Table 1.
Raman and ROA bands for the Hairpin, Mismatch, Bulge and EMCV RNAs
| Raman band (cm−1)a | Assignment | Intensity relative to Hairpin (%)b | |||
|---|---|---|---|---|---|
| Mismatch | Bulge | EMCV | |||
| Bands arising from ribose/phosphate/backbone | |||||
| c | 601 wk | Ribose (32) | +6 | +30 | +55 |
| h | 813 str | O–P–O symmetric stretching, marker for A-form helix (2,9–11,28,32,34,36) | −9 | +36 | +18 |
| i | 856 wk | Ribose–phosphate (32) | −19 | −68 | −56 |
| k | 919 wk | Ribose–phosphate, –C–O– stretching (32,34) | −15 | −5 | 0 |
| l | 977 wk | Ribose–phosphate, –C–O– stretching (32,34) | 0 | +21 | +24 |
| o | 1047 str | P–O stretch, sugar phosphate –C–O– stretching (30,34) | −18 | +38 | −10 |
| p | 1098 med |
 symmetric stretching (2,9–11,28,32,34,36) |
−2 | +18 | +21 |
| q | 1136 wk | Stretching at 2’ position of ribose (32) | +5 | +71 | +22 |
| Bands arising from bases | |||||
| a | 489 wk | G out of plane ring deformations (34) | −15 | +35 | +13 |
| b | 580 wk | A/U/G/C out of plane ring deformations (34) | +16 | +34 | +13 |
| d | 631 wk | A/U/G/C (10,28,34) | +5 | +49 | +46 |
| e | 670 wk | G out of plane ring deformations (9–11,32,34) | +4 | −13 | −1 |
| f | 726 wk | A ring stretching (9,11,27,32,34) | −21 | +23 | +4 |
| g | 787 str | C/U breathing/stretching (27,28,32–34,36) | +3 | +47 | +45 |
| j | 876 wk | A/U/G/C out of plane ring deformations, backbone (10,28,34) | −16 | −50 | −56 |
| r | 1182 wk | A/U/G/C ring; external C–N stretching (9,10,28,34) | +9 | −24 | +32 |
| s | 1253 med | U/C ring stretching (2,9,11,27,32–34) | +9 | +62 | +44 |
| t | 1300 sh | C/A ring stretching (10,11,32–34) | −10 | −20 | +12 |
| u | 1316 med | A/G ring stretching (2,9–11,28,32,34) | −7 | +12 | +13 |
| v | 1336 med/sh | A/G/U (2,9–11,28,32,34) | −22 | +22 | +12 |
| w | 1380 wk | A/G/U (10,11,28,32,34,36) | −11 | −39 | −22 |
| x | 1425 wk | A/G ring stretching, CH deformations (28,32,34) | −14 | +66 | +17 |
| y | 1460 med | U/C ring stretching, CH deformations (28,32,34) | −17 | +8 | −19 |
| z | 1485 str | A/G ring stretching/planar vibrations (9,10,28,32,34) | −3 | −20 | +3 |
| aa | 1532 wk | A/G/C ring stretching (10,27,28,32,34) | +78 | −100 | +110 |
| ab | 1578 str | A/G ring stretching (9,10,27,28,32,34) | −6 | −10 | +1 |
| Bands with no previous assignment | |||||
| m | 1002 wk | +3 | +16 | +26 | |
| n | 1025 med/sh | −16 | +63 | 0 | |
| ROA band (cm−1) | Assignment | Intensity relative to Hairpin (%) | |||
|---|---|---|---|---|---|
| Mismatch | Bulge | EMCV | |||
| ac | 994-1093 | Triplet; A-form RNA (13) | +26 | −16 | +46 |
| ad | 1650-1750 | Couplet; right-handed helix (13) | +14 | −19 | +2 |
aLetters identifying each peak correspond to those given in Figure 3. Band positions given are those observed in the spectrum of the Hairpin RNA, and may differ slightly for the other three oligonucleotides. Intensity key: wk: weak, med: medium, str: strong, sh: shoulder.
bThe intensities for each of the other three oligonucleotides are given as percentages of the Hairpin RNA intensity for each band.