit comprises basic materials and reagents for labelling and modifying nucleic acids according to the described process.
  • An inventive kit may include at least one nucleoside/nucleotide analogue comprising ethenyl aromatic groups and a reagent comprising a tetrazine linked to a directly or indirectly detectable group.
  • Certain inventive kits may further comprise additives e.g. reaction buffers and/or reagents, wash buffers, fixation buffers and/or reagents. Protocols for using the components of the inventive kits may also be included.
  • the present invention also provides kits for preparing modified nucleic acids comprising at least one nucleoside/nucleotide analogue comprising ethenyl aromatic groups and a reagent comprising a tetrazine linked to a detectable group.
  • a sixth aspect of the invention relates to a use of a nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a nucleoside/nucleotide analogue according to formula (I) or (II), in preparing modified nucleic acid, in particular a modified nucleic acid according to the second aspect of the invention.
  • a seventh aspect the invention relates to at least one nucleoside/nucleotide analogue and/or at least one modified nucleic acid according to the second and third aspect of the invention for use as diagnostic substance or composition.
  • nucleoside/nucleotide analogue and/or modified nucleic acid for use as diagnostic substance or composition references is made to the detailed description of the first aspect of the invention.
  • the at least one modified nucleic acid comprising dihydropyridazine and pyridazine units may be used as diagnostic substances or compositions in vitro and/or in vivo to specifically detect, locate, capture and quantify target nucleic acid polymers.
  • FIG. 3 Selectivity of VdU for incorporation into newly synthesized cellular DNA versus RNA.
  • Cells were incubated with or without the DNA synthesis inhibitor aphidicolin (10 ⁇ ) in the presence of 30 ⁇ VdU for 16 h. After removal of aphidicoline, cells were washed three times with DMEM, and EdU (10 ⁇ ) was added for 3 hours. Afterwards, cells were fixed and modified with Tamra-Tz and AF-azide. No VdU labelling was observed in cells treated with aphidicolin. The cells could restart their DNA synthesis activities as shown by the positive staining for EdU as soon as cells were released from the aphidicolin block. Total cellular DNA was stained with DAPI. Scale bars represent 50 ⁇ .
  • DIC differential interference contrast image.
  • FIG. 4 Time-dependent modification with Tamra-Tz of VdU labelled DNA in HeLa cells. Cells were incubated with 40 ⁇ VdU for 12 h. Cells were then fixed and stained using 5 ⁇ Tamra-Tz for variable incubation times. Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a synthetic nucleoside prior to the staining reaction. Scale bars represent 50 ⁇ .
  • FIG. 5 Modification of newly synthesized DNA in HeLa cells using VdC.
  • Cells were incubated with variable concentrations of VdC for 16 h. Cells were then fixed and stained using 5 ⁇ Tamra-Tz. Total cellular DNA was stained with DAPI.
  • Negative controls received identical treatments, but were not exposed to a nucleoside analogue prior to the modification reaction. Scale bars represent 50 ⁇ .
  • DIC differential interference contrast image.
  • FIG. 6 Modification of newly synthesized DNA in HeLa cells using VdA.
  • Cells were incubated with variable concentrations of VdA for 16 h. Cells were then fixed and stained using 5 ⁇ Tamra-Tz. Total cellular DNA was stained with DAPI.
  • Negative controls received identical treatments, but were not exposed to a nucleoside analogue prior to the modification reaction. Scale bars represent 50 ⁇ .
  • DIC differential interference contrast image.
  • Figure 7 Chemical structure of different tetrazine reagents.
  • FAM-Tz tetrazine-5-fluoresceine
  • Cy3-Tz 6-methyl-tetrazine-Cy3
  • Cy5-Tz 6-methyl-tetrazine-Cy5
  • Tamra-Tz tetramethylrhodamine-dipyridyl-tetrazine
  • Figure 9 Total metabolic activities of different cell cultures according to the Alamar Blue assay in standard media (DMEM supplemented with 4.5 g/L glucose and 10% FBS) with variable concentrations of synthetic nucleosides after 72 hours. Values were normalized relative to untreated cells (DMSO only).
  • Figure 10 Total metabolic activities of different cell cultures according to the Alamar Blue assay in standard media (DMEM supplemented with 4.5 g/L glucose and 10% FBS) with variable concentrations of synthetic nucleosides after 72 hours. Values were normalized relative to untreated cells (DMSO only).
  • Figure 11 FACS analysis to assess the effect of continuous exposure of HeLa cells to 30 ⁇ VdU or 10 ⁇ EdU on the level of ⁇ 2 ⁇ .
  • Figure 13 Dual labelling of cells. Cells were treated sequentially with a pulse of EdU for 4 hours followed by a VdU "chase” for an additional 4 hours and vice versa with washing in between. Cells were fixed and stained with Tamra-Tz and AF-azide. Approximately 50% of cells stained for VdU or EdU. Alternatively, cells were treated with VdU for 12 hours, washed with medium for 2 hours and chased with EdU for additional 2 hours. Total cellular DNA was stained with DAPI. Scale bars represent 50 ⁇ .
  • Figure 14 Cell imaging analysis using Cell Profiler software. The histograms show the integrated intensity of sequentially labelled VdU and EdU cells identified according to the DAPI signal.
  • Experimental details cells were treated sequentially with a pulse of 10 ⁇ EdU for 4 hours followed by a 30 ⁇ VdU chase for an additional 4 hours with washing in between. Cells were fixed and stained with Tamra-Tz and AF-azide.
  • Figure 15 Triple labelling of newly synthesized DNA in HeLa cells by VdU, BrdU and F-ara- EdU. Controls: VdU (30 ⁇ ), BrdU (30 ⁇ ) and F-ara-EdU (10 ⁇ ) were independently added and incubated for 2 h 45 min. For control experiments (C) the nucleosides were omitted, but the cells were otherwise treated identically.
  • Figure 16 Triple labelling of newly synthesized DNA in HeLa cells by VdU, BrdU and F-ara- EdU. Triple labelling: VdU (30 ⁇ ), BrdU (30 ⁇ ) and F-ara-EdU (10 ⁇ ) were sequentially added and incubated for 2 h 45 min each.
  • nucleic acid refers to a deoxyribonucleotide (e.g DNA) or ribonucleotide (e.g. RNA) oligomer, comprising a length of 2 up to 200 nucleotide units, or polymers, comprising a length of more than 200 nucleotide units in either single- or double- stranded form.
  • RNA ribonucleotide
  • Preferred embodiments are nucleic acid polymers.
  • the nucleic acid may be a purified molecule in solution or immobilized onto a surface, or it may be located inside a cell or organism.
  • nucleic acid polymer means a nucleic acid, which bears one or more dihydropyridazine and/or pyridazine units that are formed by following the process of incorporating ethenyl aromatic groups into nucleic acids and reacting those groups with a tetrazine reagent.
  • labelled or “labelling” when used herein in reference to a nucleic acid means a nucleic acid comprising at least one ethenyl nucleotide analogue.
  • nucleotide analogue refers to a compound that is structurally and functionally similar to a natural nucleotide e.g. such as it has similar ability to base pair with one of the naturally occurring bases.
  • nucleoside analogue refers to a compound that is structurally and functionally similar to a natural nucleoside e.g. such as it has similar ability to be incorporated into DNA by DNA replication or RNA by RNA transcription.
  • Organism refers to a living system that has or can develop the ability to act or function independently. Organisms include humans, animals, plants, bacteria, protozoa, and fungi.
  • kit used herein in connection to the invention refers to a combination of two or more substances containing detailed instructions for their utilization to accomplish the invention.
  • linker used herein in connection to the invention refers to a variable covalent linkage between two or more functional groups, e.g. such as a polyethylene glycol chain separating a tetrazine group and fluorescent molecule.
  • tautomeric forms used herein in connection to the invention refers to constitutional isomers of dihydropyridazine units wherein single bonds and adjacent double bonds switch due to a formal migration of hydrogen atoms.
  • a "polynucleotide template” according to the invention comprises one or more coding and/or non-coding nucleic acids.
  • alkyl refers to a saturated straight or branched hydrocarbon moiety containing up to 10, particularly up to 6 carbon atoms.
  • alkyl groups include, without limitation, methyl, ethyl, propyl, butyl, isopropyl, n-hexyl, octyl, decyl and the like.
  • Alkyl groups typically include from 1 to about 10 carbon atoms, particularly from 1 to about 6 carbon atoms.
  • Alkyl groups as used herein may optionally include further substituent groups.
  • alkenyl refers to a straight or branched hydrocarbon chain moiety containing up to 10 carbon atoms and having at least one carbon-carbon double bond.
  • alkenyl groups include, without limitation, ethenyl, propenyl, butenyl, 1 -methyl-2-buten-1- yl, dienes such as 1 ,3-butadiene and the like.
  • Alkenyl groups typically include from 2 to about 10 carbon atoms, more typically from 2 to about 6 carbon atoms. Alkenyl groups as used herein may optionally include further substituent groups.
  • alkynyl refers to a straight or branched hydrocarbon moiety containing up to 10 carbon atoms and having at least one carbon-carbon triple bond.
  • alkynyl groups include, without limitation, ethynyl, 1 -propynyl, 1 -butynyl, and the like.
  • Alkynyl groups typically include from 2 to about 10 carbon atoms, more typically from 2 to about 6 carbon atoms.
  • Alkynyl groups as used herein may optionally include further substituent groups.
  • alkylidene refers to any of a class of divalent functional groups derived from an alkane by removal of two hydrogen atoms from the same carbon atom, the free valencies being part of a double bond.
  • aryl refers to a hydrocarbon with alternating double and single bonds between the carbon atoms forming a ring structure (in the following also “aromatic hydrocarbon”).
  • heteroaryl refers to aryl compounds in which at least one carbon atom is replaced with an oxygen, a nitrogen or a sulphur atom.
  • Aryl or hetero aryl groups as used herein may optionally include further substituent groups.
  • heterocycle refers to cycloalkyl compounds (an interconnected alkyl group forming a ring structure containing 3 to 8, particularly 5 to 6 carbon atoms) in which at least one carbon atom is replaced with an oxygen, a nitrogen or a sulphur atom forming a ring structure. Said ring structure comprising at least one double or triple bond. Heterocycle groups as used herein may optionally include further substituent groups.
  • the inventors focused on the development of alternative methods for modifying nucleic acid polymers or oligomers to address limitations of available methods mentioned above.
  • the present invention provides methods for the incorporation of ethenyl aromatic groups into nucleic acids that are reactive in the presence of a reagent comprising a tetrazine group.
  • the reaction between the labelled nucleic acid and the tetrazine group is rapid and chemically orthogonal to other reactions used for modifying nucleic acids such as, for example, azide- alkyne cycloaddition.
  • the described nucleoside/nucleotide analogues exhibit reduced genotoxicity as compared to commonly used analogues.
  • the products of the modification reaction comprise novel substances containing one or more dihydropyridazine and/or pyridazine units located at the 5-position or pyrimidines and/or the 7-position of 7-deazapurine residues.
  • This part of invention pertains to 5-ethenyl pyrimidine and 7-ethenyl-7-deazapurine nucleoside/nucleotide analogues used for the labelling nucleic acids with an ethenyl aromatic group.
  • nucleoside/nucleotide analogues suitable for the methods of the present invention include any nucleoside/nucleotide analogues of formula (I) and/or formula (II) comprising an ethenyl aromatic group that can undergo Diels-Alder cycloaddition reaction with tetrazines.
  • nucleoside/nucleotide analogues such as 5-substituted pyrimidine or 7-substituted 7-deazapurines for example have been reported in literature and are well known in the art (J. Am. Chem. Soc. 122, 5646-5647, 2000; Bioorg. Med. Chem. Lett. 1 1 , 2917-2920, 2001 ; Helv. Chim. Acta 78, 1083-1090, 1995; Bioorganic & Medicinal Chemistry Letters 21 , 7094-7098, 201 1 ).
  • Nucleoside/nucleotide analogues prepared by the present inventors are treated with metal scavenger to remove eventually remaining toxic catalysts which may be used for the synthesis of the nucleoside/nucleotide analogues.
  • nucleoside/nucleotide analogues of formula (I) and/or formula (II) can represent new chemical entities, as well as previously-known compounds that have been used in applications unrelated to the process presented within this invention.
  • the labelling process is conducted from solutions comprising at least one nucleoside analogue of 5-ethenyl pyrimidines of formula (l a ) and (l b ):
  • R 2 denotes a hydrogen (H) or hydroxyl (OH).
  • R 4 independently denotes a hydroxyl (OH), phosphate (OP0 3 2" ), triphosphate (OPO 3 PO 3 PO 3 4" ), phosphate triester (-OP0 3 (R p ) 2 ) or their derivatives in forms of acids, esters, bases and salts thereof, wherein R p is an alkylester, alkylthioester, or C-
  • the labelling process is conducted from solutions comprising at least one nucleoside analogue of 7-ethenyl-7-deazapurines of formula (ll a ) and
  • R 2 denotes a hydrogen (H) or hydroxyl (OH).
  • R 4 independently denotes a hydroxyl (OH), phosphate (OP0 3 2" ), triphosphate (OPO 3 PO 3 PO 3 4" ), phosphate triester (-OP0 3 (R p ) 2 ) or their derivatives in forms of acids, esters, bases and salts thereof, wherein R p is an alkylester, alkylthioester, or C-
  • VdA 7-vinyl-7-deaza-2'-deoxyadenosine
  • VA 7-vinyl-7-deazaadenosine
  • VdG 7-vinyl-7-deaza-2'-deoxygua
  • Nucleic acids generated according to the process presented in this invention are single- or double-stranded deoxyribonucleotide or ribonucleotide oligomers and/or polymers.
  • nucleoside/nucleotide analogues of formula (I) and/or formula (II) comprising an ethenyl aromatic group are added to enzyme mixtures containing kinases and/or phosphatases in vitro or in vivo, whereupon the 5'-position (R 4 ) is converted into a triphosphate and the resulting nucleotide triphosphate carrying the ethenyl aromatic group is incorporated into nucleic acids by means of one or more polymerases.
  • the method of the invention is practiced in a cell-free extract, wherein a polynucleotide template, nucleoside triphosphates, a nucleic acid polymerase and nucleotide analogues are provided in free solution.
  • the nucleic acid polymerase is a DNA dependent polymerase. According to another embodiment, the nucleic acid polymerase is a RNA dependent polymerase (reverse transcriptase). According to one embodiment, the nucleic acid polymerase is thermostable up to 95°C.
  • the method of the invention is practiced in a living cell, whereby the nucleoside/nucleotide analogues are provided to a cell culture medium or an organism in which the cell is present.
  • the method of the invention is practiced in a living cell, whereby the nucleoside/nucleotide analogues are provided by microinjection, electroporation, optoporation or ballistic transfer (gene gun) methods to name only a few.
  • the resulting ethenyl-labelled nucleic acid can be modified with tetrazine reagents via Diels- Alder cycloaddition reaction.
  • Diels-Alder cycloaddition reaction This version of the Diels-Alder cycloaddition reaction is termed "invers electron demand" Diels-Alder (Eur. J. Org. Chem. 1998, 2885-2896, 1998; Tetrahedron Lett. 24, 1481-1484, 1983).
  • Tetrazines of formula (III) can be added to a nucleic acid comprising one or more ethenyl aromatic groups; such that a reaction occurs between the ethenyl aromatic group and the tetrazine group to form a product of one or more dihydropyridazine and/or pyridazine units:
  • R 6 and R 7 - independently denote a hydrogen (H), halogen, methyl, trifluoromethyl (CF 3 ), trichloromethyl (CCI 3 ), cyano (CN), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-OR), thioether (-SR),
  • - and/or one or more detectable group that is attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle.
