RU2011127190A

RU2011127190A - METHOD FOR SYNTHESIS OF NUCLEIC ACIDS MODIFIED BY PHOSPHOR ATOMIC

Info

Publication number: RU2011127190A
Application number: RU2011127190/04A
Authority: RU
Inventors: Такеси ВАДА; Мамору СИМИДЗУ
Original assignee: Чиралджен, Лтд.
Priority date: 2008-12-02
Filing date: 2009-12-02
Publication date: 2013-01-10

Claims

1. A method of synthesizing a nucleic acid containing a chiral X-phosphonate moiety, which comprises reacting a molecule containing an achiral H-phosphonate moiety and a nucleoside containing a 5'-OH moiety to produce a fused intermediate; and the conversion of this intermediate to a nucleic acid containing a chiral-X-phosphonate moiety.

2. The method according to claim 1, characterized in that the reaction step of a molecule containing an achiral H-phosphonate moiety and a nucleoside containing a 5'-OH moiety to produce a condensed intermediate is a one-pot reaction.

3. The method according to claim 1, characterized in that the nucleic acid containing a chiral X-phosphonate moiety is a compound of formula 1:

where R ¹ represents —OH, —SH, —NR ^d R ^d , —N ₃ , halogen, hydrogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl -Y ¹ -, heteroaryl-Y ¹ -, -P (O) (R e) ^{_2, -HP (O) (R e} ), -OR a or -SR ^c;

Y ¹ is O, NR ^d , S or Se;

R ^a is a blocking component;

R ^c is a blocking group;

in each case R ^d is independently hydrogen, alkyl, alkenyl, alkynyl, aryl, acyl, substituted silyl, ^{carbamate, -P (O) (R e} ) ₂ or ^{-HP (O) (R e)} ;

in each case, R ^e represents, independently, hydrogen, alkyl, aryl, alkenyl, alkynyl, alkyl-Y ² -, alkenyl-Y ² -, alkynyl-Y ² -, aryl-Y ² - or heteroaryl-Y ² -, or a cation that is Na ⁺¹ , Li ⁺¹ or K ⁺¹ ;

Y ² is O, NR ^d or S;

in each case, R ² is independently hydrogen, —OH, —SH, —NR ^d R ^d , —N ₃ , halogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl-Y ¹ -, -OR ^b or -SR ^c , where R ^b is a blocking moiety;

in each case, Ba is, independently, blocked or unlocked adenine, cytosine, guanine, thymine, uracil or a modified nucleobase;

each occurrence of X is independently alkyl, alkoxy, aryl, alkylthio, acyl, -NR ^{^f} R ^f, alkenyloxy, alkynyloxy, alkenylthio, ^{^{^{alkynylthio, -S - Z +, -Se -}}} Z + or -VN ₃ ^- Z ^+;

in each case, R ^f is independently hydrogen, alkyl, alkenyl, alkynyl, or aryl;

Z ⁺ is an ammonium ion, an alkylammonium ion, a heteroaromatic iminium ion, or a heterocyclic iminium ion, each of which is a primary, secondary, tertiary or quaternary, or Z ⁺ is a monovalent metal ion;

R ³ is hydrogen, a blocking group, a binding component connected to a solid carrier, or a binding component connected to a nucleic acid; and n is an integer from 1 to about 200.

4. The method according to claim 3, characterized in that each X-phosphonate moiety of the compound of Formula 1 is more than 98% diastereomerically pure, as established using ¹³ P NMR spectroscopy or reverse phase high performance liquid chromatography.

5. The method according to claim 3, characterized in that each X-phosphonate moiety has an R _p configuration.

6. The method according to claim 3, characterized in that each X-phosphonate moiety has a S _p configuration.

7. The method according to claim 3, characterized in that each X-phosphonate moiety has, independently, R _p or S _p configuration.

8. The method according to claim 1, characterized in that the molecule containing the achiral H-phosphonate moiety is a compound of formula 2:

where R ¹ represents NR ^d R ^d , -N ₃ , halogen, hydrogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl- Y ¹ -, -P (O) (R ^e ) ₂ , -HP (O) (R ^e ), -OR ^a or -SR ^c ;

Y ¹ is O, NR ^d , S or Se;

R ^a is a blocking component;

R ^c is a blocking group;

in each case R ^d is independently hydrogen, alkyl, alkenyl, alkynyl, aryl, acyl, substituted silyl, carbamate, -P (O) (R ^e) ₂ or ^{-HP (O) (R e)} ;

in each case, R ^e is independently alkyl, aryl, alkenyl, alkynyl, alkyl-Y ² -, alkenyl-Y ² -, alkynyl-Y ² -, aryl-Y ² - or heteroaryl-Y ² -;

Y ² is O, NR ^d or S;

R ² represents hydrogen, —NR ^d R ^d , —N ₃ , halogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl- Y ¹ -, —OR ^b or —SR ^c , where R ^b is a blocking moiety; and

Ba is blocked or unblocked adenine, cytosine, guanine, thymine, uracil or a modified nucleobase; and

Z ⁺ is an ammonium ion, an alkylammonium ion, a heteroaromatic iminium ion, or a heterocyclic iminium ion, each of which is a primary, secondary, tertiary or quaternary or monovalent metal ion.

