Group frequencies nucleotides

Infrared spectroscopy of nucleic acids has progressed from the ability to identify a few group frequencies to the point where we can begin to consider the vibrational interactions of the entire molecule and its parts. This is made possible by comparison of spectra from a number of series of nucleic acid derivatives and their metal complexes. In addition, the spectra of the constituents, the nucleotides which consist of a base (purine or pyrimidine), a sugar (pentose) and the phos-... 

Lio D, Scola L, Crivello A, Bonafe M, Franceschi C, Olivieri F, Colonna-Romano G, Candore G, Caruso C. Allele frequencies of +874T—A single nucleotide polymorphism at the first intron of interferon-gamma gene in a group of Italian centenarians. Gerontology 2002 44 293-299. 

The 12 possible types of nucleotide substitution can be treated differently (assuming nonsymmetry of change, e.g., the frequency of A to C does not equal that for C to A) or treated equally, or any combination of these substitutions can be grouped. One obvious division of base substitutions is to treat transitions (changes of purine to purine or pyrimidine to pyrimidine) separately from transversions (change of purine to pyrimidine or vice versa). Insertion/deletion events can also be treated as a separate type of mutation. Additionally, nucleotide substitutions can be preferentially treated by a combination of position and mutation (e.g., transversions occurring in the first and second codon positions). 

With this normal mode description, then, it is instructive to review the resonance Raman intensity-derived excited-state structural dynamics. The first UV resonance Raman study of thymine was not done until 1994 by Lagant, et al. [113], Although Raman and IR spectra of thymine had been recorded much earlier. Most earlier studies of nucleic acid components focussed on the nucleosides and nucleotides. Indeed, much of the earlier research on nucleic acid components was done by the groups of Peticolas and Spiro, working independently. Spiro focussed more on nucleosides and larger nucleic acid structures (see below), while Peticolas examined the nucleobases initially. Peticolas s approach was to combine ab initio computations of the ground-state and excited-state structures and vibrational frequencies, with... 

Since the value of the diffusion constant of OH is less than half the value for e aq the encounter frequencies tabulated in Table II for OH are lower than those given in Table I. The measured rate constants in the last column of Table II agree well with the calculated encounter frequencies. For proteins this must be ascribed to the high reactivity of OH for several amino acid side chains and for the peptide group, linking the amino acid residues together. For DNA this can be ascribed to the reactivity of nucleotides. 

For nucleotides, the charge on the phosphate group generally precludes the use of the 1R-R2PI hole burning technique. Instead, it is possible to study ions in a trap by IR multiphoton dissociation (IRMPD). The characteristics of a free electron laser, such as FELIX, with its macro and micro pulses, are very suitable for this type of multiphoton IR spectroscopy [58]. Since there is no isomer selection in this case, the interplay with theory is especially important and the occurrence of multiple structural forms could complicate interpretation, van Zundert et al. compared results for neutral (by DRS) and protonated (by IRMPD) adenine and 9-methyladenine in the same mid-IR frequency range of 525-1,750 cm ... 

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