  • the reaction is performed with tetrazines, wherein R 7 is conjugated to a directly detectable fluorescent label attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker.
  • the reaction is performed with tetrazines, wherein R 7 is conjugated via an amide linkage to a directly detectable group, e.g. fluorophores such as tetramethylrhodamine, cyanine or fluoresceine, to name only a few.
  • the resulted modification may be indirectly detectable, e.g. wherein R 6 or R 7 is conjugated via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker to an indirectly detectable group such as hapten or biotin.
  • Tetrazine reagents linked to fluorophores are also commercially available from different companies, e.g. Jena Bioscience.
  • nucleic acid polymers comprised of one or more dihydropyridazine and/or pyridazine units located at the 5-position or pyrimidines and/or the 7-position of 7-deazapurines residues. According to certain embodiments, these products are used to analytically differentiate newly synthesized nucleic acids in cells.
  • the dihydropyridazine units and its tautomeric forms of formula (XIII) are formed by reacting ethenyl aromatic groups of formula (XII) with tetrazine reagents of formula (III):
  • R 6 and R 7 independently denote a hydrogen (H), halogen, methyl, trifluoromethyl (CF 3 ), trichloromethyl (CCI 3 ), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (- OR), thioether (-SR), and/or one or more detectable group that is attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle.
  • Nut denotes a nucleotide unit within a nucleic acid.
  • the dihydropyridazine-containing nucleic acid may be directly detectable such as it does not require any further manipulation to be detected, e.g. due to a radioactive isotope present. According to one embodiment, the dihydropyridazine-containing nucleic acid may be directly detectable such as it does not require any further manipulation to be detected, e.g. due to intrinsic fluorescence properties.
  • R 7 of the dihydropyridazine-containing nucleic acid is conjugated to a directly detectable fluorescent label attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker.
  • R 7 of the dihydropyridazine-containing nucleic acid is conjugated via an amide linkage to a directly detectable group, e.g. fluorophores such as tetramethylrhodamine, cyanine or fluoresceine, to name only a few.
  • a directly detectable group e.g. fluorophores such as tetramethylrhodamine, cyanine or fluoresceine
  • the dihydropyridazine-containing nucleic acid indirectly detectable, e.g. wherein R 7 is conjugated via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker to an indirectly detectable group such as hapten or biotin.
  • the pyridazine units of formula (XIV) are formed under oxidizing conditions by reacting ethenyl aromatic groups of formula (XII) with tetrazine reagents of formula (III):
  • R 6 and R 7 independently denote a hydrogen (H), halogen, methyl, trifluoromethyl (CF 3 ), trichloromethyl (CCI 3 ), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (- OR), thioether (-SR), and/or one or more detectable group that is attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle.
  • - Nut denotes a nucleotide unit within a nucleic acid.
  • an oxidizing agent such as 0 2
  • the pyridazine-containing nucleic acid may be directly detectable such as it does not require any further manipulation to be detected, e.g. due to a radioactive isotope present. According to one embodiment, the pyridazine-containing nucleic acid may be directly detectable such as it does not require any further manipulation to be detected, e.g. due to intrinsic fluorescence properties.
  • R 7 of the pyridazine is conjugated to a directly detectable fluorescent label attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker.
  • R 7 of the pyridazine is conjugated via an amide linkage to a directly detectable group, e.g. fluorophores such as tetramethylrhodamine, cyanine or fluoresceine, to name only a few.
  • a directly detectable group e.g. fluorophores such as tetramethylrhodamine, cyanine or fluoresceine, to name only a few.
  • the pyridazine may be indirectly detectable, e.g. wherein R 7 is conjugated via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker to an indirectly detectable group such as hapten or biotin.
  • the products of the modification reaction comprising dihydropyridazine and pyridazine units of formula (XIII) and (XIV) may be used as diagnostic substances or compositions in vitro and/or in vivo to specifically detect, locate, capture and quantify target nucleic acids.
  • the dihydropyridazine and pyridazine units may be used to localize high proliferating cancer cells as well as viral compartments/particles in patients.
  • the dihydropyridazine and pyridazine-containing nucleic acid may be directly detectable, e.g. due to a radioactive isotope present.
  • the dihydropyridazine and pyridazine units are conjugated to a directly detectable fluorescent label attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker.
  • the dihydropyridazine and pyridazine units may be indirectly detectable, e.g. wherein R 7 of formula (XIII) and(XIV) is conjugated via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker to an indirectly detectable group such as hapten or biotin.
  • Human cervical cancer cells (HeLa) were incubated with variable concentrations of 5-vinyl-2'- deoxyuridine (VdU) for 16 h. The cells were then washed, fixed and modified using a tetramethylrhodamine-dipyridyl-tetrazine conjugate ("Tamra-Tz", see Figure 7). When the cellular DNA was denatured prior to the addition of Tamra-Tz, intense nuclear staining that colocalized with the non-covalent DAPI stain was observed ( Figure 1 ). In contrast, cells not receiving VdU displayed no detectable DNA staining if subjected to the same fixation and modification procedures.
  • VdU 5-vinyl-2'- deoxyuridine
  • HeLa cells were incubated with 40 ⁇ VdU for 12 h. Following fixation of the cells, the addition of Tamra-Tz to VdU-treated cells resulted in rapid intranuclear staining after only 30 min at 37 °C ( Figure 4). Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a synthetic nucleoside prior to the staining reaction.
  • VdC 5-vinyl-2'-deoxycytidine
  • VdA 7-vinyl-7-deaza-2'- deoxyadenosine
  • Example 5 Labelling and modification of cells with VdU and different tetrazine reagents
  • HeLa cells were incubated with 30 ⁇ 5-vinyl-2'-deoxyuridine (VdU) for 16 h. The cells were then washed, fixed and modified using fluorescent tetrazines probes indicated in Figure 7. When the cellular DNA was denatured prior to the addition of reagents, intense nuclear staining that colocalized with the non-covalent DAPI stain was observed ( Figure 8). In contrast, cells not receiving VdU displayed no detectable DNA staining if subjected to the same fixation and modification procedures.
  • VdU 5-vinyl-2'-deoxyuridine
  • the biological impact of the metabolic label should be minimal during the labelling period, so that the experimental results are not influenced by excessive toxicity, cell cycle arrest, and/or activation of DNA damage pathways.
  • a standard "Alamar Blue” assay was used to assess the combined effects of proliferation and metabolism on total cellular respiration for VdU. As a comparison, BrdU and EdU were also included. The cell cultures were grown in the presence of various nucleoside concentrations for 24 - 72 hours. In all cell types tested, EdU was consistently more toxic than VdU and BrdU. EdU exhibited IC 50 values (defined as the concentrations needed to inhibit 50% of the total metabolic activity) that were 2 - 15-fold lower than VdU ( Figure 9). A standard "Alamar Blue” assay was also used to assess the combined effects of proliferation and metabolism on total cellular respiration for VdC and VdA ( Figure 10).
  • Pulse-chase labelling experiments where multiple metabolic probes are introduced into DNA over time, are used in a wide variety of important biological experiments such as characterizing the timing of DNA replication, visualizing embryogenesis, and in stem cell research (Nature 494, 476-479, 2013; Nature 425, 836-841 , 2003; Science 310, 1327-1330, 2005).
  • VdU-tetrazine ligation in combination with EdU-azide cycloaddition for introducing orthogonal chemical labels into cellular DNA.
  • VdU and EdU could, in principal, be expanded to include a third color if BrdU was included. This would provide a valuable third level of spatial and temporal resolution to pulse-chase labelling experiments.
  • VdU 1 (VdU) 2 (py 2 -Tz) 3 (VdU-Tz, 52%) 4 (VdU-Tz-ox, 29%)
  • Example 12 Verification of dihydropyridazine derivative 8 (VdA-Tz) and pyridazine 9 (VdA-Tz-ox)
  • VdC-Tz The cycloaddition product 6 VdC-Tz was investigated for its pH-dependent intrinsic fluorescence properties.
  • the quantum yield ( ⁇ ) of the product was measured to be 0.05 independent of the pH (reference: quinine sulfate).
  • the brightness was calculated as the product of molar absorptivity ( ⁇ ) and the quantum yield.
  • HeLa, U20S, MRC-5 and Vero cells were cultivated at 37°C, 5% C0 2 in DMEM (Gibco) containing 4.5 g/L glucose, 10% FBS (Gibco), 50 ⁇ 00 units Penicillin and 50 mg Streptomycin per L (Sigma Aldrich).
  • A549 cells were cultivated with additional 1 % of MEM non-essential amino acids solution 100x (Sigma). Cells were grown to confluency and passaged every 2 to 4 days using Trypsin-EDTA solution (Sigma Aldrich). Cells were counted using Scepter cell counter (Millipore) for the determination of seeding densities. Microscopy.
  • DAPI was excited at 405 nm, and emission was sampled between 420 and 470 nm; AlexaFluor 488 was excited at 488 nm, and emission was sampled between 500 and 550 nm; TamraX-550-Tz was excited at 561 nm, and emission was sampled between 570 and 630 nm, AlexaFluor 647 was excited at 633 nm, and emission was sampled between 655 and 700 nm.
  • Image analysis was performed using LAS AF 2.6.0 (Leica Microsystems), ImageJ 1.47c (National Institutes of Health, USA) and Imaris x64 7.1 .1 (Bitplane). Metabolic labelling of cellular DNA using synthetic nucleosides.
  • Cells were seeded in 100 mm round cell culture dishes (13 mL) containing glass coverslips (VWR, thickness 1.5, diameter 13 mm) at 100 ⁇ 00 - 300 ⁇ 00 cells per mL and incubated overnight to ensure an even distribution of cells.
  • the coverslips were placed in 24-well plates containing fresh media solutions with variable concentrations of nucleosides (diluted from appropriate stock solutions in DMSO). After incubating for various times, the cells were fixed in paraformaldehyde (3.7%) for 15 min at room temperature, quenched with PBS containing 50 mM glycine and 50 mM NH 4 CI for 5 min, and washed twice with PBS. Samples were then stained via invDA or CuAAC.
  • HeLa, U20S, MRC-5, Vero, or A549 cells were seeded in 96-well plates at a density of 5 ⁇ 00 - 10 ⁇ 00 cells per well and incubated overnight. The supernatant was removed, and fresh media containing variable concentrations of each nucleoside in DMSO was added (final DMSO 0.05%). Control samples contained 0.05% DMSO only. Cells were grown for 24 - 72 h. The media were removed and fresh media containing 87 ⁇ of resazurin in media (freshly prepared from an 870 ⁇ stock solution in PBS) was added.
  • Fluorescence-assisted cell sorting FACS: ⁇ 2 ⁇ immunostaining. Cells were seeded in 6-well plates at 250 ⁇ 00 cells per well and incubated overnight. The supernatant was removed, and fresh media solutions containing 30 ⁇ VdU or 10 ⁇ EdU (diluted from 2000x stock solutions in DMSO) were added. After incubating for 4 or 16 hours, the supernatant was removed.
  • the cells were washed with 1 % BSA in PBS, pelleted and resuspended in 100 ⁇ _ 1 % BSA in PBS containing mouse monoclonal anti-phospho-histone antibody (H2A.X, Ser 139; 0.5 ⁇ g/mL; Millipore) for 2 hours at room temperature. Cells were washed with 1 % BSA in PBS. After pelleting, cells were resuspended in 50 ⁇ _ 1 % BSA in PBS containing secondary antibody (AlexaFluor 488 conjugate, 2 ⁇ g / ml. ; Life technologies) for 1 hour at room temperature in the dark. Cells were washed with PBS.
  • secondary antibody AlexaFluor 488 conjugate, 2 ⁇ g / ml. ; Life technologies
  • alkyne-modified DNA was stained with AlexaFluor-488-azide (3 ⁇ AF-488-azide, 1 mM CuS0 4 , 10 mM sodium ascorbate, in PBS; 30 min, room temperature, in the dark; Life technologies). Samples were washed 0.1 % Triton X-100 in PBS, and PBS (3x). Total DNA was stained with DAPI (1 - 5 ⁇ in PBS) for 15 min at room temperature in the dark.
  • AlexaFluor-488-azide 3 ⁇ AF-488-azide, 1 mM CuS0 4 , 10 mM sodium ascorbate, in PBS; 30 min, room temperature, in the dark; Life technologies. Samples were washed 0.1 % Triton X-100 in PBS, and PBS (3x). Total DNA was stained with DAPI (1 - 5 ⁇ in PBS) for 15 min at room temperature in the dark.
  • the coverslips were washed with PBS (2x) and nanopure water and glued upside-down on microscopy slides using Glycergel (1 1 ⁇ _, Dako). Triple labelling of cellular DNA synthesis with VdU, BrdU and F-ara-EdU.
  • cells were fixed using paraformaldehyde (3.7% in PBS, 15 min, room temperature), quenched (glycine 50 mM, NH 4 CI 50 mM, in PBS; 5 min, room temperature), permeabilized with acetone (2 min at - 20°C) and washed with ice-cold PBS (3x).
  • Cells were then incubated with 2 M HCI in PBS (30 min, room temperature), washed with PBS (1 x), neutralized with 0.1 M aq. Na2B 4 O7'10H 2 O (10 min, room temperature), and washed with PBS (3x).
  • the coverslips were then incubated upside down on 25 ⁇ _- drops of mouse monoclonal BrdU antibody-AlexaFluor-488 conjugate (2 ⁇ g/mL in blocking solution; Invitrogen) for 2 hours at room temperature in the dark. Samples were washes with PBS (3x) and then the alkyne-modified DNA was stained with AlexaFluor-647-azide (10 ⁇ AF-647-azide, 1 mM CuS0 4 , 10 mM sodium ascorbate, in PBS; 1 h, room temperature, in the dark). Samples were washed with 0.1 % Triton X-100 in PBS, and PBS (3x).

Abstract

This invention pertains to the preparation of modified nucleic acids by means of enzymatic synthesis and chemical modification of nucleic acids bearing ethenyl aromatic groups with tetrazines. The invention is also directed to the products of the process; comprising nucleosides/nucleotides and nucleic acids containing one or more dihydropyridazine and/or pyridazine units located at the 5-position of pyrimidines and/or the 7-position of 7- deazapurine residues.

Description

Methods and products from the reaction of tetrazines with nucleic acids bearing ethenyl aromatic groups
FIELD OF THE INVENTION
This invention pertains to the preparation and products of modified nucleic acids by means of enzymatic synthesis and chemical modification. The invention is also directed to the products of the process; comprising nucleosides/nucleotides and nucleic acids containing one or more dihydropyridazine and/or pyridazine units located at the 5-position of pyrimidines and/or the 7-position of 7-deazapurine residues.
BACKGROUND OF THE INVENTION
Non-native functional groups can be incorporated into nucleic acids by the addition of a synthetic nucleoside/nucleotide to whole cells, cell lysates, purified enzyme mixtures, or whole animals containing appropriate nucleotide kinases and/or polymerases that incorporate the unnatural nucleotide units into newly synthesized DNA or RNA molecules. In a second step, the modification and/or detection of the non-native functional groups can be accomplished by the application of an immunohistochemical or chemical reaction. This second step is most commonly used to introduce an analytical probe that is specific for the newly-synthesized nucleic acids, such as a radiolabel, fluorescent marker, and/or biotin group.
The most widely used non-natural precursors for RNA and DNA synthesis are currently the halogenated nucleosides 5-bromouridine (BrU) (Exp. Cell Res. 260, 248-256, 2000), 5- bromo-2'-deoxyuridine (BrdU) (Brain Res Rev 53, 198-214, 2007), and their corresponding nucleotide triphosphates (NTP's). BrU and BrdU NTP's are incorporated into nucleic acids by natural RNA and DNA polymerases in the presence of unmodified NTP's to give nucleic acid polymers containing one or more bromine groups. Nucleic acids containing BrU or BrdU can be immunohistochemically modified by the addition of antibodies raised specifically for the brominated residues. This approach can be used for the characterization of newly synthesized DNA RNA polymers in vitro and in vivo, but is severely limited by the poor tissue permeability of antibodies (Proc. Natl. Acad. Sci. U. S. A. 108, 20404-20409, 201 1 ).