9. The method according to claim 1, characterized in that it further comprises a chiral reagent.

10. The method according to claim 9, characterized in that the chiral reagent is a compound of formula 3:

where W ₁ and W ₂ are independently —NG ⁵ -, —O— or —S—;

G ¹ , G ² , G ³ , G ⁴ , and G ⁵ are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, hetaryl or aryl, or two of G ¹ , G ² , G ³ , G ⁴ , and G ⁵ are G ⁶ and, taken together, form a saturated, partially unsaturated or unsaturated carbocyclic or heteroatom ring containing up to about 20 ring atoms, which is monocyclic or polycyclic, fused or non-fused, and where no more than four of G ¹ , G ² , G ³ , G ⁴ , and G ⁵ are G ⁶ .

11. The method according to claim 1, characterized in that the nucleoside containing the 5'-OH component is a compound of formula 4:

where in each case, R ² independently represents hydrogen, —NR ^d R ^d , —N ₃ , halogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl-Y ¹ -, -OR ^b or -SR ^c , where R ^b is a blocking moiety;

Y ¹ is O, NR ^d , S or Se;

R ^c is a blocking group;

in each case, R ^e represents alkyl, aryl, alkenyl, alkynyl, alkyl-Y ² -, alkenyl-Y ² -, alkynyl-Y ² -, aryl-Y ² - or heteroaryl-Y ² -;

Y ² is O, NR ^d or S;

in each case, Ba is independently blocked or unblocked adenine, cytosine, guanine, thymine, uracil or a modified nucleobase;

m is an integer from 0 to n-1;

n is an integer from 1 to about 200;

O _{A is} coupled to a trityl moiety, a silyl moiety, an acetyl moiety, an acyl moiety, an aryl moiety, an arylacyl moiety, a binder moiety, coupled to a solid carrier, or a moiety bonding to a nucleic acid;

J is O and D is H or J is S, Se, or BH ₃ , and D is a chiral ligand C _i or a component of formula A:

where W ₁ and W ₂ are independently NHG ⁵ , OH or SH;

A represents hydrogen, acyl, aryl, alkyl, aralkyl or silyl moiety; and

where G ¹ , G ² , G ³ , G ⁴ , and G ⁵ are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, heteroaryl or aryl, or two of G ¹ , G ² , G ³ , G ⁴ , and G ⁵ are G ⁶ , and taken together form a saturated, partially unsaturated or unsaturated carbocyclic or heteroatom ring containing up to about 20 ring atoms, which is monocyclic or polycyclic, fused or non-fused, and where no more than four of G ¹ , G ² , G ³ , G ⁴ , and G ⁵ are G ⁶ .

12. The method according to claim 1, characterized in that it further includes the introduction of a condensing reagent C _R , through which a molecule containing an achiral H-phosphonate moiety is activated to react with this chiral reagent to form a chiral intermediate.

13. The method according to p. 12, characterized in that the condensing reagent C _R is Ar ₃ PL ₂ , (ArO) ₃ PL ₂ ,

,

or

Where

Z ¹ , Z ² , Z ³ , Z ⁴ , Z ⁵ , Z ⁶ , Z ⁷ , Z ⁸ , Z ⁹ and Z ¹⁰ are independently alkyl, aminoalkyl, cycloalkyl, heterocycle, cycloalkylalkyl, heterocycloalkyl, aryl, heteroaryl, alkyloxy, aryloxy or heteroaryloxy, or where any of Z ² and Z ³ , Z ⁵ and Z ⁶ , Z ⁷ and Z ⁸ , Z ⁸ and Z ⁹ , Z ⁹ and Z ⁷ , or Z ⁷ and Z ⁸ , and Z ⁹ taken together with the formation of a 3-20 membered alicyclic or heterocyclic ring;

Q ^- is the counterion;

L is a leaving group;

W is an integer from 0 to 3; and

Ar is aryl, heteroaryl, and / or one of the Ar groups is attached to a polymer carrier.

14. The method according to item 13, wherein the counterion of the condensing reagent C _R is Cl ^- , Br ^- , BF ₄ ^- , PF ₆ ^- , TfO ^- , Tf ₂ N ^- , AsF ₆ ^- , ClO ₄ ^- or SbF ₆ ^- where Tf is CF ₃ SO ₂ .

15. The method according to item 13, wherein the leaving group of the condensing reagent C _R is F, Cl, Br, I, 3-nitro-1,2,4-triazole, imidazole, alkyltriazole, tetrazole, pentafluorobenzene or 1-hydroxybenzotriazole .

