Silicon and germanium dyes for use in genetic identity

1. A method of detecting the presence of a nucleic acid polymer in a sample comprising:

a) contacting a sample suspected of containing a nucleic acid polymer with a composition comprising a conjugate comprising a compound of Formula (I) and an oligonucleotide; and

b) detecting the presence or amount of the compound in the sample;

wherein the compound of formula (I) is a component in an ET cassette; and

wherein the compound of formula (I) is as shown below:

wherein

Z is Si(R 11 )(R 12 ) or Ge(R 11 )(R 12 );

each R 11 and R 12 are independently selected from C 1-10 linear, branched or cyclic alkyl, C 1-10 alkyl interrupted with one or more heteroatoms, C 6-10 aryl, heteroaryl or R 11 and R 12 may together form a ring;

each X is independently selected from OR 2 or N(R 3 )(R 4 );

each R 1 is independently selected from H, C 1-4 alkyl, sulfonate or halo;

R 2 is H, C 1-10 alkyl, L-R or L-C S ;

R 3 and R 4 are independently selected from H, C 1-4 alkyl, C 1-4 alkyl interrupted with one or more heteroatoms, C 6-10 aryl, peptidyl, heteroaryl, L-R or L-C S ;

R 6-10 are independently H, halo, alkoxy, amino, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;

L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;

R is a reactive group; or

C S is a conjugated substance;

one or more of R 3 and R 4 or R 3 and R 1 or R 4 and R 1 may together form a ring;

and

one or more of R 6-10 may together form a ring.

2. The method of claim 1 , wherein more than one nucleic acid polymer is detected in a single reaction.

3. A method of detecting the presence of a nucleic acid polymer in a sample comprising:

a) contacting a sample suspected of containing a nucleic acid polymer with a composition comprising a conjugate comprising a compound of Formula (II) and an oligonucleotide; and

b) detecting the presence or amount of the compound in the sample;

wherein the compound of formula (II) is a component in an ET cassette; and

wherein the compound of formula (II) is as shown below:

wherein

each R 1 is independently selected from H, C 1-4 alkyl, sulfonate or halo;

R 3 and R 4 are independently selected from H, C 1-4 alkyl, C 1-4 alkyl interrupted with one or more heteroatoms, L-R or L-C S ;

R 6-9 are independently H, halo, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;

R 10 is alkoxy, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, SO 2 N(R N ) 2 , CON(R N ) 2 , L-CO 2 H, L-SO 3 H, L-R or L-C S ;

each R N is independently selected from H, alkyl, aryl, heteroaryl, L-R, and L-C S

L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;

R is a reactive group; or

C S is a conjugated substance;

one or more of R 3 and R 4 or R 3 and R 1 or R 4 and R 1 may together form a ring;

and

one or more of R 6-9 may together form a ring.

4. The method of claim 3 , wherein more than one nucleic acid polymer is detected in a single reaction.

5. A compound selected from the group consisting of:

6. A kit comprising a compound according to formula (I) or (II) in an ET cassette, at least one locus-specific primer, and instructions for use; wherein the compound of formula (I) is

wherein

Z is Si(R 11 )(R 12 ) or Ge(R 11 )(R 12 );

each R 11 and R 12 are independently selected from C 1-10 linear, branched or cyclic alkyl, C 1-10 alkyl interrupted with one or more heteroatoms, C 6-10 aryl, heteroaryl or R 11 and R 12 may together form a ring;

each X is independently selected from OR 2 or N(R 3 )(R 4 );

each R 1 is independently selected from H, C 1-4 alkyl, sulfonate or halo;

R 2 is H, C 1-10 alkyl, L-R or L-C S ;

R 3 and R 4 are independently selected from H, C 1-4 alkyl, C 1-4 alkyl interrupted with one or more heteroatoms, C 6-10 aryl, peptidyl, heteroaryl, L-R or L-C S ;

R 6-10 are independently H, halo, alkoxy, amino, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;

L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;

R is a reactive group; or

C S is a conjugated substance;

one or more of R 3 and R 4 or R 3 and R 1 or R 4 and R 1 may together form a ring;

and

one or more of R 6-10 may together form a ring;

and wherein the compound of formula (II) is

wherein

each R 1 is independently selected from H, C 1-4 alkyl, sulfonate or halo;

R 3 and R 4 are independently selected from H, C 1-4 alkyl, C 1-4 alkyl interrupted with one or more heteroatoms, L-R or L-C S ;

R 6-9 are independently H, halo, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;

R 10 is alkoxy, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, SO 2 N(R N ) 2 , CON(R N ) 2 , L-CO 2 H, L-SO 3 H, L-R or L-C S ;

each R N is independently selected from H, alkyl, aryl, heteroaryl, L-R, and L-C S

L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;

R is a reactive group; or

C S is a conjugated substance;

one or more of R 3 and R 4 or R 3 and R 1 or R 4 and R 1 may together form a ring;

and

one or more of R 6-9 may together form a ring.