Bioorthogonal chemical reactions provide highly attractive alternatives for the modification of biopolymers containing non-native functional groups (Science 287, 2007-2010, 2000; J. Am. Chem. Soc. 125, 3192-3193, 2003; Chem. Commun. 49, 1 1007-1 1022, 2013). In this approach, a highly chemoselective reaction is used to chemically modify a biomolecule containing a non-native functional group. One of the most commonly used chemoselective reactions for this purpose is the copper(l)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction (Coord. Chem. Rev. 255, 2933-2945, 201 1 ). In the context of nucleic acids, 5- ethynyluridine (EU) and 5-ethynyl-2'-deoxyuridine (EdU) can be phosphorylated and incorporated into RNA molecules (Proc. Natl. Acad. Sci. U. S. A. 105, 15779-15784, 2008) and DNA molecules (Proc. Natl. Acad. Sci. U. S. A. 105, 2415-2420, 2008) by enzymes mixtures in vitro and in vivo. Further modification of the ethynyl groups in the nucleic acid polymers can be accomplished by CuAAC reactions to furnish triazole units at the 5-positions of pyrimidine residues.
Taken together, the incorporation and detection of azide/alkyne groups in nucleic acids has constituted an important invention (PCT Int. Appl. (2007), WO 200705081 1 A2 20070503). One key advantage of this approach is that CuAAC reactions exclusively utilize small molecules for modification, rather than antibodies. The sensitivity of alkyne detection using CuAAC can therefore exceed that of the immunohistochemical detection of BrU and BrdU, especially in vivo. Another key advantage of this approach is that the combination of alkyne- modified nucleic acids and CuAAC reactions can be used for preparative-scale reactions including capture experiments to provide an unambiguous assignment of labelled biomolecules and their associated components (Scientific reports 1 , 95, 201 1 ). The use of copper(l) in these experiments, however, is highly problematic, as it causes degradation of proteins and nucleic acids in the isolated samples (J. Biochem. 94, 1259-1267, 1983). This leads to a low yield of highly fragmented nucleic acids due to the CuAAC reaction itself. Yet another limitation to this approach is that the nucleoside analogues used to introduce the bioorthogonal functional groups (for example azide or alkyne) into the nucleic acids can be extremely toxic. For example, the most commonly used ethynyl nucleoside for DNA modification is 5-ethynyl-2'-deoxyuridine (EdU) which was initially developed as a chemotherapeutic drug in the 1980's (J. Med. Chem. 26, 661 -666, 1983). The addition of EdU to living cells causes extensive DNA damage, cell cycle arrest and apoptosis, even when it is applied at low concentrations (IC50 « 0.2 μΜ) (J. Med. Chem. 26, 661 -666, 1983; Bioorg. Med. Chem. 15, 3082-3088, 2007; Cytometry A 83, 979-988, 2013). These inhibitory concentrations are approximately 50-fold lower than the concentrations of EdU (10 μΜ) typically added to cells for its enzymatic incorporation into DNA (PCT Int. Appl. (2007), WO 200705081 1 A2 20070503). This causes low isolated yields of the nucleic acids when cells are treated with EdU for extended periods, and can also cause large perturbations to bioanalytical experiments that are aimed at characterizing cell cycle, DNA repair, and RNA expression, to name only a few. In diagnostic and preparative applications, the development of a new method for the preparation of modified nucleic acid polymers would facilitate applications such as, biological engineering. All previously reported methods for the bioorthogonal chemical modification of enzymatically prepared DNA and RNA molecules have hitherto utilized azide-alkyne "click" reactions. The development of alternative bioorthogonal chemical reactions for RNA and DNA labelling would be highly desirable in the following situations:
- where multiple bioorthogonal chemical reactions are required,
in situations where azide-alkyne "click" reactions are utilized for other modifications in the same system
- to potentially minimize the biological impact of the nucleoside analogue itself,
and to utilize copper-free reaction conditions for preparations of modified yet otherwise undamaged DNA or RNA molecules,
to name only a few circumstances. Thus, the objective of the present invention is to provide the materials and methods for the preparation and modification of nucleic acids, improving the above disadvantages of known methods. A further object of the invention is to provide novel modified nucleic acids and the use of reagents in providing said modified nucleic acids. Inverse electron demand Diels-Alder (invDA) reactions between electron-deficient tetrazines and electron-rich dienophiles are particularly attractive bioorthogonal chemical reactions since they are irreversible, do not require a catalyst, and are compatible with cell media (J. Am. Chem. Soc. 130, 13518-13519, 2008; Nat Chem 4, 298-304, 2012; Angew. Chem., Int. Ed. Engl. 51 , 4466-4469, 2012). To date, invDA reactions have been used for labelling synthetic oligonucleotides in vitro as well as cellular and cell surface proteins using strained dienophiles such as norbornene (Bioconjugate Chem. 19, 2297-2299, 2008; Nat Chem 4, 298-304, 2012; J. Am. Chem. Soc. 132, 8846-8847, 2010), trans-cyclooctene (Angew. Chem., Int. Ed. Engl. 51 , 4166-4170, 2012; Angew. Chem., Int. Ed. Engl. 48, 7013-7016, 2009) and cyclopropene (J. Am. Chem. Soc. 134, 18638-18643, 2012). The addition of such large substituents to nucleosides is known to inhibit their metabolism by enzymes (Biochem. J. 351 Pt 2, 319-326, 2000). We therefore sought the smallest possible dienophile to incorporate into nucleic acids. Since ethenyl aromatic compounds such as styrene are known to react with tetrazines, we identified 5-ethenyl pyrimidine and 7-ethenyl-7-deazapurine nucleosides or derivatives thereof as candidates for the preparation and modification of nucleic acids upon addition of a modifying reagent comprising a tetrazine group. The present invention is based on our surprising finding that the nucleotide triphosphate of 5- vinyl-2'-deoxyuridine (VdU) is enzymatically incorporated into the newly synthesized DNA of living cells, yet unlike 5-ethynyl-2'-deoxyuridine (EdU), it does not cause an accumulation of tetraploid (4n) cells, arrested at G2/M, that stain positively for markers of DNA damage (γΗ2ΑΧ) (DNA Repair 3, 959-967, 2004). Little or no γΗ2ΑΧ formation or G2/M cell cycle arrest was observed in cells treated with VdU, correlating with its diminished cytotoxicity as compared to EdU. While the reasons for these differences are unknown, previous studies have established a relationship between the chemical stability of modified nucleotides and their ability to initiate DNA damage response (Chinese journal of cancer 31 , 373-380, 2012). Studies conducted in vitro revealed that EdU and EdU-containing oligonucleotides decomposed with a half-life of 8 hours in a 20% aqueous methyl amine solution at room temperature (Chemistry 16, 14385-14396, 2010; PLoS One 9, e92369, 2014), while VdU exhibited no detectable decomposition even after 48 hours under these same conditions. This is especially surprising, given the nearly identical chemical structures of these nucleosides. We furthermore show that, in general, 5-ethenyl pyrimidine and 7-ethenyl-7- deazapurine nucleosides are metabolically incorporated into nucleic acids that, upon addition of a modifying reagent comprising a tetrazine group, results in a covalent modification of the nucleic acid. The novel products from these reactions are nucleic acid polymers containing one or more dihydropyridazine and/or pyridazine units located at the 5-positions of pyrimidine and/or the 7-positions of 7-deazapurine residues. These novel methods, reagents and products are expected to become an important discovery for use biological engineering and academic research; to name only a few applications.
SUMMARY OF THE INVENTION
A first aspect of the invention relates to a process for preparing at least one labelled nucleic acid, comprising steps of:
(a) providing at least one nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a 5-ethenyl pyrimidine moiety or a derivative thereof or a 7-ethenyl-7-deazapurine or a derivative thereof,
(b) contacting said at least one nucleoside/nucleotide analogue to a source of nucleic acid polymers,
(c) applying an enzymatic synthesis yielding at least one labelled nucleic acid, which comprises at least one nucleoside/nucleotide analogue incorporated into said at least one labelled nucleic acid .
According to the first aspect, labelled nucleic acids are provided.
In particular embodiments of the first aspect of the invention subsequent to the incorporation step c of the first aspect of the invention the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue is reacted with at least one reagent comprising a tetrazine moiety forming one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
Thus, modified nucleic acids are provided. A second aspect of the invention relates to a modified nucleic acid, in particular prepared according to the first aspect of the invention, comprising a. at least one dihydropyridazine unit of formula (IV) and/or the corresponding tautomeric forms of said formula and/or
b. at least one pyridazine unit of formula (V) and/or the corresponding tautomeric forms of said formulas and/or
c. at least one dihydropyridazine unit of formula (VI) and/or the corresponding tautomeric forms of said formulas and/or
d. at least one pyridazine unit of formula (VII) and/or the corresponding tautomeric forms of said formulas, in particular from at least one unit comprising the formula (IV) and/or (VI) and/or (VII),
Figure imgf000006_0001
wherein R3, R5, R6, R7, T, and L have the same meaning as discussed in the description the invention.
A third aspect of the invention relates to a nucleoside/nucleotide analogue comprising a. a nucleoside/nucleotide unit and a dihydropyridazine unit of formula (VIII) or (VIII*), in particular of formula (VIII*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000007_0001
b. a nucleoside/nucleotide unit and a pyridazine unit of formula (IX) or (IX*), in particular of formula (IX*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000007_0002
a nucleoside/nucleotide unit and a dihydropyridazine unit of formula (X) or (X*), particular of formula (X*), and/or the corresponding tautomeric forms of said formulas
Figure imgf000007_0003
(X), (X*), or d. a nucleoside/nucleotide unit and a pyridazine unit of formula (XI) or (XI*), in particular of formula (XI*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000008_0001
wherein R3, R4, R5, R6, R7, Nu, and T have the same meaning as discussed in the description of the invention.
A fourth aspect of the invention relates to methods for further modifying labelled nucleic acids by adding at least one tetrazines of formula (III) to at least one labelled nucleic acid, in particular a labelled nucleic acid according to the first aspect of the invention, comprising one or more ethenyl aromatic groups; such that a reaction occurs between the ethenyl aromatic group and the tetrazine group of formula (III):
Figure imgf000008_0002
wherein R6 and R7 are selected independently from each other from
- hydrogen (H), halogen, methyl, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano (CN), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-ORb), or thioether (-SRb), wherein Rb is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from CrC4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
- wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety.
A fifth aspect of the invention relates to a kit for preparing, in particular according to the method of the first and fourth aspect of the invention, a modified nucleic acid according to the second aspect of the invention, wherein the kit comprises at least one nucleoside/nucleotide analogue with an ethenyl aromatic moiety and/or at least one labelled nucleic acid, in particular at least one nucleoside/nucleotide analogue according to formula (I) or (II), and a reagent comprising a tetrazine moiety according to formula (III).
A sixth aspect of the invention relates to a use of a nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a nucleoside/nucleotide analogue according to formula (I) or (II), in preparing modified nucleic acids, in particular modified nucleic acid according to the second aspect of the invention.
A seventh aspect the invention relates to at least one nucleoside/nucleotide analogue and/or at least one modified nucleic acid according to the second and third aspect of the invention for use as diagnostic substance or composition.
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides methods and compositions useful for modifying nucleic acids in vitro and in vivo. The inventive methods include the incorporation of nucleoside analogues into nucleic acids and a chemical reaction between the prior labelled nucleic acid and a reagent comprising a functional, in particular a detectable group. A first aspect of the invention relates to a process for preparing at least one labelled nucleic acid, comprising steps of:
(a) providing at least one nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a 5-ethenyl pyrimidine moiety or a derivative thereof or a 7-ethenyl-7-deazapurine or a derivative thereof,
(b) contacting said at least one nucleoside/nucleotide analogue to a source of nucleic acids,
(c) applying an enzymatic synthesis yielding at least one labelled nucleic acid, which comprises at least one nucleoside/nucleotide analogue incorporated into said at least one nucleic acid.
In some embodiments, said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (lNu) or at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (llNu)
Figure imgf000009_0001
wherein - R3 is selected o in case of formula lNu from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula llNu hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH2) and the corresponding tautomeric forms of the 7- deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine;
- R5 of formula llNu is selected from hydrogen (H), hydroxyl (OH), amino (NH2), or halogen, in particular from hydrogen (H) or amino (NH2), and
- Nu is a sugar moiety or a sugar phosphate moiety, and
- T is selected from O, S or Se, in particular T is O.
In some embodiments, said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (I) or at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (II)
Figure imgf000010_0001
wherein
- R1 and R2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH2), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl, ether (-ORa), or thioether (-SRa), wherein Ra is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C-|-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl;
- R3 is selected o in case of formula I from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula II hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH2) and the corresponding tautomeric forms of the 7- deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine;
- R4 is selected from hydroxyl (OH), phosphate (OP03 2"), diphosphate (OP03P03 3"), triphosphate (OP03P03P03 4"), phosphate diester (OP02RpO"), phosphate triester (-
OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, CrC4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl; and - R5 of formula II is selected from hydrogen (H), hydroxyl (OH), amino (NH2), or halogen, in particular from hydrogen (H) or amino (NH2), and
- T is selected from O, S or Se, in particular T is O.
In some embodiments, said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (I) or ( ), in particular of formula (I*)
Figure imgf000011_0001
R1 and R2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH2), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl, ether (-ORa), or thioether (-SRa), wherein Ra is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C-|-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl;
R3 is selected from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and
R4 is selected from hydroxyl (OH), phosphate (OP03 2"), diphosphate (OP03P03 3"), triphosphate (OP03P03P03 4"), phosphate diester (OP02RpO"), phosphate triester (-OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl, and
- T is selected from O, S or Se, in particular T is O. An example for corresponding amino tautomeric forms of the pyrimidine moiety is given below. In case R3 is OH a lactim compound of a formula lta is provided and the corresponding lactam tautomeric form is shown in formula ltb.
Figure imgf000012_0001
In some embodiments, said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (II)
Figure imgf000012_0002
wherein
- R1 and R2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH2), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl, ether (-ORa), or thioether (-SRa), wherein Ra is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C-|-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl;
- R3 is selected from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine; - R4 is selected from hydroxyl (OH), phosphate (OP03 2"), diphosphate (OP03P03 3"), triphosphate (OP03P03P03 4"), phosphate diester (OP02RpO"), phosphate triester (- OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl; and
- R5 is selected from hydrogen (H), hydroxyl (OH), amino (NH2), or halogen, in particular from hydrogen (H) or amino (NH2).
Examples for corresponding amino tautomeric forms of the 7-deazapurine moiety are given below. In case R3 is NH2 and R5 is H of an amino compound of a formula l lta is provided and the corresponding imino tautomeric form is shown in formula l ltb.
Figure imgf000013_0001
In case R3 is OH and R5 is NH2 a compound of a formula lltc is provided and the corresponding lactam tautomeric form is shown in formula lltd.
Figure imgf000013_0002
In some embodiments, R1 of formula I, I* or II is selected from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH2), C1-C4 alkyl, in particular methyl, C2-C4 alkenyl, C2-C4 alkynyl, ether (-ORa), or thioether (-SRa), wherein Ra is selected from C-|-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl.