16. The method according to p. 12, characterized in that the condensing reagent is a bis (trichloromethyl) carbamate (BTK), (PhO) ₃ PCl ₂ , Ph ₃ PCl ₂ , N, N'-bis (2-oxo-3- oxazolidinyl) phosphine chloride (BopCl), 1,3-dimethyl-2- (3-nitro-1,2,4-triazol-1-yl) -2-pyrrolidin-1-yl-1,3,2-diazaphospholidinium hexafluorophosphate (MNTP), or 3-nitro-1,2,4-triazol-1-yl-tris (pyrrolidin-1-yl) phosphonium hexafluorophosphate (PyNTP).

,

17. The method according to p. 12, characterized in that it further includes the introduction of an activating reagent A _R.

18. The method according to 17, characterized in that the activating reagent A _R represents

,

or

where Z ¹¹ , Z ¹² , Z ¹³ , Z ¹⁴ , Z ¹⁵ , Z ¹⁶ , Z ¹⁷ , Z ¹⁸ , Z ¹⁹ , Z ²⁰ and Z ²¹ are independently hydrogen, alkyl, aminoalkyl, cycloalkyl, heterocycle, cycloalkylalkyl, heterocycloalkyl, aryl, heteroaryl, alkyloxy, aryloxy or heteroaryloxy, or where any of Z ¹¹ and Z ¹² , Z ¹¹ and Z ¹³ , Z ¹¹ and Z ¹⁴ , Z ¹² and Z ¹³ , Z ¹² and Z ¹⁴ , Z ¹³ and Z ¹⁴ , Z ¹⁵ and Z ¹⁶ , Z ¹⁵ and Z ¹⁷ , Z ¹⁶ and Z ¹⁷ , Z ¹⁸ and Z ¹⁹ , or Z ²⁰ and Z ²¹ are taken together with the formation of a 3-20 membered alicyclic or heterocyclic ring, or with the formation of 5 or 20 membered aromatic ring, and Q ^- is the counterion.

19. The method according to p. 18, characterized in that the counterion of the activating reagent A _R is Cl ^- , Br ^- , BF ₄ ^- , PF ₆ ^- , TfO ^- , Tf ₂ N ^- , AsF ₆ ^- , ClO ₄ ^- or SbF ₆ ^- where Tf is CF ₃ SO ₂ .

20. The method according to 17, characterized in that the activating reagent A _R is imidazole, 4,5-dicyanoimidazole (DCI), 4,5-dichloroimidazole, 1-phenylimidazole triflate (PhIMT), benzimidazole triflate (BIT), benztriazole , 3-nitro-1,2,4-triazole (NT), tetrazole, 5-ethylthiotetrazole, 5- (4-nitrophenyl) tetrazole, N-cyanomethylpyrrolidinium triflate (CMPT), N-cyanomethylpiperidinium triflate, N-cyanomethyldimethylammonium triflate.

21. The method according to 17, characterized in that the activating reagent A _R is 4,5-dicyanoimidazole (DCI), 1-phenylimidazole triflate (PhIMT), benzimidazolium triflate (BIT), 3-nitro-1,2,4 triazole (NT), tetrazole or N-cyanomethylpyrrolidinium triflate (CMPT).

,

22. The method according to 17, characterized in that the activating reagent A _R is N-cyanomethylpyrrolidinium triflate (CMPT).

23. The method according to claim 1, characterized in that the reaction is carried out in an aprotic organic solvent.

24. The method according to item 23, wherein the solvent is acetonitrile, pyridine, tetrahydrofuran or dichloromethane.

25. The method according to paragraph 24, wherein the aprotic solvent is not basic, while the base is present in the reaction stage.

26. The method according A.25, characterized in that the base is pyridine, quinoline, N, N-dimethylaniline or N-cyanomethylpyrrolidine.

27. The method according A.25, characterized in that the basis is

,

where Z ²² and Z ²³ are independently alkyl, aminoalkyl, cycloalkyl, heterocycle, cycloalkylalkyl, heterocycloalkyl, aryl, heteroaryl, alkyloxy, aryloxy, or heteroaryloxy, or where any of Z ²² and Z ²³ are taken together to form 3-10 membered alicyclic or heterocyclic rings.

28. The method according A.25, characterized in that the base is N-cyanomethylpyrrolidine.

29. The method according to item 23, wherein the aprotic solvent is anhydrous.

30. The method according to clause 29, wherein the anhydrous aprotic solvent is freshly distilled.

31. The method according to p. 30, characterized in that the freshly distilled anhydrous aprotic organic solvent is pyridine or acetonitrile.

