Cyanine Dyes

A method of synthesizing a first polynucleotide having a first nucleic acid sequence, the method comprising:

• under conditions of a template dependent polymerization reaction, contacting a nucleic acid polymerase complexed with second polynucleotide having a second nucleic acid
• sequence complementary to the first nucleic acid sequence with a cyanine compound of the formula:
• wherein
• Rf, Rg, Rh, and R′i are members independently selected from halogen, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heteroalkyl;
• Rc, and Rd are independently selected from alkyl and heteroalkyl, substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, and phosphoric acid;
• a and e are independently selected from selected from the integers 0, 1, 2, 3 and 4, with the proviso that at least one member selected from a and e is 2 or greater, such that when a is 2 or greater, each Ra is independently selected, and when e is 2 or greater, each Re is independently selected;
• wherein when a is 2 or greater, ring A is selected from phenyl substituted at least at the 4- and 6-positions with (Ra)a, and substituted or unsubstituted napthyl;
• and when e is 2, or more ring E is selected from phenyl substituted at least at the 4- and 6-positions with (Re)e, and substituted or unsubstituted naphthyl;
• Q is a member selected from
• wherein
• n is selected from the integers from 1 to 3;
• Ra and Re, are independently selected from C(O)R9, OR12, NR12R13, CR12C(O)R13, NR12C(O)2R13, SO3H, and C(O)NR12R13, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a ring structure formed by joining a member selected from two Ra moieties together with the atoms they are attached, two Re moieties together with the atoms they are attached, and a combination thereof, to form said ring structure, which is a member selected from a substituted or unsubstituted aryl and a substituted or unsubstituted heteroaryl
• wherein
• R9 is a member selected from OR10, and NH(CH2)tOR11
• wherein
• R10 is a member selected from H and substituted or unsubstituted alkyl;
• t is selected from the integers from 1 to 12;
• R11 is a nucleic acid moiety, which is a substrate for the polymerase;
• and
• R12 and R13 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl,
• thereby synthesizing the first polynucleotide.

A method of synthesizing a first polynucleotide having a first nucleic acid sequence, the method comprising:

• under conditions of a template dependent polymerization reaction, contacting a nucleic acid polymerase complexed with a second polynucleotide having a second nucleic acid sequence complementary to the first nucleic acid sequence with a cyanine compound selected from the formulae:
• wherein
• n is an integer selected from 1, 2 and 3;
• e is an integer selected from 0, 1 and 2;
• Rf, Rg, Rh, and Ri are members independently selected from halogen, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heteroalkyl, or a bond to M;
• Rc, and Rd are independently selected from a bond to M, and alkyl substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, phosphoric acid and heteroalkyl, substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, phosphoric acid;
• Ra and Re, are independently selected from C(O)R9, OR12, NR12R13, CR12C(O)R13, NR12C(O)2R13, SO3H, and C(O)NR12R13, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a bond to M,
• wherein
• R9 is a member selected from OR10, and a bond to M
• wherein
• R10 is a member selected from H and substituted or unsubstituted alkyl;
• and
• R12 and R13 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a bond to M,
• wherein
• M comprises a linker bound to a nucleic acid carrier, which is a substrate for the polymerase,
• and at least one of Ra, Rc, Rd, Rf, Rg, Rh, Ri, R9, R12 and R13 is a bond to M, thereby synthesizing the first polynucleotide.

A method of synthesizing a first polynucleotide having a first nucleic acid sequence, the method comprising:

• under conditions of a template dependent polymerization reaction, contacting a nucleic acid polymerase complexed with a second polynucleotide having a second nucleic acid sequence complementary to the first nucleic acid sequence with a cyanine compound selected from the formulae:
• wherein
• n is an integer selected from 1, 2, and 3;
• a, e, and j are independently selected from the integers 1, 2, 3, and 4, such that when a is 2 or greater, each Ra is independently selected, when e is 2 or greater, each Re is independently selected, and when j is 2 or greater, each Rj is independently selected;
• b and e′ are independently selected from the integers 0, 1, and 2, such that when b is 2, each Rb is independently selected, and when e′ is 2, each Re′ is independently selected;
• Ra, Rb, Re, Re′, and Rj, are independently selected from C(O)R9, OR12, NR12R13, CR12C(O)R13, NR12C(O)2R13, SO3H, and C(O)NR12R13, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a bond to M;
• Rf, Rg, Rh, and Ri are members independently selected from halogen, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heteroalkyl, and a bond to M;
• Rc, and Rd are independently selected from a bond to M, and alkyl substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, and phosphoric acid, and heteroalkyl substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, and phosphoric acid;
• wherein
• R9 is a member selected from OR10, and a bond to M;
• R10 is a member selected from H and substituted or unsubstituted alkyl;
• and
• R12 and R13 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a bond to M,
• wherein
• M comprises a linker bound to a nucleic acid carrier, which is a substrate for the polymerase,
• and at least one of Ra, Rb, Rc, Rd, Re, Re′, Rf, Rg, Rh, Ri, Rj, R9, R12 and R13 is a bond to M,
• thereby synthesizing the first polynucleotide.

A method of synthesizing a first polynucleotide having a first nucleic acid sequence, the method comprising:

• under conditions of a template dependent polymerization reaction, contacting a nucleic acid polymerase complexed with a second polynucleotide having a second nucleic acid sequence complementary to the first nucleic acid sequence with a cyanine
• compound selected from the formula:
• wherein
• n is selected from the integers 1 and 2;
• Ra is selected from H, a moiety according to Formula II:
• and a moiety joined with Rb, together with the atoms to which Ra and Rb are attached, forming substituted phenyl ring C:
• wherein
• each y is an independently selected integer from 0 to 10;
• Ru and Rv are independently selected from —SO3H, a moiety according to Formula II, and
• wherein
• R8 is selected from H and substituted or unsubstituted alkyl;
• x is an integer from 1 to 10
• Rb is selected from H,
• and a moiety joined with Ra forming, together with the atoms to which Ra and Rb are attached, substituted phenyl ring C;
• z is an integer from 0 to 10;
• R8 is selected from H and substituted or unsubstituted alkyl;
• Rc is selected from H,
• q is an integer from 0 to 10;
• wherein Ra, Rb and Ro are not all H;
• Rd is selected from H and OCH3;
• Re and Re′ are independently selected from
• wherein t is an integer from 1 to 10;
• Ra′ is selected from H, C(O)-M, a moiety according to Formula II, and a moiety joined with Rb′ forming, together with the atoms to which Ra′ and Rb′ are attached, substituted phenyl ring C′;
• M is selected from OH, a carboxylic acid activating moiety, a polyvalent scaffold and a carrier molecule;
• Ru′ and Rv′ are independently selected from H, a moiety according to Formula II, —SO3H, and
• wherein
• each x is an integer independently selected from 0 to 10;
• R10 is selected from H and substituted or unsubstituted alkyl;
• Rw′ is selected from H and a moiety according to Formula II;
• Rb′ is selected from H, C(O)-M, a moiety according to Formula II, a moiety joined with Ra′, together with the atoms to which Ra and Rb′ are attached, forming substituted phenyl ring C′, and
• wherein
• p is an integer from 0 to 10;
• Rc′ is selected from H, C(O)-M and —SO3H,
• wherein Ra′, Rb′ and Rc′ are not all H;
• Rd′ is selected from H and OCH3;
• and
• Rf, Rg, Rf′ and Rg′ are independently selected from CH3,
• wherein each t is an independently selected integer from 1 to 10;
• and
• at least one of Ra′, Rb′ and Rc′, Re, Re′, Rf, Rg, Rf′ and Rg′ comprises M