In some embodiments, R1 of formula I, I* or II is selected from hydrogen (H), hydroxyl (OH), fluoride (F) or methyl. In some embodiments, R2 of formula I, I* or II is selected from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH2), C1-C4 alkyl, in particular methyl, C2-C4 alkenyl, C2-C4 alkynyl, ether (-ORa), or thioether (-SRa), wherein Ra is selected from C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl. In some embodiments, R2 of formula I, I* or II is selected from hydrogen (H), hydroxyl (OH), fluoride (F) or methyl.
In some embodiments, R3 of formula I, I* is selected from hydroxyl (OH), halogen, methyl, or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine. In some embodiments, R3 of formula I, I* is selected from hydroxyl (OH), halogen, or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine.
In some embodiments, R3 of formula II is selected from hydroxyl (OH), halogen, methyl, or amino group (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine.
In some embodiments, R3 of formula II is selected from hydroxyl (OH), halogen, or amino (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7- deazaadenine and 7-deazaguanine.
In some embodiments, R4 of formula I, I* or II is selected from phosphate diester (OP02RpO" ), phosphate triester (-OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl.
In some embodiments, R4 of formula I or II is selected from hydroxyl (OH). In some embodiments, R5 of formula II is selected from hydrogen (H), hydroxyl (OH), amino (NH2), or halogen.
In some embodiments, R5 of formula II is selected from hydrogen (H), amino (NH2), or halogen.
In some embodiments, R5 of formula II is selected from hydrogen (H) or amino (NH2). In preferred embodiments, T of formula I is O.
In some embodiments,
- R1 and R2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH2), C1-C4 alkyl, in particular methyl, C2-C4 alkenyl, C2-C4 alkynyl, ether (-0Ra), or thioether (-SRa), wherein Ra is selected from Ci-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl; and
- R3 is selected a. in case of formula I, I* from hydroxyl (OH), halogen, methyl, or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and b. in case of formula II from hydroxyl (OH), halogen, methyl, or amino group (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine; and - R4 is selected from phosphate diester (OP02RpO"), phosphate triester (-OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C-|-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl; and - R5 of formula II is selected from hydrogen (H), amino (NH2), or halogen, and
- T is O.
In some embodiments,
- R1 and R2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), fluoride (F) or methyl; and - R3 is selected a. in case of formula I, I* from hydroxyl (OH), halogen, or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and b. in case of formula II hydroxyl (OH), halogen, or amino (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7- deazaadenine and 7-deazaguanine; and
- R4 is selected from hydroxyl (OH); and
- R5 of formula II is selected from hydrogen (H) or amino (NH2), and
- T is O. In some embodiments said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (I), wherein T is O, and i. R1 is H, R2 is H, R3 is OH, R4 is OH; or ii. R1 is F, R2 is H, R3 is OH, R4 is OH; or iii. R1 is H, R2 is H, R3 is OH, R4 is triphosphate, or iv. R1 is H, R2 is OH, R3 is OH, R4 is OH, or v. R1 is H, R2 is OH, R3 is OH, R4 is triphosphate; or vi. R1 is H, R2 is H, R3 is NH2, R4 is OH, or vii. R1 is H, R2 is H, R3 is NH2, R4 is triphosphate; or viii. R1 is H, R2 is OH, R3 is NH2 and R4 is OH, or ix. R1 is H, R2 is OH, R3 is NH2, R4 is triphosphate.
In some embodiments said at least one nucleoside/nucleotide analogue is selected from at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (II), wherein i. R1 is H, R2 is H, R3 is OH, R4 is OH, R5 is NH2; or ii. R1 is H, R2 is H, R3 is OH, R4 is triphosphate, R5 is NH2; or iii. R1 is H, R2 is OH, R3 is OH, R4 is OH, R5 is NH2; or iv. R1 is H, R2 is OH, R3 is OH, R4 is triphosphate, R5 is NH2; or v. R1 is H, R2 is H, R3 is NH2, R4 is OH, R5 is H; or vi. R1 is H, R2 is H, R3 is NH2, R4 is triphosphate, R5 is H, or vii. R1 is H, R2 is OH, R3 is NH2, R4 is OH, R5 is H, or viii. R1 is H, R2 is OH, R3 is NH2, R4 is triphosphate, R5 is H. some embodiments, the nucleic acid source is selected from a. a nucleic acid template, in particular a polynucleotide template; b. cells; or c. organisms; or d. cell extracts; or and/or wherein the enzymatic synthesis is conducted with a. a purified enzyme; or b. a purified enzyme mixture. The previous discussed embodiments of the present invention provide methods for labelling nucleic acids by enzymatic synthesis.
In particular, embodiments of the invention, subsequent to the incorporation step c the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue is reacted with at least one reagent comprising a tetrazine moiety forming one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
In some embodiments, the at least one tetrazine is selected from a tetrazine of formula (I I I):
Figure imgf000017_0001
wherein R6 and R7 are selected independently from each other from
- hydrogen (H), halogen, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano (CN), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-ORb), or thioether (-SRb), wherein Rb is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
- wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety.
In some embodiments, the at least one tetrazine is selected from a tetrazine of formula (I I I):
Figure imgf000017_0002
wherein R6 and R7 are selected independently from each other from
- a heteroaryl group, in particular 2-pyridine and 2-pyrimidine, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
- wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety.
In some embodiments the detectable group comprises at least one detectable moiety that is attached to the tetrazine moiety via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle. In some embodiments, the detectable group comprises a directly or indirectly detectable moiety.
In some embodiments, the detectable group comprises a detectable moiety selected from a. a luminescent agent, in particular a fluorescent agent; or b. a biotin; or c. a hapten; or
In some embodiments, the labelled nucleic acid, which comprises the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue, provided by step c, is reacted directly after the step c with the at least one reagent comprising a tetrazine moiety forming one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
In some embodiments, the labelled nucleic acid, which comprises the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue, provided by step c, is separated, in particular purified, prior to the reaction with the at least one reagent comprising a tetrazine moiety forming one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
The process of preparing the modified nucleic acid comprises two steps; first, the addition of one or more 5-ethenyl pyrimidine and/or 7-ethenyl-7-deazapurine derivatives to enzyme mixtures that incorporate the ethenyl nucleotides into the nucleic acids providing the labelled nucleic acids; second, the addition of a tetrazine reagent that undergoes a [4+2] Diels-Alder cycloaddition with the ethenyl aromatic groups providing the modified nucleic acid.
Thus, the inventive methods comprise steps of: contacting cell lysates, enzyme mixtures, cells or organisms with an effective amount of nucleoside analogues of formula I, and II, wherein R1, R2, R3, R4, R5 and T have the meaning indicated above, such that one or more nucleoside analogues are incorporated into nucleic acids
contacting the ethenyl-modified nucleic acids within aqueous solutions, cell lysates, enzyme mixtures, cells or organisms with a reagent comprising a tetrazine of formula III, wherein R6 and R7 have the meaning indicated above, such that Diels-Alder cycloaddition reaction occurs between the incorporated nucleoside analogue and the reagent.
According to the second aspect the invention relates to a modified nucleic acid, in particular prepared according to the first of the invention, comprising at least one dihydropyridazine unit formula (IV) or (IV*), in particular of formula (IV*) and/or the corresponding tautomeric forms of said formulas:
Figure imgf000019_0001
at least one pyridazine unit of formula (V) or (V*), in particular of formula (V*) and/or the corresponding tautomeric forms of said formulas:
Figure imgf000019_0002
at least one dihydropyridazine unit of formula (VI) and/or the corresponding tautomeric forms of said formula:
+ (VI) and/or at least one pyridazine unit of formula (VII) and/or the corresponding tautomeric forms of said formulas:
Figure imgf000019_0003
in particular the modified nucleic acid comprises at least one unit comprising the formula (IV) and/or (VI) and/or (VII), wherein - R3 is selected o in case of formula IV, IV*, V and V* from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula VI and VII hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7- deazaguanine; and
- R5 denotes a hydrogen (H), hydroxyl (OH), amino (NH2), or halogen, in particular from hydrogen (H) or amino (NH2);
- R6 and R7 are selected independently from each other from o hydrogen (H), halogen, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano (CN), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-ORb), or thioether (-SRb), wherein Rb is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, o wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety, and
- T is selected from O, S or Se, in particular from O, and
- L is a sugar-phosphate linkage to a nucleic acid.
Thus, the sugar-phosphate linkage L is part of the nucleic acid backbone.
In some embodiments, L is a sugar-phosphate linkage to a nucleic acid derived from a reaction of the sugar moiety L* of the compound according to formula I or II
Figure imgf000020_0001
with R1, R2, and R4 having the same meaning as defined previously, and a corresponding sugar/sugar-phosphate moiety of the nucleic acid.
The compound according to formula I or II is connected to a preceding or subsequent monomer or building block in the nucleic acid via a covalent bond, particularly via a phosphodiester bond. Thus, the invention also includes the Diels-Alder cycloaddition products comprised of one or more dihydropyridazine and/or pyridazine units that are formed between the ethenyl aromatic groups and the tetrazine reagent within the nucleic acid.
Concerning further specifications and preferred embodiments of the modified nucleic acid of the second aspect of the invention references is made to the detailed description of the first aspect of the invention.
According to a third aspect the invention relates to a nucleoside/nucleotide analogue comprising
a. a nucleoside/nucleotide unit and a dihydropyridazine unit of formula (VIII) or (VIII*), in particular of formula (VIII*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000021_0001
b. a nucleoside/nucleotide unit and a pyridazine unit of formula (IX) or (IX*), in particular of formula (IX*):
Figure imgf000021_0002
(IX), (IX*), a nucleoside/nucleotide unit and a dihydropyridazine unit of formula (X) or (X*), particular of formula (X*), and/or the corresponding tautomeric forms of said formulas
Figure imgf000022_0001
a nucleoside/nucleotide unit and a pyridazine unit of formula (XI) or (XI*), in particular of formula (XI*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000022_0002
wherein
R1 and R2 have the same meaning as discussed previously, in particular in the first aspect of the invention,
R3 is selected o in case of formula VIII and VIII* from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding amino and amido tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and o in case of formula IX and IX* from halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding amino and amido tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and o in case of formula X, X*, XI and XI* hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH2) and the corresponding amino and amido tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine;
- R4 is selected from hydroxyl (OH), phosphate diester (OP02RpO") or phosphate triester (-OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl;
- R5 denotes a hydrogen (H), amino (NH2), or halogen group;
- R6 and R7 are selected independently from each other from o hydrogen (H), halogen, methyl, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano (CN), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (- ORb), or thioether (-SRb), wherein Rb is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, o wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety;
- Nu is a sugar moiety or a sugar phosphate moiety; and
- T is selected from O, S or Se, in particular from O. Concerning further specifications and preferred embodiments of the nucleoside/nucleotide analogue of the third aspect of the invention references is made to the detailed description of the first aspect of the invention.
According to the fourth aspect, the present invention provides methods for modifying labelled nucleic acids by adding at least one tetrazines of formula (III) to at least one labelled nucleic acid, in particular a labelled nucleic acid according to the first aspect of the invention, comprising one or more ethenyl aromatic groups; such that a reaction occurs between the ethenyl aromatic group and the tetrazine group of formula (III):
Figure imgf000023_0001
O N )
R6 and R7 are selected independently from each other from - hydrogen (H), halogen, methyl, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano
(CN), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-ORb), or thioether (-SRb), wherein Rb is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety,
- wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety.
Concerning further specifications and preferred embodiments of the methods for modifying labelled nucleic acids of the fourth aspect of the invention references is made to the detailed description of the first aspect of the invention.
In some embodiments, the at least one tetrazine is selected from a tetrazine of formula (I I I):
Figure imgf000024_0001
wherein R6 and R7 are selected independently from each other from
- a heteroaryl group, in particular 2-pyridine and 2-pyrimidine, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
- wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety.
According to a fifth aspect the invention relates to a kit for preparing, in particular according to the method of the first and fourth aspect of the invention, a modified nucleic acid according to the second aspect of the invention, wherein the kit comprises at least one nucleoside/nucleotide analogue with an ethenyl aromatic moiety and/or at least one labelled nucleic acid, in particular at least one nucleoside/nucleotide analogue according to formula (I) or (I I), and a reagent comprising a tetrazine moiety according to formula (I I I).
Concerning further specifications and preferred embodiments of the kit for preparing modified nucleic acids of the fifth aspect of the invention references is made to the detailed description of the first aspect of the invention.
In some embodiment, the kit comprises basic materials and reagents for labelling and modifying nucleic acids according to the described process.
An inventive kit may include at least one nucleoside/nucleotide analogue comprising ethenyl aromatic groups and a reagent comprising a tetrazine linked to a directly or indirectly detectable group. Certain inventive kits may further comprise additives e.g. reaction buffers and/or reagents, wash buffers, fixation buffers and/or reagents. Protocols for using the components of the inventive kits may also be included. Thus, the present invention also provides kits for preparing modified nucleic acids comprising at least one nucleoside/nucleotide analogue comprising ethenyl aromatic groups and a reagent comprising a tetrazine linked to a detectable group.
A sixth aspect of the invention relates to a use of a nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a nucleoside/nucleotide analogue according to formula (I) or (II), in preparing modified nucleic acid, in particular a modified nucleic acid according to the second aspect of the invention.
Concerning further specifications and preferred embodiments of the use of a nucleoside/nucleotide analogue of the sixth aspect of the invention references is made to the detailed description of the first aspect of the invention.
A seventh aspect the invention relates to at least one nucleoside/nucleotide analogue and/or at least one modified nucleic acid according to the second and third aspect of the invention for use as diagnostic substance or composition.
Concerning further specifications and preferred embodiments of the nucleoside/nucleotide analogue and/or modified nucleic acid for use as diagnostic substance or composition references is made to the detailed description of the first aspect of the invention.
In some embodiments, the at least one modified nucleic acid comprising dihydropyridazine and pyridazine units may be used as diagnostic substances or compositions in vitro and/or in vivo to specifically detect, locate, capture and quantify target nucleic acid polymers. BRIEF DESCRIPTION OF THE FIGURES
Figure 1 : Modification of newly synthesized DNA in HeLa cells using VdU. Cells were incubated with variable concentrations of VdU for 16 h. Cells were then fixed and stained using 5 μΜ Tamra-Tz. Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a nucleoside analogue prior to the modification reaction. Scale bars represent 50 μηη. DIC = differential interference contrast image.
Figure 2: Modification of newly synthesized DNA in U20S, A549, Vero and MRC-5 cells using VdU. Cells were incubated with 30 μΜ VdU for 16 h. Cells were then fixed and stained using 5 μΜ Tamra-Tz. Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a nucleoside analogue prior to the modification reaction. Scale bars represent 50 μηη. DIC = differential interference contrast image.
Figure 3: Selectivity of VdU for incorporation into newly synthesized cellular DNA versus RNA. Cells were incubated with or without the DNA synthesis inhibitor aphidicolin (10 μΜ) in the presence of 30 μΜ VdU for 16 h. After removal of aphidicoline, cells were washed three times with DMEM, and EdU (10 μΜ) was added for 3 hours. Afterwards, cells were fixed and modified with Tamra-Tz and AF-azide. No VdU labelling was observed in cells treated with aphidicolin. The cells could restart their DNA synthesis activities as shown by the positive staining for EdU as soon as cells were released from the aphidicolin block. Total cellular DNA was stained with DAPI. Scale bars represent 50 μηη. DIC = differential interference contrast image.
Figure 4: Time-dependent modification with Tamra-Tz of VdU labelled DNA in HeLa cells. Cells were incubated with 40 μΜ VdU for 12 h. Cells were then fixed and stained using 5 μΜ Tamra-Tz for variable incubation times. Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a synthetic nucleoside prior to the staining reaction. Scale bars represent 50 μηη.