32. The method according to claim 1, characterized in that the step of converting the condensed intermediate to a compound of formula 1 includes: capping the condensed intermediate and modifying the capped condensed intermediate to obtain a compound of formula 5:

where R ¹ represents —NR ^d R ^d , —N ₃ , halogen, hydrogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, apkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl -Y ^l -, -P (O) (Re) 2, -HP (O) (Re), -ORa or -SRc;

Y ¹ is O, NRd, S or Se;

R ^a is a blocking component;

R ^c is a blocking group;

in each case, R ^e represents, independently, alkyl, aryl, alkenyl, alkynyl, alkyl-Y ² -, alkenyl-Y ² -, alkynyl-Y ² -, aryl-Y ² - or heteroaryl-Y ² -;

Y ² is O, NR ^d or S;

in each case, R ² is independently hydrogen, —NR ^d R ^d , —N ₃ , halogen, alkyl, alkeyyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl- Y ¹ -, heteroaryl-Y ¹ -, —OR ^b or —SR ^c , where R ^b is a blocking moiety;

in each case, J is S, Se or BH ₃ ;

v is an integer from 2 to n-1;

O _{A is} bonded to a binding moiety that is bonded to a solid support or a bonding moiety to a nucleic acid;

A represents an acyl, aryl, alkyl, aralkyl or silyl moiety; and

G ¹ , G ² , G ³ , G ⁴ and G ⁵ are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, heteroaryl or aryl, or two of G ¹ , G ² , G ³ , G ⁴ and G ⁵ are G ⁶ , and taken together form a saturated, partially unsaturated or unsaturated carbocyclic or heteroatom ring containing up to about 20 ring atoms, which is monocyclic or polycyclic, fused or non-fused, and where no more than four of G ¹ , G ² , G ³ , G ⁴ and G ⁵ are G ⁶ .

33. The method according to p, characterized in that it further comprises the steps of: (a) unlocking R ^{1 a} compound of formula 5 to obtain a compound of formula 4, where m is at least 1, J is S, Se, or BH3 and D is a component of formula A; (b) reacting a compound of formula 4 using the method of claim 10, wherein the step of converting the condensed intermediate compound comprises capping the condensed intermediate compound and modifying the capped condensed intermediate to obtain a compound of formula 5, where v is greater than 2 and less than about 200; and (c) is a repetition, if necessary, of steps (a) and (b) to obtain a compound of formula 5, where v is greater than 3 and less than approximately 200.

34. The method according to p, characterized in that it further comprises the step of converting a compound of formula 5 into a compound of formula 1, wherein each Ba component is unlocked; R ¹ represents —OH, —SH, —NR ^d R ^d , —N ₃ , halogen, hydrogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl- Y ¹ -, heteroaryl-Y ¹ -, -P (O) (R e) ^{_2, -HP (O) (R e} ), -OR a or -SR ^c;

Y ¹ is O, NR ^d , S or Se;

R ^a is a blocking component;

R ^c is a blocking group;

in each case, R ^e is independently hydrogen, alkyl, aryl, alkenyl, alkynyl, alkyl-Y ² -, alkenyl-Y ² -, alkyl-Y ² -, aryl-Y ² - or heteroaryl-Y ² - or a cation, which is Na ⁺¹ , Li ⁺¹ or K ⁺¹ ;

Y ² is O, NR ^d or S;

in each case, R ² represents hydrogen ,, —OH, —SH, —NR ^d R ^d , —N ₃ , halogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl-Y ¹ -;

R ³ is H;

each occurrence of X is independently ^{^{^{-S - Z +, -Se - Z}}} + or -VN ₃ ^- Z ^+; and

Z ⁺ is an ammonium ion, alkylammonium ion, heteroaromatic iminium ion or heterocyclic iminium ion, any of which is primary, secondary, tertiary or quaternary, or Z ⁺ is a monovalent metal ion.

35. The method according to claim 1, characterized in that the step of converting the condensed intermediate to a compound of formula 1 comprises acidifying the condensed intermediate to produce a compound of Formula 4, wherein m is at least one, J is O, and D is H .

36. The method according to clause 35, wherein the condensed intermediate compound contains a component of the formula A ':

where a is hydrogen; and

where G ¹ and G ² are independently alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, gstsroaryl or aryl, and G ³ , G ⁴ , and G ⁵ are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, heteroaryl, or acyl, or two of G ¹ , G ² , G ³ , G ⁴ and G ⁵ are G ⁶ , and taken together form a saturated, partially unsaturated or unsaturated carbocyclic or hsteroatom ring containing up to about 20 ring atoms, which is monocyclic or polycyclic, merged or unfused, and where not e four of G ^1, G ^2, G ^3, G ^4, G ⁵ and G ⁶ are.

