Table 1.
Sequences and hybridization properties of oligonucleotides and DNA mimics used in this study
| Oligomer sequence (target)a | Complementary oligonucleotidea | ODN Tm, °C (Δα;Δ)b | HypNA-pPNA Tm, °C(Δα;Δ)b | pHypNA Tm, °C (Δα;Δ)b |
|---|---|---|---|---|
| TCACTCAACACTCAC-Flu | d(GTGAGTGTTGAGTGA) | 57 | 58 | 55 |
| TGGCGTCGGTGACCAT (FLuc) | d(ATGGTCACCGACGCCA) | 64 | 65 | 67 |
| TGGCGTCGGTGACCAT (FLuc) | r(AUGGUCACCGACGCCA) | 56 | 73 | 72 |
| TGGaGTCGGcGACCAT (FLuc) | d(ATGGTCACCGACGCCA) | ∼25 (−36) | ∼26 (−39) | ∼28 (−39) |
| TGGaGTCGGcGACCAT (FLuc) | r(AUGGUCACCGACGCCA) | 32 (−24) | 48 (−25) | 45 (−27) |
| GCTCTCGTCGCTCTCCAT (GFP) | d(CATGGAGAGCGACGAGAGCGGC) | 69 | 65 | 63 |
| GCTCTCGTCGCTCTCCAT (GFP) | r(CAUGGAGAGCGACGAGAGC)dTT | 68 | 76 | 75 |
| GCTCTaGTCGCTaTCCAT (GFP) | d(CATGGAGAGCGACGAGAGCGGC) | 34 (−35) | 31 (−34) | ∼26 (−37) |
| GCTCTaGTCGCTaTCCAT (GFP) | r(CAUGGAGAGCGACGAGAGC)dTT | 49 (−19) | 51 (−25) | 49 (−26) |
| r(GCUCUCGUCGCUCUCCAUG)dTT (GFP) | r(CAUGGAGAGCGACGAGAGC)dTT | 86 | - | - |
| TGCGCTTTCTTTTGTCTG (Ras-dva) | r(CAGACAAAAGAAAGCGCA) | 60 | 64 | 67 |
| TGCtCTTTCTTcTGTCTG (Ras-dva) | r(CAGACAAAAGAAAGCGCA) | 35 (−25) | 43 (−21) | 38 (M29) |
aThe sequence is shown from 5′ to 3′end of an oligonucleotide, or from pseudo-5′ to pseudo-3′end of a mimic oligomer. Lowercase base represents a mismatch position.
bThe value in brackets shows the difference between the melting temperature of duplexes formed by the oligomers with matched and mismatched sequences with complementary targets.