Figure 5: Modification of newly synthesized DNA in HeLa cells using VdC. Cells were incubated with variable concentrations of VdC for 16 h. Cells were then fixed and stained using 5 μΜ Tamra-Tz. Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a nucleoside analogue prior to the modification reaction. Scale bars represent 50 μηη. DIC = differential interference contrast image.
Figure 6: Modification of newly synthesized DNA in HeLa cells using VdA. Cells were incubated with variable concentrations of VdA for 16 h. Cells were then fixed and stained using 5 μΜ Tamra-Tz. Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a nucleoside analogue prior to the modification reaction. Scale bars represent 50 μηη. DIC = differential interference contrast image.
Figure 7: Chemical structure of different tetrazine reagents. In the figure are shown: tetrazine-5-fluoresceine (FAM-Tz), 6-methyl-tetrazine-Cy3 (Cy3-Tz), 6-methyl-tetrazine-Cy5 (Cy5-Tz) and tetramethylrhodamine-dipyridyl-tetrazine (Tamra-Tz).
Figure 8: Modification of newly synthesized DNA in HeLa cells using VdU and different tetrazine reagents (Figure 7). Cells were incubated with 30 μΜ VdU for 16 h. Cells were then fixed and stained using 5 μΜ tetrazine-5-fluoresceine (FAM-Tz), 6-methyl-tetrazine-Cy3 (Cy3-Tz) or 6-methyl-tetrazine-Cy5 (Cy5-Tz) (Jena Bioscience). Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a nucleoside analogue prior to the modification reaction. Scale bars represent 50 μηη. DIC = differential interference contrast image.
Figure 9: Total metabolic activities of different cell cultures according to the Alamar Blue assay in standard media (DMEM supplemented with 4.5 g/L glucose and 10% FBS) with variable concentrations of synthetic nucleosides after 72 hours. Values were normalized relative to untreated cells (DMSO only). Figure 10: Total metabolic activities of different cell cultures according to the Alamar Blue assay in standard media (DMEM supplemented with 4.5 g/L glucose and 10% FBS) with variable concentrations of synthetic nucleosides after 72 hours. Values were normalized relative to untreated cells (DMSO only). Figure 11 : FACS analysis to assess the effect of continuous exposure of HeLa cells to 30 μΜ VdU or 10 μΜ EdU on the level of γΗ2ΑΧ. Cells were untreated (control, ctl) or treated with nucleosides for 4 or 16 hours. For a positive control, cells were exposed to CPT (camptothecin, 0.5 μΜ) for 1 hour. γΗ2ΑΧ positive cells were detected immunocytochemically with a phosphospecific antibody. A) HeLa: n = 5, *P<0.02, **P<0.002, ***P<0.0001 ; U20S: n = 3, *P<0.03, **P<0.005, ***P<0.0001 ; ns = not significant as compared to the control. B) The dotplots illustrate the expression of γΗ2ΑΧ in relation to cellular DNA content (cell cycle phase). The insets display the histograms of the distribution of the DNA content. The upper dashed line gives the threshold of γΗ2ΑΧ positive cells according to the control.
Figure 12: Orthogonality of EdU and VdU staining. HeLa cells were independently treated with EdU or VdU, fixed and stained with Tamra-Tz followed by AF-azide under CuAAC conditions. The Tamra-Tz and AF-azide dyes did not show any cross-reactivity with EdU and VdU, respectively. Total cellular DNA was stained with DAPI. Scale bars represent 50 μηη. DIC = differential interference contrast image.
Figure 13: Dual labelling of cells. Cells were treated sequentially with a pulse of EdU for 4 hours followed by a VdU "chase" for an additional 4 hours and vice versa with washing in between. Cells were fixed and stained with Tamra-Tz and AF-azide. Approximately 50% of cells stained for VdU or EdU. Alternatively, cells were treated with VdU for 12 hours, washed with medium for 2 hours and chased with EdU for additional 2 hours. Total cellular DNA was stained with DAPI. Scale bars represent 50 μηη. Figure 14: Cell imaging analysis using Cell Profiler software. The histograms show the integrated intensity of sequentially labelled VdU and EdU cells identified according to the DAPI signal. The threshold is set at 2-fold higher intensity than the background (number of identified nuclei = 1650). Experimental details: cells were treated sequentially with a pulse of 10 μΜ EdU for 4 hours followed by a 30 μΜ VdU chase for an additional 4 hours with washing in between. Cells were fixed and stained with Tamra-Tz and AF-azide.
Figure 15: Triple labelling of newly synthesized DNA in HeLa cells by VdU, BrdU and F-ara- EdU. Controls: VdU (30 μΜ), BrdU (30 μΜ) and F-ara-EdU (10 μΜ) were independently added and incubated for 2 h 45 min. For control experiments (C) the nucleosides were omitted, but the cells were otherwise treated identically. Figure 16: Triple labelling of newly synthesized DNA in HeLa cells by VdU, BrdU and F-ara- EdU. Triple labelling: VdU (30 μΜ), BrdU (30 μΜ) and F-ara-EdU (10 μΜ) were sequentially added and incubated for 2 h 45 min each. The cells were washed 15 min with fresh media between each nucleoside. Following the last nucleoside treatment and washing, cells were fixed, permeabilized, denatured and stained with Tamra-Tz (5 μΜ in PBS), mouse monoclonal BrdU antibody-AF-488 conjugate (2 μg/mL in blocking solution) and AF-647- azide (10 μΜ in PBS under CuAAC). The order of nucleoside addition did not influence the labelling results, demonstrating that none of the three nucleosides interfered with metabolism or detection of the other two. Total DNA was stained with DAPI. Scale bars represent 5 μηη, BrdU = Ab-AF-488, VdU = Tamra-550-Tz, F-ara-EdU = AF-647-azide.
Figure 17: Excitation and emission spectra of the cycloaddition product 6 VdC-Tz. VdC-Tz showed a 50 fold increase in excitation (light grey) and emission (dark grey) at pH 4 (solid line) compared to pH 7 (dotted line).
Figure 18: Modification of newly synthesized RNA in HeLa cells using VU. HeLa cells were incubated with 1 mM VU for 12 h. Cells were then fixed and stained using 5 μΜ Tamra-Tz. Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a nucleoside analogue prior to the modification reaction. Scale bars represent 50 μηη. DIC = differential interference contrast image.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Definitions
For purpose of clarity, various terms and phrases used throughout this specification and the appended claims are presented and defined below:
The term "nucleic acid" refers to a deoxyribonucleotide (e.g DNA) or ribonucleotide (e.g. RNA) oligomer, comprising a length of 2 up to 200 nucleotide units, or polymers, comprising a length of more than 200 nucleotide units in either single- or double- stranded form. Preferred embodiments are nucleic acid polymers. The nucleic acid may be a purified molecule in solution or immobilized onto a surface, or it may be located inside a cell or organism.
The term "modified", "modifying" or "modification" when used herein in reference to a nucleic acid polymer means a nucleic acid, which bears one or more dihydropyridazine and/or pyridazine units that are formed by following the process of incorporating ethenyl aromatic groups into nucleic acids and reacting those groups with a tetrazine reagent. The term "labelled" or "labelling" when used herein in reference to a nucleic acid means a nucleic acid comprising at least one ethenyl nucleotide analogue. The term "nucleotide analogue" refers to a compound that is structurally and functionally similar to a natural nucleotide e.g. such as it has similar ability to base pair with one of the naturally occurring bases.
The phrase "nucleoside analogue" refers to a compound that is structurally and functionally similar to a natural nucleoside e.g. such as it has similar ability to be incorporated into DNA by DNA replication or RNA by RNA transcription.
The term "organism" refers to a living system that has or can develop the ability to act or function independently. Organisms include humans, animals, plants, bacteria, protozoa, and fungi.
The term "kit" used herein in connection to the invention refers to a combination of two or more substances containing detailed instructions for their utilization to accomplish the invention.
The term "linker" used herein in connection to the invention refers to a variable covalent linkage between two or more functional groups, e.g. such as a polyethylene glycol chain separating a tetrazine group and fluorescent molecule.
The phrase "tautomeric forms" used herein in connection to the invention refers to constitutional isomers of dihydropyridazine units wherein single bonds and adjacent double bonds switch due to a formal migration of hydrogen atoms.
A "polynucleotide template" according to the invention comprises one or more coding and/or non-coding nucleic acids.
The term "alkyl," refers to a saturated straight or branched hydrocarbon moiety containing up to 10, particularly up to 6 carbon atoms. Examples of alkyl groups include, without limitation, methyl, ethyl, propyl, butyl, isopropyl, n-hexyl, octyl, decyl and the like. Alkyl groups typically include from 1 to about 10 carbon atoms, particularly from 1 to about 6 carbon atoms. Alkyl groups as used herein may optionally include further substituent groups.
The term "alkenyl," refers to a straight or branched hydrocarbon chain moiety containing up to 10 carbon atoms and having at least one carbon-carbon double bond. Examples of alkenyl groups include, without limitation, ethenyl, propenyl, butenyl, 1 -methyl-2-buten-1- yl, dienes such as 1 ,3-butadiene and the like. Alkenyl groups typically include from 2 to about 10 carbon atoms, more typically from 2 to about 6 carbon atoms. Alkenyl groups as used herein may optionally include further substituent groups.
The term "alkynyl," refers to a straight or branched hydrocarbon moiety containing up to 10 carbon atoms and having at least one carbon-carbon triple bond. Examples of alkynyl groups include, without limitation, ethynyl, 1 -propynyl, 1 -butynyl, and the like. Alkynyl groups typically include from 2 to about 10 carbon atoms, more typically from 2 to about 6 carbon atoms. Alkynyl groups as used herein may optionally include further substituent groups.
The term "alkylidene" refers to any of a class of divalent functional groups derived from an alkane by removal of two hydrogen atoms from the same carbon atom, the free valencies being part of a double bond.
The term "aryl" refers to a hydrocarbon with alternating double and single bonds between the carbon atoms forming a ring structure (in the following also "aromatic hydrocarbon"). The term "heteroaryl" refers to aryl compounds in which at least one carbon atom is replaced with an oxygen, a nitrogen or a sulphur atom. Aryl or hetero aryl groups as used herein may optionally include further substituent groups.
The term " heterocycle" refers to cycloalkyl compounds (an interconnected alkyl group forming a ring structure containing 3 to 8, particularly 5 to 6 carbon atoms) in which at least one carbon atom is replaced with an oxygen, a nitrogen or a sulphur atom forming a ring structure. Said ring structure comprising at least one double or triple bond. Heterocycle groups as used herein may optionally include further substituent groups.
General description
The inventors focused on the development of alternative methods for modifying nucleic acid polymers or oligomers to address limitations of available methods mentioned above. The present invention provides methods for the incorporation of ethenyl aromatic groups into nucleic acids that are reactive in the presence of a reagent comprising a tetrazine group. The reaction between the labelled nucleic acid and the tetrazine group is rapid and chemically orthogonal to other reactions used for modifying nucleic acids such as, for example, azide- alkyne cycloaddition. According to certain embodiments, the described nucleoside/nucleotide analogues exhibit reduced genotoxicity as compared to commonly used analogues. According to other embodiments, the products of the modification reaction comprise novel substances containing one or more dihydropyridazine and/or pyridazine units located at the 5-position or pyrimidines and/or the 7-position of 7-deazapurine residues.
I. Labelling of nucleic acids
This part of invention pertains to 5-ethenyl pyrimidine and 7-ethenyl-7-deazapurine nucleoside/nucleotide analogues used for the labelling nucleic acids with an ethenyl aromatic group.
Nucleoside/nucleotide analogues: The nucleoside/nucleotide analogues suitable for the methods of the present invention include any nucleoside/nucleotide analogues of formula (I) and/or formula (II) comprising an ethenyl aromatic group that can undergo Diels-Alder cycloaddition reaction with tetrazines.
Procedures for preparing nucleoside/nucleotide analogues such as 5-substituted pyrimidine or 7-substituted 7-deazapurines for example have been reported in literature and are well known in the art (J. Am. Chem. Soc. 122, 5646-5647, 2000; Bioorg. Med. Chem. Lett. 1 1 , 2917-2920, 2001 ; Helv. Chim. Acta 78, 1083-1090, 1995; Bioorganic & Medicinal Chemistry Letters 21 , 7094-7098, 201 1 ).
Nucleoside/nucleotide analogues prepared by the present inventors are treated with metal scavenger to remove eventually remaining toxic catalysts which may be used for the synthesis of the nucleoside/nucleotide analogues.
It should be noted that nucleoside/nucleotide analogues of formula (I) and/or formula (II) can represent new chemical entities, as well as previously-known compounds that have been used in applications unrelated to the process presented within this invention. According to preferred embodiments, the labelling process is conducted from solutions comprising at least one nucleoside analogue of 5-ethenyl pyrimidines of formula (la) and (lb):
Figure imgf000031_0001
wherein
- R2 denotes a hydrogen (H) or hydroxyl (OH).
- R4 independently denotes a hydroxyl (OH), phosphate (OP03 2"), triphosphate (OPO3PO3PO3 4"), phosphate triester (-OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, or C-|-C4 alkyl, alkenyl, or alkynyl group.
Exemplary nucleoside analogues that may be used in the practice of the present invention include 5-vinyl-2'-deoxyuridine (also termed here VdU, wherein R2 = H, R4 = OH of formula (la)), 5-vinyluridine (VU, wherein R2 = OH, R4 = OH of formula (la)) and/or 5-vinyl-2'- deoxycytidine (VdC, wherein R2 = H, R4 = OH of formula (lb)), 5-vinylcytidine (VC, wherein R2 = OH, R4 = OH of formula (lb)). According to preferred embodiments, the labelling process is conducted from solutions comprising at least one nucleoside analogue of 7-ethenyl-7-deazapurines of formula (lla) and
(llb):
Figure imgf000032_0001
wherein
- R2 denotes a hydrogen (H) or hydroxyl (OH).
- R4 independently denotes a hydroxyl (OH), phosphate (OP03 2"), triphosphate (OPO3PO3PO3 4"), phosphate triester (-OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, or C-|-C4 alkyl, alkenyl, or alkynyl group.
Exemplary nucleoside analogues that may be used in the practice of the present invention include 7-vinyl-7-deaza-2'-deoxyadenosine (also termed here VdA, wherein R2 = H, R4 = OH of formula (lla)), 7-vinyl-7-deazaadenosine (VA, wherein R2 = OH, R4 = OH of formula (lla)) and/or 7-vinyl-7-deaza-2'-deoxyguanosine (VdG, wherein R2 = H, R4 = OH of formula (llb)), 7- vinyl-7-deazaguanosine (VG, wherein R2 = OH, R4 = OH of formula (llb)).
Nucleic acids:
Nucleic acids generated according to the process presented in this invention are single- or double-stranded deoxyribonucleotide or ribonucleotide oligomers and/or polymers. For generating nucleic acids, nucleoside/nucleotide analogues of formula (I) and/or formula (II) comprising an ethenyl aromatic group are added to enzyme mixtures containing kinases and/or phosphatases in vitro or in vivo, whereupon the 5'-position (R4) is converted into a triphosphate and the resulting nucleotide triphosphate carrying the ethenyl aromatic group is incorporated into nucleic acids by means of one or more polymerases.
According to one embodiment, the method of the invention is practiced in a cell-free extract, wherein a polynucleotide template, nucleoside triphosphates, a nucleic acid polymerase and nucleotide analogues are provided in free solution.
According to one embodiment, the nucleic acid polymerase is a DNA dependent polymerase. According to another embodiment, the nucleic acid polymerase is a RNA dependent polymerase (reverse transcriptase). According to one embodiment, the nucleic acid polymerase is thermostable up to 95°C.
According to another embodiment, the method of the invention is practiced in a living cell, whereby the nucleoside/nucleotide analogues are provided to a cell culture medium or an organism in which the cell is present.