37. The method according to p. 35, characterized in that it further includes: (a) a reaction of a compound of formula 4, where m is at least one, J is O and D is H, using the method of claim 10, where the step of converting the condensed intermediate to a compound of formula 1 involves acidifying the condensed intermediate to obtain a compound of formula 4, wherein m is at least 2 and less than about 200; J is O and D is H, and (b) repeating, if necessary, step (a) to obtain a compound of formula 4, where m is greater than 2 and less than about 200.

38. The method according to p. 35 or 37, wherein the acidification comprises the addition of such a quantity of Bronsted or Lewis acid that is effective for converting the condensed intermediate to a compound of formula 4 without removing the purine or pyrimidine components from the condensed intermediate.

39. The method according to § 38, wherein the acidification comprises adding 1% trifluoroacetic acid in an organic solvent.

40. The method according to p. 35 or 37, wherein the acidification further includes the addition of a cation scavenger.

41. The method according to p, characterized in that the cation scavenger is triethylsilane or triisopropylsilane.

42. The method according to p. 35 or 37, characterized in that the step of converting the condensed intermediate to a compound of formula 1 further comprises unlocking R ¹ before the step of acidifying the condensed intermediate.

43. The method according to p, characterized in that it further includes the step of modifying the compound of formula 4 to introduce the X component to obtain in this way a compound of formula 1, where R ³ is a blocking group or a binding component connected to a solid carrier.

44. The method according to item 43, wherein it further includes processing the product according to item 35 to obtain a compound of formula 1, where R ¹ represents —OH, —SH, —NR ^d R ^d , —N ₃ , halogen, hydrogen , alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl-Y ¹ -, -P (O) (R ^e) _2, -HP (O) (R ^e ), -OR ^a or -SR ^c ;

Y ¹ is O, NR ^d , S or Se;

R ^a is a blocking component;

R ^c is a blocking group;

in each case R ^d is independently hydrogen, alkyl, alkenyl, alkynyl, aryl, acyl, substituted silyl, ^{carbamate, -P (O) (R e} ) or ^{-HP (O) (R e)} ;

Y ² is O, NR ^d or S;

in each case, R ² is independently hydrogen, —OH, —SH, —NR ^d R ^d , —N ₃ , halogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl- Y ¹ -, aryl-Y ¹ -, heteroaryl-Y ¹ -;

each VA component is unlocked;

R ³ is H;

each occurrence of X is independently alkyl, alkoxy, aryl, alkylthio, acyl, -NR ^{^f} R ^f, alkenyloxy, alkynyloxy, alkenylthio, ^{^{^{alkynylthio, -S - Z +, -Se -}}} Z + or -BH ₃ ^- Z ^+;

in each case, R ^f is independently hydrogen, alkyl, alkenyl, alkynyl or aryl;

Z ⁺ is an ammonium ion, an alkylammonium ion, a heteroaromatic iminium ion or a heterocyclic iminium ion, any of which is a primary, secondary, tertiary or quaternary, or Z ⁺ is a monovalent metal ion; and

n is greater than 1 and less than approximately 200.

45. The method according to p. 32 or 33, characterized in that the stage of modification is carried out using a borating agent, sulfur electrophile or selenium electrophile.

46. The method according to item 45, wherein the sulfur electrophile is a compound having one of the following formulas:

, Z ²⁴ -SSZ ²⁵ or Z ²⁴ -SXZ ²⁵ ,

where Z ²⁴ and Z ²⁵ are independently alkyl, aminoalkyl, cycloalkyl, heterocycle, cycloalkylalkyl, heterocycloalkyl, aryl, heteroaryl, alkyloxy, aryloxy, heteroaryloxy, acyl, amide, imide or thiocarbonyl, or Z ²⁴ and Z ²⁵ are taken together to form 3 -8 membered alicyclic or heterocyclic rings, which may be substituted or unsubstituted;

X is SO ₂ , O, or NR ^f ; and R ^f represents hydrogen, alkyl, alkenyl, alkynyl or aryl.

47. The method according to item 46, wherein the sulfur electrophile is a compound of formula B, C, D, E or F:

,

48. The method according to item 45, wherein the selenium electrophile is a compound having one of the following formulas:

, Z ²⁶ -Se-Se-Z ^27f or Z ²⁶ -Se-XZ ²⁷ ,

where Z ²⁶ and Z ²⁷ are independently alkyl, aminoalkyl, cycloalkyl, heterocycle, cycloalkylalkyl, heterocycloalkyl, aryl, heteroaryl, alkyloxy, aryloxy, heteroaryloxy, acyl, amide, imide, or thiocarbonyl, or Z ²⁶ and Z ²⁷ are taken together to form 3-8 membered alicyclic or heterocyclic rings, which may be substituted or unsubstituted;

X is O ₂ , O, S or NR ^f ; and R ^f is hydrogen, alkyl, alkenyl, alkynyl or aryl.

49. The method according to p, characterized in that the selenium electrophile is a compound of the formula G, H, I, J, K or L.

