Table 1.
Oligonucleotides used in this study and their analysis by MALDI-TOF MS. 1 is the unmodified DNA control strand for strand 4; 2 is the control strand for 5 ~ 8; 3 is the hairpin template; 9 is the control for nuclease digestion, UnUc represents two uridine residues linked by both 3′,5′-phosphate diester linkage and 2′,2′-amide linkage; 10 is ligated product from 4 and 5, UnUc represents two uridine residuals linked by only 2′,2′-amide linkage. (For structures UnUc and UnUc of see Fig. 4)
| Mass
|
|||
|---|---|---|---|
| ODNs | Sequence | Calculated | Found |
| 1 | 5′-AACACGGACATAGT-3′ a | -- | -- |
| 2 | 5′-TCCTCGTGTTGTGGAC-3′ a | -- | -- |
| 3 | 5′-GCACGTATGCTGTTTTCAGCATACGTGCG--TCCACAACACGAGGAACTATGTCCGTGTT-3′ a | -- | -- |
| 4 | 5′-AACACGGACATAGUn-3′ | 4371.0 | 4370.9 |
| 5 | 5′-UcCCTCGTGTTGTGGAC-3′ | 4998.4 | 4996.2 |
| 6 | 5′-TCCUcCGTGTTGTGGAC-3′ | 4998.4 | 4995.4 |
| 7 | 5′-TCCTCGUcGTTGTGGAC-3′ | 4998.4 | 4997.4 |
| 8 | 5′-TCCTCGTGTUcGTGGAC-3′ | 4998.4 | 4997.9 |
| 9 | 5′-GCATAGTTUnUcTTGTCTAC-3′ b | 5660.9 | 5661.3 |
| 10 | 5′-AACACGGACATAGUnUcCCTCGTGTTGTGGAC-3′ | 9348.4 | 9347.7 |
a
Strands 1, 2 and 3 were obtained from Integrated DNA Technologies (Coralville, IA) and purified by denaturing gel electrophoresis.
b
For synthesis and thermal denaturing study of strand 9 see reference.13