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Pyrimidine derivatives for labeled binding partners

  • US 6,414,127 B1
  • Filed: 09/21/1999
  • Issued: 07/02/2002
  • Est. Priority Date: 11/07/1997
  • Status: Expired due to Term
First Claim
Patent Images

1. A compound having the structure (1):

  • embedded imageand tautomers, solvates and salts thereof, whereinR1 is —

    H or a binding partner having the structure 2, 2(A), 2(B), or 2(C);

    embedded imagewhereinD is —

    OH, protected —

    OH, an oligonucleotide coupling group or a solid support;

    D1 is an oligonucleotide coupling group, —

    OH, protected —

    OH or a solid support, wherein D1 is bonded to one 2′

    or 3′

    position in the oligonucleotide of structure (2) and the adjacent 2′

    or 3′

    position in structure (2) is substituted with R21, provided that D and D1 are not both an oligonucleotide coupling group or they are not both a solid support;

    D2 is —

    CO2R5, —

    C(O)N(R5)2, —

    SO3R5, —

    SO2N(R5)2 or an activated derivative of —

    CO2H or —

    SO3H;

    D3 is a protecting group, —

    H or —

    (CH2)2-6

    N(R5)2, R4 independently a phosphodiester linkage or a phosphodiester substitute linkage, wherein R4 is bonded to one 2′

    or 3′

    position in the structure (2) oligonucleotide and the adjacent 2′

    or 3′

    position in structure (2) substituted with R21;

    R5 is independently —

    H or a protecting group;

    R21 is independently —

    H, —

    OH, halogen or a moiety that enhances the oligonucleotide against nuclease cleavage;

    R37 is independently —

    O—

    , —

    CH2

    or —

    CF2

    ;

    n is an integer from 0 to 98; and

    B independently is a purine or pyrimidine base or a protected derivative thereof, provided that at least one B is a base of structure (3) embedded imageR2 is A(Z)X1, wherein A is a spacer and Z independently is a label bonding group optionally bonded to a detectable label, but R2 is not amine, protected amine, nitro or cyano;

    R27 is independently —

    CH═

    , —

    N═

    , —

    C(C1-C8 alkyl)═

    or —

    C(halogen)═

    , but no adjacent R27 are both —

    N═

    , or two adjacent R27 are taken together to form a ring having the structure, embedded image

    where Ra is independently —

    CH═

    , —

    N═

    , —

    C(C1-C8 alkyl)═

    or —

    C(halogen)═

    , but no adjacent Ra are both —

    N═

    ;

    R34 is —

    O—

    , —

    S—

    or —

    N(CH3)—

    ;

    R40 independently is hydrogen, C1-C12 alkyl, C1-C12 substituted alkyl, a protecting group or both R40 together with the nitrogen atom to which they are attached form;

    embedded imageand X1 is 1, 2 or 3.

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