,

50. The method according to item 45, wherein the boron agent is borane-N, N-diisopropylethylamine (BH3 · DIPEA), borane-pyridine (BH3 · Py), borane-2-chloropyridine (BH3 · CPy), borane -aniline (BH3 · An), borane-tetrahydrofuran (BH3 · THF) or borane-dimethyl sulfide (BH3 · Me2S).

51. The method according to item 43, wherein the modification step is carried out using a silylating reagent, then a sulfur electrophile, a selenium electrophile, a boron agent, an alkylating agent, an aldehyde or an acylating agent.

52. The method according to 51, wherein the silylating reagent is chlorotrimethylsilane (TMS-Cl), triisopropylsilyl chloride (TIPS-Cl), N-butyldimethylsilyl chloride (TBDMS-Cl), t-butyldiphenylsilyl chloride (TBDFS-Cl) , 1,3,3,3-hexamethyldisilisane (HMDS), N-trimethylsilyldimethylamine (TMSDMA), N-trimethylsilyldiethylamine (TMSDEA), N-trimethylsilylacetamide (TMSA), N, O-bis (trimethylsilyl) acetamide (BSA) or N, O-bis (trimethylsilyl) trifluoroacetamide (BSTFA).

53. The method according to 51, wherein the sulfur electrophile is a compound having one of the following formulas:

, Z ²⁴ -SSZ ²⁵ or Z ²⁴ -SXZ ²⁵ ,

54. The method according to item 53, wherein the sulfur electrophile is a compound of formula B, C, D, E or F:

,

55. The method according to § 51, wherein the selenium electrophile is a compound having one of the following formulas:

, Z ²⁶ -Se-Se-Z ²⁷ or Z ²⁶ -Se-XZ ²⁷ ,

where Z ²⁶ and Z ²⁷ are independently alkyl, aminoalkyl, cycloalkyl, heterocycle, cycloalkylalkyl, heterocycloalkyl, aryl, heteroaryl, alkyloxy, aryloxy, heteroaryloxy, acyl, amide, imide or thiocarbonyl, or Z ²⁶ and Z ²⁷ are taken together to form 3 -8 membered alicyclic or heterocyclic rings, which may be substituted or unsubstituted;

X is SO ₂ , S, O or NR ^f ; and R ^f represents hydrogen, alkyl, alkenyl, alkynyl or aryl.

56. The method according to § 51, wherein the selenium electrophile is a compound of the formula G, H, I, J, K or L.

,

57. The method according to 51, wherein the boron agent is borane-N, N-diisopropylethylamine (BH3 · DIPEA), borane-pyridine (BH3 · Py), borane-2-chloropyridine (BH3 · CPy), bran- aniline (BH3 · An), borane-tetrahydrofuran (BH3 · THF) or borane-dimethyl sulfide (BH3 · Me2S).

58. The method according to 51, wherein the alkylating agent is an alkyl halide, alkenyl halide, alkynyl halide, alkyl sulfonate, alkenyl sulfonate or alkynyl sulfonate.

59. The method of claim 51, wherein the aldehyde is (para) formaldehyde, alkyl aldehyde, alkenyl aldehyde, alkynyl aldehyde or aryl aldehyde.

60. The method according to § 51, wherein the acylating agent is a compound of formula M or N:

where G ⁷ represents alkyl, cycloalkyl, heterocycle, cycloalkylalkyl, heterocycloalkyl, aryl, heteroaryl, alkyloxy, aryloxy or heteroaryloxy; and M is F, Cl, Br, I, 3-nitro-1,2,4-triazole, imidazole, alkyltriazole, tetrazole, pentafluorobenzene or 1-hydroxybenzotriazole.

61. The method according to item 43, wherein the stage of modification is carried out by reaction with a halogenating reagent, then reaction with a nucleophile.

62. The method according to 61, wherein the halogenating reagent is CCl4, CBr4, Cl2, Br2, I2, sulfuryl chloride (SO2Cl2), phosgene, bis (trichloromethyl) carbonate (BTK), sulfur monochloride, sulfur dichloride, chloroamine, CuCl2 N-chlorosuccinimide (NCS), CI4, N-bromosuccinimide (NBS) or N-iodosuccinimide (NIS).

63. The method according to p, characterized in that the nucleophile is NRfRfH, RfDH, or RfSH, where Rf is hydrogen, alkyl, alkenyl, alkyyl or aryl, and at least one of Rf NRfRfH is not hydrogen.

64. The method according to claim 10, characterized in that the chiral reagent is a compound of Formula 3, where W ₁ is NHG ⁵ and W ₂ is O.

65. The method according to claim 10, characterized in that the chiral reagent has the formula O or the formula P:

66. The method according to claim 10, characterized in that the chiral reagent has the formula Q or the formula R:

67. The method according to claims 3, 8, 32 or 34, characterized in that Ra is substituted or unsubstituted trityl or substituted silyl.