According to another embodiment, the method of the invention is practiced in a living cell, whereby the nucleoside/nucleotide analogues are provided by microinjection, electroporation, optoporation or ballistic transfer (gene gun) methods to name only a few.
II. Modification of labelled nucleic acids
The resulting ethenyl-labelled nucleic acid can be modified with tetrazine reagents via Diels- Alder cycloaddition reaction. This version of the Diels-Alder cycloaddition reaction is termed "invers electron demand" Diels-Alder (Eur. J. Org. Chem. 1998, 2885-2896, 1998; Tetrahedron Lett. 24, 1481-1484, 1983).
Tetrazines: Tetrazines of formula (III) can be added to a nucleic acid comprising one or more ethenyl aromatic groups; such that a reaction occurs between the ethenyl aromatic group and the tetrazine group to form a product of one or more dihydropyridazine and/or pyridazine units:
Figure imgf000033_0001
wherein R6 and R7 - independently denote a hydrogen (H), halogen, methyl, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano (CN), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (-OR), thioether (-SR),
- and/or one or more detectable group that is attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle.
According to one embodiment, the reaction is performed with tetrazines, wherein R7 is conjugated to a directly detectable fluorescent label attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker. According to one embodiment, the reaction is performed with tetrazines, wherein R7 is conjugated via an amide linkage to a directly detectable group, e.g. fluorophores such as tetramethylrhodamine, cyanine or fluoresceine, to name only a few.
According to one embodiment, the resulted modification may be indirectly detectable, e.g. wherein R6 or R7is conjugated via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker to an indirectly detectable group such as hapten or biotin.
According to one embodiment, the reaction is performed with tetrazines, wherein R6 = pyridine-2-yl or pyrimidien-2-yl and R7 = aminopyridine-2-yl or aminopyrimidine-2-yl independently.
Procedures for preparing above mentioned tetrazines have been reported in literature and are well known in the art (Bioconjugate Chem. 19, 2297-2299, 2008; Nat Chem 4, 298-304, 2012; Eur. J. Org. Chem. 2009, 6121 -6128, 2009; Angew. Chem., Int. Ed. Engl. 2014). Tetrazine reagents linked to fluorophores are also commercially available from different companies, e.g. Jena Bioscience.
III. Methods and Products of modification reaction
The addition of tetrazine reagents that undergo a [4+2] Diels-Alder cycloaddition with the ethenyl aromatic groups of nucleic acids furnishes modified nucleic acid polymers comprised of one or more dihydropyridazine and/or pyridazine units located at the 5-position or pyrimidines and/or the 7-position of 7-deazapurines residues. According to certain embodiments, these products are used to analytically differentiate newly synthesized nucleic acids in cells.
Dihydropyridazines:
The dihydropyridazine units and its tautomeric forms of formula (XIII) are formed by reacting ethenyl aromatic groups of formula (XII) with tetrazine reagents of formula (III):
Figure imgf000035_0001
(XII) (XIII)
Figure imgf000035_0002
(XIII) (X|H) wherein
- R6 and R7 independently denote a hydrogen (H), halogen, methyl, trifluoromethyl (CF3), trichloromethyl (CCI3), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (- OR), thioether (-SR), and/or one or more detectable group that is attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle.
- Nut denotes a nucleotide unit within a nucleic acid.
According to one preferred embodiment, the above mentioned reaction is conducted under a reducing environment and aqueous conditions using the nucleoside analogues 5-vinyl-2'- deoxyuridine (VdU), 5-vinyl-2'-deoxycytidine (VdC), 7-vinyl-7-deaza-2'-deoxyadenosine (VdA) and 7-vinyl-7-deaza-2'-deoxyguanosine (VdG) with a tetrazine reagent of formula (III) wherein R6 and R7 = pyridine-2-yl.
According to one embodiment, the above mentioned reaction is performed in buffered aqueous media using nucleic acids comprising one or more ethenyl aromatic groups with tetrazine reagents of formula (III) wherein R6 = pyridine-2-yl and R7 = aminopyridine-2-yl attached to a detectable group.
According to one embodiment, the dihydropyridazine-containing nucleic acid may be directly detectable such as it does not require any further manipulation to be detected, e.g. due to a radioactive isotope present. According to one embodiment, the dihydropyridazine-containing nucleic acid may be directly detectable such as it does not require any further manipulation to be detected, e.g. due to intrinsic fluorescence properties.
According to one embodiment, R7 of the dihydropyridazine-containing nucleic acid is conjugated to a directly detectable fluorescent label attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker.
According to one embodiment, R7 of the dihydropyridazine-containing nucleic acid is conjugated via an amide linkage to a directly detectable group, e.g. fluorophores such as tetramethylrhodamine, cyanine or fluoresceine, to name only a few.
According to one embodiment, the dihydropyridazine-containing nucleic acid indirectly detectable, e.g. wherein R7 is conjugated via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker to an indirectly detectable group such as hapten or biotin.
Pyridazines:
The pyridazine units of formula (XIV) are formed under oxidizing conditions by reacting ethenyl aromatic groups of formula (XII) with tetrazine reagents of formula (III):
Figure imgf000036_0001
wherein - R6 and R7 independently denote a hydrogen (H), halogen, methyl, trifluoromethyl (CF3), trichloromethyl (CCI3), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (- OR), thioether (-SR), and/or one or more detectable group that is attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle. - Nut denotes a nucleotide unit within a nucleic acid.
According to one preferred embodiment, the above mentioned reaction is conducted in the presence of an oxidizing agent (such as 02) under aqueous conditions using the nucleoside analogues 5-vinyl-2'-deoxyuridine (VdU), 5-vinyl-2'-deoxycytidine (VdC), 7-vinyl-7-deaza-2'- deoxyadenosine (VdA) and 7-vinyl-7-deaza-2'-deoxyguanosine (VdG) with a tetrazine reagent of formula (III) wherein R6 and R7 = pyridine-2-yl.
According to one embodiment, the above mentioned reaction is performed in the presence of an oxidizing agent in buffered aqueous media using nucleic acids comprising one or more ethenyl aromatic groups with tetrazine reagents of formula (III) wherein R6 = pyridine-2-yl and R7 = aminopyridine-2-yl attached to a detectable group.
According to one embodiment, the pyridazine-containing nucleic acid may be directly detectable such as it does not require any further manipulation to be detected, e.g. due to a radioactive isotope present. According to one embodiment, the pyridazine-containing nucleic acid may be directly detectable such as it does not require any further manipulation to be detected, e.g. due to intrinsic fluorescence properties.
According to one embodiment, R7 of the pyridazine is conjugated to a directly detectable fluorescent label attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker.
According to one embodiment, R7 of the pyridazine is conjugated via an amide linkage to a directly detectable group, e.g. fluorophores such as tetramethylrhodamine, cyanine or fluoresceine, to name only a few.
According to one embodiment, the pyridazine may be indirectly detectable, e.g. wherein R7 is conjugated via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker to an indirectly detectable group such as hapten or biotin.
IV. Methods of Use
Diagnostic use, diagnostic compositions The products of the modification reaction comprising dihydropyridazine and pyridazine units of formula (XIII) and (XIV) may be used as diagnostic substances or compositions in vitro and/or in vivo to specifically detect, locate, capture and quantify target nucleic acids. Preferably, the dihydropyridazine and pyridazine units may be used to localize high proliferating cancer cells as well as viral compartments/particles in patients. According to one embodiment, the dihydropyridazine and pyridazine-containing nucleic acid may be directly detectable, e.g. due to a radioactive isotope present.
According to one preferred embodiment, the dihydropyridazine and pyridazine units are conjugated to a directly detectable fluorescent label attached via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker.
According to one preferred embodiment, the dihydropyridazine and pyridazine units may be indirectly detectable, e.g. wherein R7 of formula (XIII) and(XIV) is conjugated via a linear, branched, or cyclic alkyl, alkenyl, alkynyl, alkylidene, aryl, ester, ether, amide, carbamate, urea, heteroaryl group or carbocycle linker to an indirectly detectable group such as hapten or biotin.
EXAMPLES
Example 1 :
Labelling and modification of cells with VdU and tetrazine
Human cervical cancer cells (HeLa) were incubated with variable concentrations of 5-vinyl-2'- deoxyuridine (VdU) for 16 h. The cells were then washed, fixed and modified using a tetramethylrhodamine-dipyridyl-tetrazine conjugate ("Tamra-Tz", see Figure 7). When the cellular DNA was denatured prior to the addition of Tamra-Tz, intense nuclear staining that colocalized with the non-covalent DAPI stain was observed (Figure 1 ). In contrast, cells not receiving VdU displayed no detectable DNA staining if subjected to the same fixation and modification procedures. Similar results were observed in all cell lines evaluated, including human bone osteosarcoma cells (U20S), human lung cancer cells (A549), african green monkey epithelial kidney cells (Vero) and human fetal lung fibroblast cells (MRC-5) (Figure 2).
To evaluate the selectivity of VdU for incorporation into cellular DNA versus RNA, living HeLa cells were treated with the nuclear DNA replication inhibitor aphidicolin in the presence of 30 μΜ of VdU for 16 hours (Figure 3). After removal of aphidicoline, cells were washed three times with DMEM, and EdU (10 μΜ) was added for 3 hours. Afterwards, cells were fixed and stained with Tamra-Tz and AF-azide. No VdU labelling was observed in cells treated with aphidicolin. The cells could restart their DNA synthesis activities as shown by the positive staining for EdU as soon as cells were released from the aphidicolin block. These results demonstrate that the nuclear staining by Tamra-Tz results from the selective metabolic incorporation of VdU into cellular DNA of replicating cells. Example 2:
Labelling of cells with VdU and time-dependent modification with tetrazine
HeLa cells were incubated with 40 μΜ VdU for 12 h. Following fixation of the cells, the addition of Tamra-Tz to VdU-treated cells resulted in rapid intranuclear staining after only 30 min at 37 °C (Figure 4). Total cellular DNA was stained with DAPI. Negative controls received identical treatments, but were not exposed to a synthetic nucleoside prior to the staining reaction.
Example 3:
Labelling and modification of cells with VdC and tetrazine HeLa cells were incubated with variable concentrations of 5-vinyl-2'-deoxycytidine (VdC) for 16 h. The cells were then washed, fixed and modified using Tamra-Tz. When the cellular DNA was denatured prior to the addition of Tamra-Tz, intense nuclear staining that colocalized with the non-covalent DAPI stain was observed (Figure 5). In contrast, cells not receiving VdC displayed no detectable DNA staining if subjected to the same fixation and modification procedures.
Example 4:
Labelling and modification of cells with VdA and tetrazine
HeLa cells were incubated with variable concentrations of 7-vinyl-7-deaza-2'- deoxyadenosine (VdA) for 16 h. The cells were then washed, fixed and modified using Tamra-Tz. When the cellular DNA was denatured prior to the addition of Tamra-Tz, intense nuclear staining that colocalized with the non-covalent DAPI stain was observed (Figure 6). In contrast, cells not receiving VdA displayed no detectable DNA staining if subjected to the same fixation and modification procedures.
Example 5: Labelling and modification of cells with VdU and different tetrazine reagents
HeLa cells were incubated with 30 μΜ 5-vinyl-2'-deoxyuridine (VdU) for 16 h. The cells were then washed, fixed and modified using fluorescent tetrazines probes indicated in Figure 7. When the cellular DNA was denatured prior to the addition of reagents, intense nuclear staining that colocalized with the non-covalent DAPI stain was observed (Figure 8). In contrast, cells not receiving VdU displayed no detectable DNA staining if subjected to the same fixation and modification procedures.
Example 6:
Toxicity of nucleoside analogues
The biological impact of the metabolic label should be minimal during the labelling period, so that the experimental results are not influenced by excessive toxicity, cell cycle arrest, and/or activation of DNA damage pathways. A standard "Alamar Blue" assay was used to assess the combined effects of proliferation and metabolism on total cellular respiration for VdU. As a comparison, BrdU and EdU were also included. The cell cultures were grown in the presence of various nucleoside concentrations for 24 - 72 hours. In all cell types tested, EdU was consistently more toxic than VdU and BrdU. EdU exhibited IC50 values (defined as the concentrations needed to inhibit 50% of the total metabolic activity) that were 2 - 15-fold lower than VdU (Figure 9). A standard "Alamar Blue" assay was also used to assess the combined effects of proliferation and metabolism on total cellular respiration for VdC and VdA (Figure 10).
Example 7:
DNA damage analysis of nucleoside analogues
The genotoxic effects of EdU are only partially understood. Meanwhile, it is known that EdU induces cell cycle arrest at G2/M and activation of DNA damage response pathways (Cytometry A 83, 979-988, 2013; Chromosome Res. 21 , 87-100, 2013; J. Med. Chem. 24, 1537-1540, 1981 ). These circumstances can greatly impact the validity of cell cycle studies conducted with EdU (The Journal of Immunology 190, 1085-1093, 2013; Cell death & disease 4, e656, 2013). When HeLa cells were incubated with the standard labelling concentration of EdU (10 μΜ) for 4 - 16 hours, no changes in cellular morphology or total cellular respiration were observed, but a dramatic accumulation of tetraploid (4n) cells that stained positively for the phosphorylation of histone H2AX was detected (Figure 1 1 ). Similar results were obtained when using U20S cells. γΗ2ΑΧ formation is a critical step in DNA damage signalling and repair that is predominantly associated with double strand breaks (DNA Repair 3, 959-967, 2004; Nat. Cell Biol. 13, 1 161-1 169, 201 1 ). Little or no γΗ2ΑΧ formation or cell cycle arrest was observed for cells treated with 30 μΜ of VdU under the same conditions (Figure 1 1 ). Taken together, these results indicate that standard labelling concentrations of EdU cause large perturbations to cell cycle progression and activation of DNA damage response after only 4 - 16 hours, whereas VdU exhibits very limited genotoxic effects.
Example 8:
Orthogonality for dual labelling by VdU and EdU
Pulse-chase labelling experiments, where multiple metabolic probes are introduced into DNA over time, are used in a wide variety of important biological experiments such as characterizing the timing of DNA replication, visualizing embryogenesis, and in stem cell research (Nature 494, 476-479, 2013; Nature 425, 836-841 , 2003; Science 310, 1327-1330, 2005). We therefore examined the possibility of using VdU-tetrazine ligation in combination with EdU-azide cycloaddition for introducing orthogonal chemical labels into cellular DNA. To test the chemical orthogonality of VdU and EdU in the context of cellular DNA, HeLa cells were independently treated with EdU or VdU, fixed and stained with Tamra-Tz followed by AlexaFluor-azide (AF-azide) under CuAAC conditions. Thereby, Tamra-Tz did not show any cross-reactivity with EdU-treated cells, and, VdU-treated cells did not exhibit any staining by AF-azide (Figure 12).
To evaluate the orthogonality of VdU and EdU in cells containing both labels, cells were treated sequentially with a pulse of EdU for 4 hours followed by a VdU "chase" for additional 4 hours. The cells were then fixed and stained with Tamra-Tz and AF-azide. The resulting staining revealed cells containing only one of the two labels as well as cells with well- resolved signals from both labels (Figure 13) consistent with the differing stages of proliferation present in asynchronous cell cultures. The order of nucleoside addition did not influence these results (Figure 13). Quantitative image analyses indicated that VdU and EdU were incorporated and detected in the cells with very similar efficiencies (Figure 14). Taken together, these results indicate that the methods used for chemical modification of VdU and EdU within nucleic acid polymers are both efficient and mutually orthogonal.
