Methods for enhancing nucleic acid hybridization

1. A composition, comprising:

a first oligonucleotide having the structure 5′-Y 1 -L 1 -X-L 2 -Y 2 -3′, wherein:

Y 1 comprises a sequence of DNA or RNA nucleotides, including a first nucleotide N 1 having a 3′ phosphate covalently linked to L 1 ;

Y 2 comprises a sequence of DNA or RNA nucleotides, including a second nucleotide N 2 having a 5′ phosphate covalently linked to L 2 ;

L 1 and L 2 each independently are a direct bond or a C 1 -C 7 alkyl, alkynyl, alkenyl, heteroalkyl, substituted alkyl, aryl, heteroaryl, substituted aryl, cycloalkyl, alkylaryl, or alkoxyl group;

X is

R 1 is a hydrogen or a C 1 -C 8 alkyl; and

M is

L 3 is a direct bond or a C 1 -C 8 alkyl, alkenyl, heteroalkyl, substituted alkyl cycloalkyl, or alkoxyl;

R 2 -R 6 each independently are a hydrogen, an alkyl, an alkenyl, a heteroalkyl, a substituted alkyl, an aryl, a heteroaryl, a substituted aryl, a cycloalkyl, an alkylaryl, an alkoxyl, an electron withdrawing group, or an electron donating group, and one of

R 2 -R 6 is

wherein P is

and

R 7 -R 9 each independently are a hydrogen, an alkoxyl, an alkyl, an alkylamino, an arylamino, a cycloalkyl, a heteroalkoxyl, a heteroalkyl, or an amino; and

R 10 -R 13 each independently are a hydrogen, a nitro, a cyano, a carboxylate, a sulfonyl, a sulfamoyl, an alkenyl, an alkynyl, an amino, an aryl, a heteroaryl, a biaryl, a bialkenyl, a bialkynyl, an alkoxycarbonyl or a carbamoyl, or

wherein P is

and

R 14 -R 19 each independently are a hydrogen, an alkyl, a heteroalkyl, an aryl, a heteroaryl, an electron withdrawing group, or a five or six membered ring structure formed from the R 1 , R 2 pair, the R 3 , R 4 pair, the R 4 , R 5 , Pair or the R 5 , R 6 pair;

wherein the first oligonucleotide is hybridized to a second oligonucleotide having the structure 3′-Y 3 -Y 4 -5′, wherein:

Y 3 comprises a sequence of DNA or RNA nucleotides, including a third nucleotide N 3 ; and

Y 4 comprises a sequence of DNA or RNA nucleotides, including a fourth nucleotide N 4 that is directly attached to nucleotide N 3 ;

wherein N 1 base pairs with N 3 and N 2 base pairs with N 4 such that the duplex has a T m that is greater than the T m of a duplex formed between the second oligonucleotide and a third oligonucleotide having the structure 5′-Y 1 -Y 2 -3′.

2. The composition of claim 1 , wherein L 1 and L 2 each is a C 1 -C 7 alkyl.

3. The composition of claim 2 , wherein L 1 and L 2 are C 2 alkyls.

4. The composition of claim 1 , wherein the 3′ phosphate that is covalently linked to L 1 , and the 5′ phosphate that is covalently linked to L 2 , each independently are a phosphodiester, a phosphothioate, a phosphodithioate, a methyl phosphonate, a phosphoramidate, a phosphoramidite or a phosphotriester.

5. The composition of claim 1 , wherein:

R 9 is

6. The composition of claim 1 , wherein the first oligonucleotide is labeled with a fluorophore.

7. The composition of claim 6 , wherein the fluorophore is 6-carboxyfluorescein (FAM), 2′7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE), tetrachlorofluorescein (TET), 6-carboxyrhodamine (R6G), N,N,N;N′-tetramethyl-6-carboxyrhodamine (TAMRA), 6-carboxy-X-rhodamine (ROX); 1-dimethylaminonaphthyl-5-sulfonate, 1-anilino-8-naphthalene sulfonate, 2-p-toluidinyl-6-naphthalene sulfonate, 5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS), a coumarin dye, an acridine dye, indodicarbocyanine 3 (Cy3), indodicarbocyanine 5 (Cy5), indodicarbocyanine 5.5 (Cy5.5), 3-1-carboxy-pentyl)-3′-ethyl-5,5′-dimethyloxacarbocyanine (CyA); 1H,5H, 11H,15H-Xantheno[2,3,4-ij:5,6,7-i′j′]diquinolizin-18-ium, 9-[2(or 4)-[[[6-[2,5-dioxo-1-pyrrolidinyl)oxy]-6-oxohexyl]amino]sulfonyl]-4(or 2)-sulfophenyl]-2,3,6,7,12,13,16,17-octahydro-inner salt (TR or Texas Red), a BODIPY™ dye, benzoxaazole, stilbene or pyrene.

8. The composition of claim 6 , wherein the fluorophore is attached to the 5′ phosphate at the end of the oligonucleotide.

9. The composition of claim 6 , wherein the first oligonucleotide is labeled with a second quencher.