68. The method according to item 44, wherein Ra is substituted or unsubstituted trityl, or substituted silyl.

69. The method according to claims 3, 8, 11 or 32, characterized in that Rb is substituted or unsubstituted trityl, substituted silyl, acetyl, acyl or substituted methyl ether.

70. The method according to claim 3, characterized in that R ³ is a blocking group, which is a substituted trityl, acyl, substituted silyl or substituted benzyl.

71. The method according to claim 3, characterized in that R ³ is a binding component connected to a solid carrier.

72. The method according to claims 3, 8, 11 or 32, characterized in that the blocking group Ba component is benzyl, acyl, formyl, dialkylformamidinyl, isobutyryl, phenoxyacetyl or trityl component, any of which may be substituted or unsubstituted.

73. The method according to claims 3, 8 or 34, characterized in that R1 is —N3, —NRdRd, alkynyloxy or —OH.

74. The method according to item 43, wherein R1 is —N3, —NRdRd, alkynyloxy or OH.

75. The method according to claims 3, 8, 11, 32 or 34, characterized in that R2 is —NRdRd, alkyl, alkenyl, alkynyl, alkyl-Y1-, alkenyl-Y1-, alkynyl-Y1-, aryl-Y1 -, heteroaryl-Y1, and is substituted by fluorescent or biomolecular binding moieties.

76. The method according to item 43, wherein R2 is —NRdRd, alkyl, vkenenyl, alkynyl, alkyl-Y1-, alkenyl-Y1-, alkynyl-Y1-, aryl-Y1-, heteroaryl-Y1 and is substituted fluorescent or biomolecular binding components.

77. The method according to item 75, wherein the substituent PA R2 is a fluorescent component.

78. The method according to item 75, wherein the substituent PA R2 is a biotype or avidin.

79. The method according to p, characterized in that the substituent on R2 is a fluorescent component.

80. The method according to p, characterized in that the substituent on R ² is biotin or avidin.

81. The method according to claims 3, 8, 11, 32, 34 or 43, characterized in that R ² represents —OH, —N ₃ , hydrogen, halogen, alkoxy or alkynyloxy.

82. The method according to claims 3, 8, 11, 32 or 34, characterized in that R2 is —OH, —N ₃ , hydrogen, halogen, alkoxy or alkynyloxy.

83. The method according to item 43, wherein the Ba is 5-bromouracil, 5-iodouracil or 2, 6-diaminopurin.

84. The method according to claims 3, 8, 11, 32 or 34, characterized in that Ba is modified by replacing a fluorescent or biomolecular binding component.

85. The method according to item 43, wherein the Ba is modified by replacing a fluorescent or biomolecular binding component.

86. The method according to p, characterized in that the substitute for Ba is a fluorescent component.

87. The method according to claim 84, wherein the substitute for Ba is biotin or avidin.

88. The method according to p, characterized in that the substitute for Ba is a fluorescent component.

89. The method of claim 85, wherein the substitute for Ba is biotin or avidin.

90. The method according to claims 3, 8 or 34, characterized in that Z is a pyridinium ion, triethylammonium ion, N, N-diisopropylethylammonium ion, 1,8-diazabicyclo [5.4.0] undec-7-ene ion, sodium ion or potassium ion.

91. The method according to item 43, wherein Z is a pyridinium ion, triethylammonium ion, N, N-diisylpropylethylammonium ion, 1,8-diazabicyclo [5.4.0] undec-7-ene ion, sodium ion or potassium ion.

92. The method according to claims 3 or 34, wherein X is alkyl, alkoxy, -NRfRf, -S-Z + or -BH3-Z +.

93. The method according to item 43, wherein X is alkyl, alkoxy, -NRfRf, -S-Z + or -BH3-Z +.

94. The method according to item 47, wherein the sulfur electrophile has the formula F, formula E or formula B.

95. The method according to item 54, wherein the sulfur electrophile has the formula F, formula E or formula B.

96. The method according to 49, characterized in that the selenium electrophile has the formula G or formula J.

97. The method according to p, characterized in that the selenium electrophile has the formula G or formula J.

98. The method according to p. 50 or 57, wherein the boron agent is borane-N, N-diisopropylethylamine (BH ₃ · DIPEA), borane-2-chloropyridine (BH ₃ · CPy), borane-tetrahydrofuran (BH ₃ · THF) or borane-dimethyl sulfide (BH ₃ · Me ₂ S).

99. The method according to claim 62, wherein the halogenating agent is CCl ₄ , CBr ₄ , Cl ₂ , sulfuryl chloride (SO ₂ Cl ₂ ) or N-chlorosuccinimide (NCS).

100. The method according to clause 16, wherein the condensing reagent is a bis (trichloromethyl) carbonate (BTK), (PhO) ₃ PCl ₂ , Ph ₃ PCl ₂ or N, N-bis (2-oxo-3-oxazolidinyl ) phosphinium chloride (BopCl).