Example 9: Triple labelling of HeLa cells with VdU, BrdU and F-ara-EdU
The orthogonal labelling of VdU and EdU could, in principal, be expanded to include a third color if BrdU was included. This would provide a valuable third level of spatial and temporal resolution to pulse-chase labelling experiments. Previous studies, however, have demonstrated that BrdU and EdU are incompatible since EdU pulses inhibit subsequent incorporation of BrdU (Proc. Natl. Acad. Sci. U. S. A. 108, 20404-20409, 201 1 ) and most anti-BrdU antibodies (~ 90%) exhibit cross-reactivity with EdU (PLoS One 7, e51679, 2012). We therefore selected F-ara-EdU as a relatively non-toxic EdU analogue that is compatible with subsequent BrdU incorporation and detection (Proc. Natl. Acad. Sci. U. S. A. 108, 20404-20409, 201 1 ). It was unclear, however, if VdU incorporation and detection would be compatible with BrdU and vice-versa. To investigate the compatibility of VdU with BrdU and F-ara-EdU, HeLa cells were sequentially treated with BrdU (30 μΜ), VdU (30 μΜ) and F-ara- EdU (10 μΜ) for 2 hours 45 min each. Subsequent staining revealed well-resolved, non- overlapping fluorescent signals that together display the spatial and temporal organization consistent with the progression of the S-phase in single cells (Figure 15 and 16) (Cold Spring Harbor perspectives in biology 2, a000737, 2010). The first label stained euchromatin in the early S-phase as numerous small replication foci throughout the cell nucleus. The second marker, was found on a fewer number of larger foci located around the nucleoli consistent with mid S-phase. The final label, gave staining in distinct globular regions of peripheral heterochromatin located at the nuclear envelope and perinucleolar heterochromatin around the nucleoli corresponding to late S-phase (Cold Spring Harbor perspectives in biology 2, a000737, 2010). The order of nucleoside addition did not influence the labelling results, demonstrating that none of the three nucleosides interfered with metabolism or detection of the other two (Figure 16).
Example 10:
Preparation of dihydropyridazine derivative 3 (VdU-Tz) and pyridazine 4 (VdU-Tz-ox)
Figure imgf000042_0001
1 (VdU) 2 (py2-Tz) 3 (VdU-Tz, 52%) 4 (VdU-Tz-ox, 29%)
In this example 5-vinyl-2'-deoxy-uridine (VdU, 23 mg, 90 μηηοΙ) and 3,6-di-2-pyridyl-1 ,2,4,5- tetrazine (py2-Tz, 25 mg, 106 μηηοΙ, 1 .2 eq) were dissolved in a dioxane/water mixture (2/1 , 3 ml.) and stirred at room temperature overnight. After consumption of VdU, the mixture was evaporated to dryness and purified by silica gel chromatography (CHCl3/MeOH/NH4OH (33% NH3 in H20) 90/9/1 ) as a mixture of compounds 3 (incl. isomers, 52%) and 4 (29%) - (total 34 mg, 81 % according to MW 462.46 of VdU-Tz). A small fraction was subjected to a second column chromatography (EtOAc/MeOH/NH4OH (33% NH3 in H20) 90/9/1 ) for characterization of VdU-Tz-ox 4. 1H-NMR of 4: (500 MHz, CD3OD) δ: 8.78 (m, 1 H, CH-N pyridyl), 8.66 (s, 1 H, H-pyridazine), 8.64 (d, J = 8.0, 1 H, pyridyl), 8.55 (m, 1 H, CH-N pyridyl), 8.31 (s, 1 H, H-6), 8.09 (d, J = 7.9, 1 H, pyridyl), 8.07 - 8.00 (m, 2H, 2x pyridyl), 7.58 - 7.46 (m, 2H, 2x pyridyl), 6.32 (t, J = 6.6, 1 H, H-V), 4.38 (m, 1 H, H-3'), 3.92 (m, 1 H, H-4'), 3.77 - 3.66 (m, 2H, H-5', H-5"), 2.35 - 2.18 (m, 2H, H-2 H-2"). HR-ESI-MS (MeOH, pos. mode): 3 [M+H]+ calculated for C23H22N605 463.17244, found 463.17290; 4 [M+H]+ calculated for C23H20N6O5 461 .15679, found 461.15668; [M+Na]+ 483.13874, found 483.13844. Example 1 1 :
Preparation of dihydropyridazine derivative 6 (VdC-Tz)
Figure imgf000042_0002
5 (VdU) 2 (py2-Tz) 6 (VdC-Tz) In this example 5-vinyl-2'-deoxy-cytidine (VdC, 20 mg, 79 μηηοΙ) and 3,6-di-2-pyridyl-1 ,2,4,5- tetrazine (py2-Tz, 28 mg, 1 19 μηηοΙ, 1.5 eq) were dissolved in a dioxane/water/ethanol mixture (1/1/1 , 9 ml.) and stirred at room temperature overnight. After consumption of VdC, the mixture was evaporated to dryness and purified by silica gel chromatography (CH2CI2/MeOH 92/8 - 89/1 1 ) to give compound 6 (84%, 1/1 mixture of diastereomers A and B). 1H-NMR of 6: (500 MHz, dmso) δ: 8.81 (d, 2H), 8.67 (m, 2H, 2x CH-N pyridyl B), 8.60 (m, 2H, 2x CH-N pyridyl A), 8.81 (d, 2H), 8.08 (s, 1 H, H-6), 7.98 (s, 1 H, H-6), 7.95 (m, 2H, 2x pyridyl B), 7.87 - 7.83 (m, 4H, pyridyl A+B), 7.74 (m, 2H, 2x pyridyl A), 7.48 (m, 2H 2x pyridyl B), 7.27 (m, 2H, 2x pyridyl A), 6.16 (m, 2H, H-V A+B), 5.19 (m, 3'-OH A+B), 5.09 (t, J = 5.0, 5'-OH A), 4.95 (t, J = 5.0, 5'-OH B), 4.68 - 4.62 (m, 2H, 2x H A+B), 4.24 - 4.17 (m, 2H, H-3' A+B), 3.81 - 3.76 (m, 2H, H-4' A+B), 3.64 - 3.54 (m, 4H, H-5' A+B, H-5" A+B), 2.35 (m, 2H, 2x H A+B), 2.12 - 1 .65 (m, 6H, 2x H A+B, H-2' A+B, H-2" A+B). HR-ESI-MS (MeOH, pos. mode): 6 [M+H]+ calculated for C23H24N704 462.18843, found 462.18852.
Example 12: Verification of dihydropyridazine derivative 8 (VdA-Tz) and pyridazine 9 (VdA-Tz-ox)
Figure imgf000043_0001
7 (VdA) 2 (py2-Tz) 8 (VdA-Tz) 9 (VdA-Tz-ox)
In this example the product formation between 7-vinyl-2'-deoxy-7-deazaadenosine (VdA, 200 μΜ) and 3,6-di-2-pyridyl-1 ,2,4,5-tetrazine (py2-Tz, 20 μΜ) in methanol/water (1/1 ) was analyzed by LC-HR-ESI-MS after 12 h. HR-ESI-MS (MeOH, pos. mode): 8 and its tautomeric forms [M+H]+ calculated for C25H25N803 484.20496, found 485.2051 1 ; 9 [M+H]+ calculated for C25H23N803 483.18931 , found 483.18940.
Example 13:
Kinetic analysis of the Diels-Alder cycloaddition reaction
Second-order rate constants were determined under pseudo first order conditions with dienophiles used in large excess over tetrazine 2 (py2-Tz). Separate solutions of dienophiles (10 mM) and tetrazine 2 (0.2 mM) were freshly prepared in MeOH/H20 1/1 at 25°C and checked for their stability. The solutions were mixed (10- to 50-fold excess of dienophiles) into thermostated quartz cuvettes for UV measurements (SpectraMax M5 and Varian Cary 300 Bio UV/Vis spectrometer). The progress of the reaction was followed by monitoring the disappearance of the n → ττ* absorption of the tetrazine 2 at λ = 530 nm at 25°C. The reported rate constant values are arithmetic means, determined from at least three independent measurements. All data processing was performed with Kaleidagraph software (Synergy Software, Reading, UK) using a mono exponential fitting equation.
Figure imgf000044_0001
Example 14:
Analysis of intrinsic fluorescence properties of the cycloaddition products
The cycloaddition product 6 VdC-Tz was investigated for its pH-dependent intrinsic fluorescence properties. The quantum yield (Φ) of the product was measured to be 0.05 independent of the pH (reference: quinine sulfate). Interestingly, VdC-Tz showed a 50 fold increase in brightness at lower pH (Figure 17), e.g. brightness (pH 4) = 308.9 M"1cm"1 compared to brightness (pH 7) = 6.4 M"1cm"1. The brightness was calculated as the product of molar absorptivity (ε) and the quantum yield. Although the present invention is described herein with reference to specific embodiments, the invention is not intended to be limited to the details shown.
Example 15:
Modification of newly synthesized RNA in HeLa cells using VU
Human cervical cancer cells (HeLa) were incubated with 1 mM of 5-vinyl-uridine (VU) for 12 h. The cells were then washed, fixed and modified using a tetramethylrhodamine-dipyridyl- tetrazine conjugate ("Tamra-Tz", see Figure 7). Staining of the nucleoli within the nuclei of each cell was observed (Figure 18). This staining pattern is consistent with RNA labelling. In contrast, cells not receiving VU displayed no detectable RNA staining if subjected to the same fixation and modification procedures (Figure 18). General protocols:
Cell culture medium and handling.
For all experiments, HeLa, U20S, MRC-5 and Vero cells were cultivated at 37°C, 5% C02 in DMEM (Gibco) containing 4.5 g/L glucose, 10% FBS (Gibco), 50Ό00 units Penicillin and 50 mg Streptomycin per L (Sigma Aldrich). A549 cells were cultivated with additional 1 % of MEM non-essential amino acids solution 100x (Sigma). Cells were grown to confluency and passaged every 2 to 4 days using Trypsin-EDTA solution (Sigma Aldrich). Cells were counted using Scepter cell counter (Millipore) for the determination of seeding densities. Microscopy.
Images were acquired on a CLSM Leica SP2 (Leica Microsystems, HCX PL APO CS 63x oil immersion objective, NA 1 .4), CLSM Leica SP5 Mid UV-VIS (63x oil immersion objective, NA 1.4) and Leica TCS SP8 upright confocal microscopes (63x oil immersion objective, NA 1 .4). DAPI was excited at 405 nm, and emission was sampled between 420 and 470 nm; AlexaFluor 488 was excited at 488 nm, and emission was sampled between 500 and 550 nm; TamraX-550-Tz was excited at 561 nm, and emission was sampled between 570 and 630 nm, AlexaFluor 647 was excited at 633 nm, and emission was sampled between 655 and 700 nm. Image analysis was performed using LAS AF 2.6.0 (Leica Microsystems), ImageJ 1.47c (National Institutes of Health, USA) and Imaris x64 7.1 .1 (Bitplane). Metabolic labelling of cellular DNA using synthetic nucleosides.
Cells were seeded in 100 mm round cell culture dishes (13 mL) containing glass coverslips (VWR, thickness 1.5, diameter 13 mm) at 100Ό00 - 300Ό00 cells per mL and incubated overnight to ensure an even distribution of cells. The coverslips were placed in 24-well plates containing fresh media solutions with variable concentrations of nucleosides (diluted from appropriate stock solutions in DMSO). After incubating for various times, the cells were fixed in paraformaldehyde (3.7%) for 15 min at room temperature, quenched with PBS containing 50 mM glycine and 50 mM NH4CI for 5 min, and washed twice with PBS. Samples were then stained via invDA or CuAAC.
InvDA staining of fixed cells. Cells were washed with 0.2% Triton X-100 in PBS for 5 min, then denatured using 2 M HCI for 30 min at room temperature. Cell were then washed once with PBS, neutralized with 0.1 M aq. Borax (Na2B4O7«10H2O) solution for 10 min and washed twice with PBS. The coverslips were incubated upside-down with 25 μί drops of freshly diluted 5 μΜ TamraX- 550-Tz in PBS (from a 400x stock solution in DMSO) for 1 - 4 h at room temperature or 37°C in the dark. Cells were washed with 0.1 % Triton X-100 in PBS, and with PBS (3x). Cellular DNA was non-covalently stained with DAPI (1 - 5 μΜ in PBS, Sigma Aldrich) for 15 min at room temperature in the dark. The coverslips were then washed with PBS (2x) and nanopure water, and glued upside-down on microscopy slides using Glycergel (1 1 μί, Dako). Note: when using other, less reactive tetrazine dyes where the substituents on the tetrazine are different than pyridine-2-yl, careful optimization of the staining conditions have to be performed to achieve an appropriate signal to noise ratio.
Selectivity of VdU for DNA synthesis: Cyclin A immunostaining. Cells were seeded in 100 mm round cell culture dishes (13 mL) containing glass coverslips (thickness 1.5, diameter 13 mm, VWR) with 250Ό00 cells per mL and incubated overnight. The coverslips were placed in 24-well plates containing fresh media solutions with or without aphidicolin (10 μΜ, DNA synthesis inhibitor) in the presence of 30 μΜ VdU for 16 h. The cells were then washed with PBS once, fixed in paraformaldehyde (3.7%, 15 min at room temperature), quenched with PBS containing 50 mM glycine and 50 mM NH4CI (5 min), and washed twice with PBS. Cells were treated with 0.2% Triton X-100 in PBS for 5 min, washed once with PBS, denatured using 2 M HCI for 30 min at room temperature, washed once with PBS, neutralized with 0.1 M aq. Borax (Na2B4O7«10H2O) solution for 10 min and washed twice with PBS. Coverslips were incubated upside-down on 25
Figure imgf000046_0001
of freshly diluted 5 μΜ Tamra-Tz in PBS (from a 400 x stock solution in DMSO) for 4 h at 37°C in the dark. After washing with 0.1 % Triton X-100 in PBS, PBS (3x) and blocking with 3% FBS in PBS (60 min, room temperature), coverslips were incubated upside-down on 25
Figure imgf000046_0002
of primary rabbit polyclonal cyclin A (H-432) antibody (2 μg / mL in 3% FBS in PBS; Santa Cruz Biotechnology) at 4°C overnight in a humidified chamber. After washing with PBS (3x 5 min), cells were further subjected to 25
Figure imgf000046_0003
of secondary antibody (AlexaFluor 647 conjugate, 2 μg / mL in 3% FBS in PBS; Life technologies) for 1 hour at room temperature. Cell were washed with PBS (3x) and stained with DAPI (1 - 5 μΜ in PBS) for 15 min at room temperature in the dark. The coverslips were washed with PBS (2x) and nanopure water and glued upside-down on microscopy slides using Glycergel (1 1 μί, Dako). Toxicity assays.
HeLa, U20S, MRC-5, Vero, or A549 cells were seeded in 96-well plates at a density of 5Ό00 - 10Ό00 cells per well and incubated overnight. The supernatant was removed, and fresh media containing variable concentrations of each nucleoside in DMSO was added (final DMSO 0.05%). Control samples contained 0.05% DMSO only. Cells were grown for 24 - 72 h. The media were removed and fresh media containing 87 μΜ of resazurin in media (freshly prepared from an 870 μΜ stock solution in PBS) was added. After incubation for 2 - 3 hours, the fluorescence intensity at 590 nm (excitation 560 nm) was measured using a SpectraMax M5 plate reader. All compound solutions and activity measures were prepared and measured in two or more independent trials. Fluorescence-assisted cell sorting (FACS): γΗ2ΑΧ immunostaining. Cells were seeded in 6-well plates at 250Ό00 cells per well and incubated overnight. The supernatant was removed, and fresh media solutions containing 30 μΜ VdU or 10 μΜ EdU (diluted from 2000x stock solutions in DMSO) were added. After incubating for 4 or 16 hours, the supernatant was removed. For control experiments (ctrl) the nucleosides were omitted; for a positive control cells were treated 1 hour with CPT (camptothecin, 0.5 μΜ). Cells were detached from their surface using Trypsin-EDTA solution (Sigma Aldrich) and pelleted by centrifugation. The cells were washed once with PBS and then fixed with paraformaldehyde (3.7% in PBS, 15 min, room temperature), washed with PBS and permeabilized (0.2% Triton X-100 in PBS, 15 min on ice). The cells were washed with 1 % BSA in PBS, pelleted and resuspended in 100 μΙ_ 1 % BSA in PBS containing mouse monoclonal anti-phospho-histone antibody (H2A.X, Ser 139; 0.5 μg/mL; Millipore) for 2 hours at room temperature. Cells were washed with 1 % BSA in PBS. After pelleting, cells were resuspended in 50 μΙ_ 1 % BSA in PBS containing secondary antibody (AlexaFluor 488 conjugate, 2 μg / ml. ; Life technologies) for 1 hour at room temperature in the dark. Cells were washed with PBS. After DAPI staining (5 μΜ in PBS, 30 min, room temperature in the dark), cell suspensions were analyzed using a CyAn ADP 9 flow cytometer (Beckman Coulter). Data was analyzed using Summit 4.3 (Beckman Coulter).
Dual labelling of cellular DNA synthesis by VdU and EdU.
Coverslips placed in 24-well plates were separately (Figure S 14) or sequentially (Figure S 15) treated with VdU (30 μΜ) and/or EdU (10 μΜ) and incubated for 4 h each. Cells were washed with fresh medium (3x) after each nucleoside treatment. For control experiments, both analogs were added simultaneously for 8 h (Figure 4, C), or were completely omitted. Afterwards, cells were fixed using paraformaldehyde (3.7% in PBS, 15 min, room temperature), quenched (glycine 50 mM, NH4CI 50 mM, in PBS; 5 min, room temperature), treated with 0.2% Triton X-100 (5 min, room temperature) and washed with PBS. Cells were then incubated with 2 M HCI in PBS (30 min, room temperature), washed with PBS (1x), neutralized with 0.1 M aq. Na2B4O7«10H2O (10 min, room temperature), and washed with PBS (3x). Coverslips were incubated upside-down on 25
Figure imgf000047_0001
of freshly diluted 5 μΜ Tamra-Tz in PBS (from a 400x stock solution in DMSO) for 4 hours at 37°C in the dark. After washing with 0.1 % Triton X-100 in PBS, and with PBS (3x), alkyne-modified DNA was stained with AlexaFluor-488-azide (3 μΜ AF-488-azide, 1 mM CuS04, 10 mM sodium ascorbate, in PBS; 30 min, room temperature, in the dark; Life technologies). Samples were washed 0.1 % Triton X-100 in PBS, and PBS (3x). Total DNA was stained with DAPI (1 - 5 μΜ in PBS) for 15 min at room temperature in the dark. The coverslips were washed with PBS (2x) and nanopure water and glued upside-down on microscopy slides using Glycergel (1 1 μΙ_, Dako). Triple labelling of cellular DNA synthesis with VdU, BrdU and F-ara-EdU.
Cells were seeded in 100 mm round cell culture dishes (13 ml.) containing glass coverslips (thickness 1.5, diameter 13 mm, VWR) with 300Ό00 cells per ml. and incubated overnight. The coverslips were placed in 24-well plates, sequentially treated with VdU (30 μΜ), BrdU (30 μΜ), and F-ara-EdU (10 μΜ) and incubated for 2 h 45 min each. Cells were washed with fresh DMEM medium (3x) for 15 min between each nucleoside treatment. For control experiments, nucleoside analogs were omitted. Afterwards, cells were fixed using paraformaldehyde (3.7% in PBS, 15 min, room temperature), quenched (glycine 50 mM, NH4CI 50 mM, in PBS; 5 min, room temperature), permeabilized with acetone (2 min at - 20°C) and washed with ice-cold PBS (3x). Cells were then incubated with 2 M HCI in PBS (30 min, room temperature), washed with PBS (1 x), neutralized with 0.1 M aq. Na2B4O7'10H2O (10 min, room temperature), and washed with PBS (3x). Coverslips were incubated upside-down on 25
Figure imgf000048_0001
of freshly diluted 5 μΜ Tamra-Tz in PBS (from a 400x stock solution in DMSO) for 4 hours at 37°C in the dark. After washing with 0.1 % Triton X-100 in PBS, and with PBS (3x), cells were treated with blocking solution (10% NGS Normal Goat Serum, 1 % BSA Bovine Serum Albumin in PBS with 0.3% Triton X-100; 30 min, room temperature in the dark). The coverslips were then incubated upside down on 25 μΙ_- drops of mouse monoclonal BrdU antibody-AlexaFluor-488 conjugate (2 μg/mL in blocking solution; Invitrogen) for 2 hours at room temperature in the dark. Samples were washes with PBS (3x) and then the alkyne-modified DNA was stained with AlexaFluor-647-azide (10 μΜ AF-647-azide, 1 mM CuS04, 10 mM sodium ascorbate, in PBS; 1 h, room temperature, in the dark). Samples were washed with 0.1 % Triton X-100 in PBS, and PBS (3x). Total DNA was stained with DAPI (1 - 5 μΜ in PBS) for 15 min at room temperature in the dark. The coverslips were washed with PBS (2x) and nanopure water and glued upside-down on microscopy slides using Glycergel (1 1 μΙ_, Dako).

Claims

Claims
1 . A process for preparing at least one labelled nucleic acid, comprising steps of:
(a) providing at least one nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety, in particular a 5-ethenyl pyrimidine moiety or a derivative thereof or a 7-ethenyl-7-deazapurine or a derivative thereof,
(b) contacting said at least one nucleoside/nucleotide analogue to a source of nucleic acids,
(c) applying an enzymatic synthesis yielding at least one labelled nucleic acid comprising at least one nucleoside/nucleotide analogue incorporated into said at least one labelled nucleic acid.
2. The process according to claim 1 , wherein said at least one nucleoside/nucleotide analogue is selected from
- at least one nucleoside/nucleotide analogue of 5-ethenyl pyrimidines of formula (I) or ( ), in particular of formula (I*)
Figure imgf000049_0001
- at least one nucleoside/nucleotide analogue of 7-ethenyl deazapurines of formula (II)
Figure imgf000049_0002
wherein
- R1 and R2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), halogen, thiol (SH), seleno (SeH), amino (NH2), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl, ether (-ORa), or thioether (-SRa), wherein Ra is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl;
- R3 is selected o in case of formula I or I* from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula II hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH2) and the corresponding tautomeric forms of the 7- deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine;
- R4 is selected from hydroxyl (OH), phosphate (OP03 2"), diphosphate (OPO3PO3 3"), triphosphate (OP03P03P03 4"), phosphate diester (OP02RpO"), phosphate triester (- OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl; and
- R5 of formula II is selected from hydrogen (H), hydroxyl (OH), amino (NH2), or halogen, in particular from hydrogen (H) or amino (NH2); and
- T is selected from 0,S or Se, in particular T is O. The process according to claim 2, wherein
- R1 and R2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), fluoride (F) or methyl; and
- R3 is selected a. in case of formula I or I* from hydroxyl (OH), halogen, methyl, or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and b. in case of formula II from hydroxyl (OH), halogen, methyl, or amino group (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7-deazaguanine; and/or
- R4 is selected from phosphate (OP03 2"), diphosphate (OP03P03 3"), triphosphate (OP03P03P03 4"), phosphate diester (OP02RpO"), phosphate triester (-OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl; and
- R5 of formula II is selected from hydrogen (H), amino (NH2), or halogen, and
- T is O.
The process according to claim 2 or 3, wherein
- R1 and R2 are each selected independently from each other from hydrogen (H), hydroxyl (OH), fluoride (F) or methyl; and
- R3 is selected a. in case of formula I or I* from hydroxyl (OH), halogen, or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine, and b. in case of formula II hydroxyl (OH), halogen, or amino (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7- deazaadenine and 7-deazaguanine; and/or
- R4 is hydroxyl (OH); and
- R5 of formula II is selected from hydrogen (H) or amino (NH2), and
- T is O.
The process according to any one of claim 2 to 4, wherein
a. in case of formula (I) T is O and i. R1 is H, R2 is H, R3 is OH, R4 is OH; or ii. R1 is F, R2 is H, R3 is OH, R4 is OH; or iii. R1 is H, R2 is H, R3 is OH, R4 is triphosphate, or iv. R1 is H, R2 is OH, R3 is OH, R4 is OH, or v. R1 is H, R2 is OH, R3 is OH, R4 is triphosphate; or vi. R1 is H, R2 is H, R3 is NH2, R4 is OH, or vii. R1 is H, R2 is H, R3 is NH2, R4 is triphosphate; or viii. R1 is H, R2 is OH, R3 is NH2 and R4 is OH, or ix. R1 is H, R2 is OH, R3 is NH2, R4 is triphosphate, and b. in case of formula II i. R1 is H, R2 is H, R3 is OH, R4 is OH, R5 is NH2; or ii. R1 is H, R2 is H, R3 is OH, R4 is triphosphate, R5 is NH2; or iii. R1 is H, R2 is OH, R3 is OH, R4 is OH, R5 is NH2; or iv. R1 is H, R2 is OH, R3 is OH, R4 is triphosphate, R5 is NH2; or v. R1 is H, R2 is H, R3 is NH2, R4 is OH, R5 is H; or vi. R1 is H, R2 is H, R3 is NH2, R4 is triphosphate, R5 is H, or vii. R1 is H, R2 is OH, R3 is NH2, R4 is OH, R5 is H, or viii. R1 is H, R2 is OH, R3 is NH2, R4 is triphosphate, R5 is H.
The process according to any one of claim 1 to 5, wherein the nucleic acid source is selected from a. a nucleic acid template, in particular a polynucleotide template; or b. cells; or c. organisms; or d. cell extracts; or and/or wherein the enzymatic synthesis is conducted with a. a purified enzyme; or b. a purified enzyme mixture.
The process according to any one of claim 1 to 6, wherein subsequent to the incorporation step c forming the labelled nucleic acid, the at least one ethenyl aromatic moiety of the incorporated at least one nucleoside/nucleotide analogue is reacted with at least one reagent comprising a tetrazine moiety forming a modified nucleic acid comprising one or more dihydropyridazine and/or pyridazine moieties under conditions allowing for the reaction of the ethenyl aromatic moiety with the tetrazine moiety.
The process according to claim 7, wherein the at least one tetrazine is selected from a tetrazine of formula (III):
Figure imgf000052_0001
wherein R6 and R7 are selected independently from each other from - hydrogen (H), halogen, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano (CN), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, in particular 2-pyridyl or 2-pyrimidyl, ether (-ORb), or thioether (-SRb), wherein Rb is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, and
- wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety.
9. The process according to any one of claim 7 or 8, wherein the detectable group comprises a detectable moiety selected from a. a luminescent agent, in particular a fluorescent agent; or b. a biotin; or c. a hapten.
10. A modified nucleic acid, in particular prepared according to any one of the claims 1 to 9, comprising a. at least one dihydropyridazine unit of formula (IV) or (IV*), in particular of formula (IV*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000053_0001
b. at least one pyridazine unit of formula (V) or (V*), in particular of formula (V*) and/or the corresponding tautomeric forms of said formulas:
Figure imgf000053_0002
(V), (V*), and/or c. at least one dihydropyridazine unit of formula (VI) and/or the corresponding tautomeric forms of said formula:
Figure imgf000054_0001
d. at least one pyridazine unit of formula (VII) and/or the corresponding tautomeric forms of said formula:
Figure imgf000054_0002
in particular a modified nucleic acid comprising at least one unit comprising the formula (IV) and/or (VI) and/or (VII), wherein
- R3 is selected o in case of formula IV, IV*, V and V* from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula VI and VII from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH2) and the corresponding tautomeric forms of the 7-deazapurine nucleobase including 7-deazaadenine and 7- deazaguanine; and
- R5 is selected from a hydrogen (H), hydroxyl (OH), amino (NH2), or halogen, in particular from hydrogen (H) or amino (NH2);
- R6 and R7 are selected independently from each other from o hydrogen (H), halogen, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano (CN), alkyl, in particular methyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, in particular 2-pyridyl or 2-pyrimidyl, ether (-ORb), or thioether (-SRb), wherein R is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from Ci- C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, o wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety, and
- T is selected from O, S or Se, in particular from O, and
- L is a sugar-phosphate linkage to a nucleic acid. 1. A nucleoside/nucleotide analogue comprising
a. a nucleoside/nucleotide unit and a dihydropyndazine unit of formula (VIII) or (VIII*), in particular of formula (VIII*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000055_0001
b. a nucleoside/nucleotide unit and a pyridazine unit of formula (IX) or (IX*), in particular of formula (IX*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000055_0002
c. a nucleoside/nucleotide unit and a dihydropyndazine unit of formula (X) or (X*), in particular of formula (X*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000056_0001
d. a nucleoside/nucleotide unit and a pyridazine unit of formula (XI) or (XI*), in particular of formula (XI*), and/or the corresponding tautomeric forms of said formulas:
Figure imgf000056_0002
R1 and R2 have the same definitions as in claims 2 to 5, R3 is selected o in case of formula VIII and VIII* from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding amino and amido tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula IX and IX* from halogen, methyl, thiol (SH), seleno (SeH), or amino (NH2) and the corresponding amino and amido tautomeric forms of the pyrimidine nucleobase including uracil and cytosine and o in case of formula X, X*, XI and XI* from hydroxyl (OH), halogen, methyl, thiol (SH), seleno (SeH), or amino group (NH2) and the corresponding amino and amido tautomeric forms of the 7-deazapurine nucleobase including 7- deazaadenine and 7-deazaguanine; and - R4 is selected from hydroxyl (OH), phosphate diester (OP02RpO") or phosphate triester (-OP03(Rp)2) or their derivatives in forms of acids, esters, bases and salts thereof, wherein Rp is an alkylester, alkylthioester, alkyl, alkenyl, or alkynyl, alkyl, alkenyl, alkynyl, or aryl, in particular an alkylester, alkylthioester, C1-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or aryl
- R5 denotes a hydrogen (H), amino (NH2), or halogen group;
- R6 and R7 are selected independently from each other from o hydrogen (H), halogen, methyl, trifluoromethyl (CF3), trichloromethyl (CCI3), cyano (CN), alkyl, alkenyl, alkynyl, alkylidene, aryl, heteroaryl group, ether (- ORb), or thioether (-SRb), wherein Rb is selected from alkyl, alkenyl, alkynyl, or aryl, in particular from C-|-C4 alkyl, C2-C4 alkenyl, C2-C4 alkynyl, or a functional group, in particular a detectable group comprising at least one detectable moiety, o wherein at least one of R6 and R7 is a functional group, in particular a detectable group comprising at least one detectable moiety, and
- Nu is a sugar moiety or a sugar phosphate moiety, and
- T is selected from O, S or Se, in particular from O.
12. A kit for preparing, in particular according to a method with respect to claim 1 to 9, modified nucleic acids according to claim 10 comprising at least one nucleoside/nucleotide analogue comprising an ethenyl aromatic moiety according to the definition of claim 1 to 5 and a reagent comprising a tetrazine moiety according to the specification any one of claims 7 to 9.
13. Use of a nucleoside/nucleotide analogue according to the definition of claim 1 to 5 in preparing modified nucleic acids.
14. At least one modified nucleic acid according to claim 10 and/or at least one nucleoside/nucleotide analogue according to claim 1 1 for use as diagnostic substance or composition.
PCT/EP2015/064165 2014-06-25 2015-06-23 Methods and products from the reaction of tetrazines with nucleic acid polymers bearing ethenyl aromatic groups WO2015197655A1 (en)

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