Building blocks · nucleic acids
Nucleic-acid IR data
IR of DNA and RNA splits into two informative windows: the base region (1750–1550 cm⁻¹), where carbonyl and ring modes report base identity, pairing and stacking, and the backbone region (1250–800 cm⁻¹), where the phosphate and sugar bands report helix conformation. Positions below are solution values from the Banyay–Sarkar–Gräslund library.
Nucleobase marker bands (1750–1500 cm⁻¹)
| Base | Marker bands (cm⁻¹) | Note | Measured ↗ |
|---|
Sugar–phosphate backbone (1250–800 cm⁻¹)
| Mode | Band (cm⁻¹) | Note |
|---|
Individual nucleotides
Base + sugar + phosphate-monoester bands for the eight ribo- and deoxyribonucleotide 5′-monophosphates. Ribonucleotides add the ribose 2′-OH band (~1120) absent in DNA. Reconstructed from literature positions; the Measured ↗ links reach real solid-state / aqueous FTIR.
| Nucleotide | Bands (cm⁻¹) | Type | Measured ↗ |
|---|
Measured nucleic-acid IR
Amino acids and nucleotides are involatile, so they are absent from the gas-phase NIST experimental database — the entries here are reconstructions. Real measured FTIR for these exists in SDBS and SpectraBase (linked per row above) and in the dedicated NAIRDB nucleic-acid FTIR database.
Conformation markers — the phosphate diagnostic
The asymmetric phosphate stretch νas(PO₂⁻) and the sugar-phosphate bands move with helix geometry — the single most-used IR readout of nucleic-acid conformation.
| Form | ν_as(PO₂⁻) | Sugar-phosphate markers | Geometry |
|---|---|---|---|
| B-DNA | ~1225 | 835 | Right-handed, C2′-endo, hydrated. |
| A-form (A-DNA / dsRNA) | ~1240 | 860, 807 | Right-handed, C3′-endo, dehydrated / RNA. |
| Z-DNA | ~1215 | 925, 865 | Left-handed, alt. syn/anti, high salt. |
| RNA (ss/ds) | ~1240 | 813; +1120 (2′-OH) | A-form; ribose 2′-OH band absent in DNA. |
What the bands tell you
A ~1225 → ~1240 shift of νas(PO₂⁻) signals a B→A transition (dehydration, or RNA character); a ~1215 band with a 925 marker flags Z-DNA. In the base region, the guanine C6=O (~1689→~1710 on pairing) and thymine twin carbonyls (1694/1663) track base pairing and stacking; their hypochromism on duplex formation is a melting/hybridisation probe. The ribose 2′-OH (~1120) band distinguishes RNA from DNA.
Simulate & compare
Defaults overlay B-DNA and A-form to show the phosphate marker shift. Add Z-DNA and RNA, or isolate individual bases.
References
- Banyay, M., Sarkar, M. & Gräslund, A. A library of IR bands of nucleic acids in solution, Biophys. Chem. 104 (2003) 477.
- Tsuboi, M. Application of infrared spectroscopy to structure studies of nucleic acids, Appl. Spectrosc. Rev. 3 (1969) 45.
- Taillandier, E. & Liquier, J. Infrared spectroscopy of DNA, Methods Enzymol. 211 (1992) 307.