Raman spectroscopy base pairing

The combination of Raman spectroscopy and Raman optical activity provides spectral signatures to assess valuable information on RNA structural motifs in the encephalomyocarditis virus (EMCV). Raman and ROA spectra were collected for RNA oligonucleotides to investigate contributions of helix, tetraloop, mismatch base pairs, and asymmetric bulge structures of the RNA... 

While the importance of IR and Raman spectroscopy for the structural elucidation of purine bases has diminished over the last few decades, its advantages for the study of oligo- and polynucleotides in particular with respect to base pairing is apparent. The IR absorption spectrum of a single-stranded polynucleotide is very similar to that of its component nucleotides, but drastic changes occur on formation of hydrogen-bonded helical structures. 

GC base pairs appear to be the preferred site of fixation of platinum(II) compounds on DNA. This conclusion is supported by three types of arguments. First, the rate of fixation of eis-DDP to DNA is correlated with its GC content (53). Hence, if ( is-DDP is mixed with two DNAs of different GC content, it will fix preferentially to the DNA with highest percentage of guanine (54, 55) Second, the quantity of purine bases which have not reacted with platinum can be determined by means of paper chromatography of the depurinated platinum-DNA complex. This experiment shows that d is-DDP reacts with guanine before it binds to adenine (56). Finally, raman spectroscopy of platinum-DNA complexes reveals that fresh aqueous solutions of c is-DDP react preferentially with guanine at r 0.2 and also with adenine at r = 0.4 whereas no reaction with cytosine or thymine was observed (37). 

The purpose of this review has been to illustrate and document the kinds of information about non-aqueous solvent systems which have been obtained by vibrational spectroscopy. We have seen that these include insight into intermolecular forces and structure of the pure solvents, the nature of the solvation shell around ions and their solvation numbers, the identification of ion pairs and complexes, measurement of mass law constants and their dependence on the polarity of the solvent, the detection and characterisation of the hydrogen bond and measurement of acid and base strengths. Little kinetic data have so far been obtained by Raman spectroscopy but recent progress in the study of ultra-fast proton transfer and the detection of associated ions of type [Br , (Bra)] during the bromination of acetic acid presage considerable advance in this area in the future. ... 

Aqueous solutions of complementary purine and pyrimidine base pairs, when examined by Raman spectroscopy (Lord and Thomas, 1967a), revealed no signs of specific base-pair interactions, although interactions between soluble nucleosides and heavy-metal ions have been detected, e.g., cytidine-HgCl2 complex. Aqueous solutions of RNA derivatives have been examined (Lord and Thomas, 19676). This work represents an application of growing importance, where further progress will be... 

The final class of modified base pairing system is metal-mediated base pairs. It has previously been shown that a T-T or a C-C mismatch can be stabilised by Hg(II) or Ag(I) ions respectively. It has been shown that the T-Hg(II)-T base pair can be detected by Raman spectroscopy, having a specific Raman band at 1586 cm. Formation of Hg(II)-mediated base pairs between two thymine residues has been monitored by FRET. Primer extension reactions with DNA polymerases and Ag(I) ions have been performed and a new base pair identified being the Ag(I)-mediated mispair between cytidine and adenosine. " It has also been shown that Ag(I) ions mediate a base pair between two imidazole nucleotide residues, as well as between pyrroloytosine and cytosine. ... 

---