101. A method for identifying or detecting a target molecule in a sample, comprising: contacting the sample, which is supposed to contain the target molecule, with a nucleic acid sensor molecule according to claim 3, where a change in the signal generated by the signal generation unit indicates the presence of said target in the specified sample.

102. The method according to p. 101, characterized in that it further includes quantifying the change in the signal generated by the signal generation unit for quantifying the target molecules in a given sample.

103. The method according to p. 101, characterized in that the signal generation unit detects fluorescence, surface plasmon resonance, quenching of fluorescence, chemiluminescence, interferometry or measurement of refractive index.

104. The method according to p. 101, characterized in that the sample is an environmental sample, a biohazardous material, an organic sample, a medicine, a toxin, a flavoring, fragrance or a biological sample.

105. The method according to p. 101, wherein the sample is a biological sample, which is a cell, cell extract, cell lysate, tissue, tissue extract, body fluid, serum, blood or blood product.

106. The method according to p. 101, characterized in that the nucleic acid sensor molecule binds in a specific manner to the target molecule.

107. The method according to p. 101, characterized in that the presence of the target molecule indicates the presence of a pathological condition.

108. A method for amplifying the necessary nucleic acid regions from a nucleic acid matrix, which comprises: (a) introducing a plurality of first PCR primers having a fixed nucleotide sequence region complementary to the desired consensus sequence; (b) introducing a plurality of second PCR primers, (c) amplifying a nucleic acid matrix by PCR (polymerase chain reaction) using a plurality of first PCR primers and a plurality of second PCR primers under conditions where a subset of the plurality of first primers binds to the desired consensus sequence under conditions where a subset of this set of first primers binds to the required consensus sequence to a large extent where this occurs in the matrix, and a subset of this a number of second primers binds to the matrix at locations remote from the first primers so that specific amplification of nucleic acid regions flanked by the first primer and second primer occurs, and where the plurality of first PCR primers and / or the plurality of second PCR are nucleic acid molecules according to claim 3 .

109. The method of claim 108, wherein said matrix is genomic DNA.

110. The method according to p, characterized in that the matrix is eukaryotic genomic DNA.

111. The method of claim 108, wherein said matrix is human genomic DNA.

112. The method of claim 108, wherein said matrix is prokaryotic DNA.

113. The method according to p, characterized in that the matrix is DNA, which is a cloned genomic DNA, subgenomic DNA region, chromosome or subchromosomal region.

114. The method according to p, characterized in that the matrix is RNA.

115. The method according to claim 1, characterized in that the step of converting the condensed intermediate to a compound of formula 1 includes: modifying the condensed intermediate to obtain a compound of formula 5:

where R ¹ represents —NR ^d R ^d , —N ₃ , halogen, hydrogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkynyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl -Y ¹ -, -P (O) (Re) ₂ , -HP (O) (R ^e ), -OR ^a or -SR ^c ;

Y1 is O, NRd, S or Se;

R ^a is a blocking component;

R ^c is a blocking group;

In each case, R ^d is independently hydrogen, alkyl, alkenyl, alkynyl, aryl, acyl, substituted silyl, carbamate, -P (O) (P ^e) ₂ or ^{-HP (O) (R e)} ;

in each case, R ^e is independently alkyl, aryl, alkenyl, alkynyl, alkyl-Y ² -, alkenple-Y ² -, alkipyl-Y ² -, aryl-Y ² - or heteroaryl-Y ² -;

Y ² is O, NR ^d or S;

in each case, R ² is independently hydrogen, —NR ^d R ^d , —N ³ , halogen, alkyl, alkenyl, alkynyl, alkyl-Y ¹ -, alkenyl-Y ¹ -, alkynyl-Y ¹ -, aryl-Y ¹ -, heteroaryl-Y ¹ -, —OR ^b or —SR ^c , where R ^b is a blocking moiety;

in each case, Ba is a blocked or unblocked adenine, cytosine, guanine, thymine, uracil or a modified nucleobase;

in each case, J is S, Se or BH ₃ ;

v is an integer equal to 1;

O _{A is} coupled to a binding moiety linked to a solid support or a binding moiety linked to a nucleic acid;

A represents an acyl, aryl, alkyl, aralkyl or silyl moiety; and

G ¹ , G ² , G ³ , G ⁴ , and C ⁵ are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, heteroaryl or aryl, or two of G ¹ , G ² , G ³ , G ⁴ and G ⁵ are G ⁶ , and taken together form a saturated, partially unsaturated or unsaturated carbocyclic or heteroatom ring containing up to about 20 ring atoms, which is monocyclic or polycyclic, fused or non-fused, where no more than four of G ¹ , G ² , G ³ , G ⁴ and G ⁵ are G ⁶ .