Fluorescence energy transfer probes with stabilized conformations

1 . A compound having a structure selected from:

X—R-A-Q-(Y) n , R—X-A-(Y) n -Q, R—X-A-Q-(Y) n , and

X—R-A-(Y) n -Q

wherein,

A is a nucleic acid chain comprising nucleic acid monomers selected from the group consisting of natural nucleic acids, modified nucleic acids and combinations thereof;

R is a molecular energy transfer donor;

Q is a molecular energy acceptor; and

X and Y are the same or different and are non-nucleic acid stabilizing moieties that interact to bring R and Q into operative proximity, thereby enabling transfer of energy from R to Q; and

n is 0 or 1.

2 . The compound according to claim 1 , wherein said molecular energy donor is a fluorophore.

3 . The compound according to claim 1 , wherein said molecular energy acceptor is a fluorescence quencher.

4 . The compound according to claim 1 , wherein X and Y are both hydrophobic moieties.

5 . The compound according to claim 4 , wherein X and Y are members independently selected from the group consisting of saturated hydrocarbons, unsaturated hydrocarbons, steroids, fatty acids, fatty alcohols and hydrophobic peptides.

6 . The compound according to claim 1 , wherein natural nucleic acids are members selected from the group consisting of deoxyribonucleotides, ribonucleotides and combinations thereof.

7 . The compound according to claim 6 , wherein said modified nucleic acids are peptide nucleic acids.

8 . The compound according to claim 1 , wherein said nucleic acid monomers are joined by linkages that are members independently selected from the group consisting phosphodiesters and modified phosphodiesters.

9 . The compound according to claim 8 , wherein said modified phosphodiesters are members selected from the group consisting of phosphorothioates and phosphoramidates.

10 . The compound according to claim 1 , wherein said nucleic acid sequence further comprises a hybridization enhancing moiety.

11 . The compound according to claim 10 , wherein said hybridization enhancing moiety is a member selected from the group consisting of intercalating agents, minor groove binders and modified exocyclic bases.

12 . The compound according to claim 1 wherein X and Y are independently attached to members selected from the group consisting of a natural base of said nucleic acid chain, a modified base of said nucleic acid chain, a 3′-hydroxyl group of said nucleic acid chain, a 5′-hydroxyl group of said nucleic acid chain, a 2′-hydroxyl group of said nucleic acid chain, and a linkage joining nucleic acid groups in said nucleic acid chain.

13 . The compound according to claim 1 , wherein said compound is immobilized on a solid surface.

14 . A method for amplifying a polynucleotide, wherein a compound according to claim 1 is a primer in said method.

15 . The method according to claim 14 , wherein said method comprises a member selected from the group consisting of polymerase chain reaction (PCR), nucleic acid sequence based amplification (NASBA), strand displacement amplification (SDA) and combinations thereof.

16 . A method for analyzing or quantitating DNA, wherein the compound according to claim 1 is used as a probe.

17 . The method according to claim 16 , wherein said method comprises a member selected from the group consisting of 5′-nuclease assay, rolling circle amplification and combinations thereof.

18 . A kit for quantitating nucleic acid, said kit comprising a compound according to claim 1 .

19 . A compound having the formula:

wherein,

CHOL is a cholesterol derivative;

R 1 , R 2 , R 3 and R 4 are linker moieties independently selected from the group consisting of substituted or unsubstituted alkyl and substituted or unsubstituted heteroalky;

Nu 1 and Nu 2 are independently selected nucleotide residues;

NA is a nucleic acid sequence;

D is a donor of light energy; and

Q is a quencher of light energy.

20 . The compound according to claim 19 , wherein R 1 and R 2 are independently selected and have structures according to the formula:

wherein,

R 11 is a member selected from the group consisting of substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl;

PEG is polyethylene glycol;

Y 3 is an organic functional group adjoining said PEG to said CHOL.

21 . The compound according to claim 20 , wherein said PEG has from about 2 to about 20 ethylene glycol subunits.

22 . The compound according to claim 20 in which R 11 is substituted or unsubstituted alkyl.

23 . The compound according to claim 22 , wherein R 11 is C 1 -C 6 substituted or unsubstituted alkyl.

24 . The compound according to claim 20 , wherein Y 3 —CHOL has the structure:

25 . The compound according to claim 19 , wherein Nu 1 and Nu 2 are nucleotides having an exocyclic amine group to which —R 1 -D and —R 4 Q are attached, respectively.

26 . A compound having the structure:

wherein,

X and Y are non nucleotide stabilizing moieties

NA is a nucleic acid sequence;

Nu 1 and Nu 2 are independently selected nucleotide residues;

Y 1 and Y 2 are linking groups independently selected from the group consisting of substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl;

R 5 and R 6 are linking groups independently selected from the group consisting of substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl;

D is a donor of light energy; and

Q is a quencher of light energy.

27 . The compound according to claim 26 , wherein Y 1 and Y 2 are members independently selected from substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl.

28 . The compound according to claim 27 , wherein Y 1 and Y 2 are polyethylene glycol.

29 . The compound according to claim 28 , wherein said PEG has from about 2 to about 20 ethylene glycol subunits.

30 . The compound according to claim 26 , wherein Y 1 —X and Y 2 —Y have the structure:

31 . The compound according to claim 19 , wherein Nu 1 and Nu 2 are nucleotides having an exocyclic amine group to which —R 5 -D and —R 6 Q are attached, respectively.