Fluorescent chemical compounds having high selectivity for double stranded DNA, and methods for their use
Chemical compounds having a high selectivity for double stranded DNA over RNA and single stranded DNA are disclosed. The chemical compounds are stains that become fluorescent upon illumination and interaction with double stranded DNA, but exhibit reduced or no fluorescence in the absence of double stranded DNA. The compounds can be used in a variety of biological applications to qualitatively or quantitatively assay DNA, even in the presence of RNA.
1. A chemical compound having the structure:
wherein:
n is 0;
X is oxygen;
R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 10 , and R 11 independently comprise hydrogen, a hydroxyl group, an alkoxy group, a thiol, a thioalkyl, a thioaryl, a halogen, an alkyl group, an alkenyl group, an alkynyl group, an aromatic group, a primary amine group, a secondary amine group, a tertiary amine group, a reactive group, or combinations thereof, wherein at least one of R 1 , R 2 , R 3 , and R 4 comprises an aromatic group or an alkynyl group;
R 9 comprises an aromatic group or alkyl-aromatic group; and
R 12 is an alkyl group.
2. The chemical compound of claim 1 , wherein:
R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 10 , and R 11 are independently hydrogen, a hydroxyl group, an alkoxy group, a thiol, a thioalkyl, a thioaryl, a halogen, an alkyl group, an alkenyl group, an alkynyl group, an aromatic group, a primary amine group, a secondary amine group, a tertiary amine group, a reactive group, or combinations thereof, wherein at least one of R 1 , R 2 , R 3 , and R 4 comprises an aromatic group or an alkynyl group.
3. The chemical compound of claim 1 , wherein R 10 is an amine group.
4. The chemical compound of claim 1 , wherein:
at least one of R 1 , R 2 , R 3 , and R 4 comprises an aromatic group or an alkynyl group;
R 9 comprises an aromatic group or alkyl-aromatic group; and
R 10 comprises an amine group.
5. The chemical compound of claim 1 , wherein R 12 is a C 1 -C 8 alkyl group.
6. The chemical compound of claim 1 , wherein R 12 is a methyl group.
7. The chemical compound of claim 1 , further comprising one or more cations or anions.
8. A kit comprising:
DNA, RNA, or both DNA and RNA; and
a chemical compound having the structure:
wherein:
n is 0;
X is oxygen;
R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 10 , and R 11 independently comprise hydrogen, a hydroxyl group, an alkoxy group, a thiol, a thioalkyl, a thioaryl, a halogen, an alkyl group, an alkenyl group, an alkynyl group, an aromatic group, a primary amine group, a secondary amine group, a tertiary amine group, a reactive group, or combinations thereof, wherein at least one of R 1 , R 2 , R 3 , and R 4 comprises an aromatic group or an alkynyl group;
R 9 comprises an aromatic group or alkyl-aromatic group; and
R 12 is an alkyl group.
9. The compound of claim 1 , wherein the compound is: