Compounds for fluorescence sensing of duplex formation

A compound of Formula I:

• wherein
• R is NR2R3 and R is at the ortho, meta, meta′, or para position relative to the NH moiety of Formula I;
• X is O, C═O, NR4, S, S═O, or S(═O)2;
• Gx is Formula X1 or X2:
• Y is H, OH, halo, or Me;
• Z is OH, O(dimethoxytrityl), guanidinium, phosphate, diphosphate, triphosphate, phosphoramidite, phosphorothioate, or —O2P(═O)(3′-X1A) wherein Formula X1A is,
• RZ is H, —P(N(R4)2)(OCH2CH2CN), or —O2P(═O)(5′-X1A);
• R1, R2, and R3 are each independently CH3, CH2CH3, or (C3-C12)alkyl wherein alkyl is optionally branched;
• R4 is H, CH3, or CH2CH3, CH(CH3)2;
• each Q is independently H, CH3, CH2CH3, (C3-C12)alkyl wherein alkyl is optionally branched, or —(CH2CH2O)n(C1-C4)alkyl where n is 1-20, and when Q is not H the carbon of the CH-Q bond is a stereocenter having an (R)-configuration, or an (S)-configuration;
• RA is H, CH3, CH2CH3, (C3-C12)alkyl wherein alkyl is optionally branched, or an amide bond to X2A wherein Formula X2A is:
• RB is H, CH3, CH2CH3, (C3-C12)alkyl wherein alkyl is optionally branched, or a protecting group;
• RC is OH, OCH3, OCH2CH3, O(C3-C12)alkyl wherein alkyl is optionally branched, or an amide bond to X2A;
• each J is independently O or S, and when J is S the phosphorous stereocenter has an (R)-configuration, or an (S)-configuration;
• each W is independently adenine (A), thymine (T), cytosine (C), guanine (G), or Formula IA, wherein Formula IA is,
• wherein R of Formula IA is OR1 or NR2R3;
• and
• d is 1 to about 50.