Table 1.
Descriptions and sequences of nucleic acid hybrids used in SPR
| Hairpin Length (bp) | Content | %GCa | Hybrid nameb | Oligonucleotide Sequencec,d |
|---|---|---|---|---|
| 0 | Equal Mix | 50 | 30ssD | CGGTGTGGTCGCTGTAATCAGAAAACGTGT |
| 23 | AT-rich | 17.4 | 23ATDD | AATTACATTGATAGAATTATTAGTTTTCTAATAATTCTATCAATGTAATT |
| 23 | GC-rich | 82.6 | 23GCDD | GGCGGTCCCAGCGAGGCCGCCGATTTTTCGGCGGCCTCGCTGGGACCGCC |
| 23 | AU-rich | 17.4 | 23AURR | rArArUrUrArCrArUrUrGrArUrArGrArArUrUrArUrUrArGrUrUrUrUrCrUrArArUrArArUrUrCrUrArUrCrArArUrGrUrArArUrU |
| 23 | GC-rich | 82.6 | 23GCRR | rGrGrCrGrGrUrCrCrCrArGrCrGrArGrGrCrCrGrCrCrGrArUrUrUrUrUrCrGrGrCrGrGrCrCrUrCrGrCrUrGrGrGrArCrCrGrCrC |
| 23 | AT-rich | 17.4 | 23ATDR | AATTACATTGATAGAATTATTAGTTTTrCrUrArArUrArArUrUrCrUrArUrCrArArUrGrUrArArUrU |
| 23 | GC-rich | 82.6 | 23GCDR | GGCGGTCCCAGCGAGGCCGCCGATTTTrUrCrGrGrCrGrGrCrCrUrCrGrCrUrGrGrGrArCrCrGrCrC |
| 23 | Equal Mix | 52.2 | 23MDR | CGGTGTGGTCGCTGTAATCAGAATTTTrUrUrCrUrGrArUrUrArCrArGrCrGrArCrCrArCrArCrCrG |
| 15 | Equal Mix | 53.3 | 15MDR | CGGTGTGAATCAGACTTTTrGrUrCrUrGrArUrUrCrArCrArCrCrG |
| 10 | Equal Mix | 60 | 10MDR | CGTGTCAGACTTTTrGrUrCrUrGrArCrArCrG |
| 8 | Equal Mix | 50 | 8MDR | GAGAACTGTTTTrCrArGrUrUrCrUrC |
| 6 | Equal Mix | 50 | 6MDR | GAACTGTTTTrCrArGrUrUrC |
| 4 | Equal Mix | 50 | 4MDR | GACTTTTTrArGrUrC |
a
GC content is calculated for the hybrid portion of the oligonucleotides, which does not include the four thymidine bases encompassing the turn. “Equal mix” denotes 40-60% GC content.
b
For example, “30ssD” is an abbreviation of “30-nucleotide single stranded DNA”.
AT = AT-rich, GC = GC-rich, DD = DNA-DNA hairpin, RR = RNA-RNA hairpin, DR = DNA-RNA hairpin, M=equal mix of AT and GC.
c
Thymidines and uracils (T, rU) in bold and underline do not participate in base pairing.
d
5′(Biotin-TEG) linker is at the 5′ end of all sequences