Chemical Structures of bisPNA Fluorescent Tags
|
Tag name |
Chemical Structure |
|---|---|
| H-1TMR | TMR-OO-Lys-Lys-TCC TTC TC-OOO-JTJ TTJ JT-Lys-OO-Lys-O |
| H-2TMR | TMR-OO-Lys-Lys-TCC TTC TC-OOO-JTJ TTJ JT-Lys-OO-Lys(TMR)-O |
| bis7 | TMR-OO-Lys-Lys-TCC TTC T-OOO-TJT TJJ T-Lys-Lys |
| S-1TMR | TMR-OO-Lys-Lys-TTT CTC TT-OOO-TTJ TJT TT-Lys-Lys |
| S-2TMR | TMR-OO-Lys-Lys-TTT CTC TT-OOO-TTJ TJT TT-Lys-OO-Lys(TMR)-O |
| S-1Alx | Alexa-OO-Lys-Lys-TTT CTC TT-OOO-TTJ TJT TT-Lys-Lys |
| S-2Alx
|
Alexa-OO-Lys-Lys-TTT CTC TT-OOO-TTJ TJT TT-Lys-Lys-OO-Lys(Alexa)-O
|
-
The tags include tetramethylrhodamine (TMR) or Alexa 546 fluorophores, which are conjugated to amino-terminal or lysine side-chain amino groups. Fluorophores, Watson-Crick (T+C) strand, and Hoogsteen (T+J) strand are connected with -O- linkers (8-amino-3,6-dioxa-octanoic acid), which form flexible hydrophilic tethers. (T) Thymine; (C) cytosine; (J) pseudoisocytosine. The replacement of C with J in the Hoogsteen strand promotes hybridization of this bisPNA at pH > 6.5 (Kuhn et al. 1999). The lysines introduce positive charges to improve hybridization efficiency (Demidov and Frank-Kamenetskii 2001). The sequences are presented from amino terminus (left) to carboxyl terminus (right). Amino- and carboxy-termini of Watson-Crick strand of PNA (bold) hybridize to 3′- and 5′-termini of DNA target, respectively, whereas amino- and carboxy-termini of Hoogsteen strand of PNA hybridize to 5- and 3′-termini of DNA target, respectively (Nielsen and Egholm 1999).
