Nucleic acid bromination

Protocol for Labeling Nucleic Acids by N-Bromosuccinimide Activation Bromination... 

The above two methods for derivative preparation have been successfully used in the phasing of both nucleic acids and proteins. However, an additional method has been used for phasing of nucleic acids, in which the heavy atom is synthetically incorporated into the molecule. For example. Drew et al. (1980) determined the structure of d(CGCG)2 by incorporating 5-bromocytosine into the synthesis of their nucleic acid and then using the bromine atoms for phasing. 

In contrast to MPO, eosinophil peroxidase (EPO) prefers to oxidize plasma level bromide (20-100 pM) to hypobromous acid (HOBr) and several biological targets are implicated, including nucleic acids and nucleosides (1480, 1482, 2376), proteins (1812, 1813, 2377, 2378), unsaturated fatty acids (2379), and low-density lipoprotein (2380, 2381). This EPO-dependent bromination is suggested to be involved in the pathogenesis of asthma (2382). Accordingly, both 3-bromotyrosine and 3,5-dibromotyrosine (1812,1813) are produced by EPO-induced bromination of tyrosine residues in lung tissue (1813, 2382). 

Other peroxidase enzymes have been found to halogenate various substrates. Thus lac-toperoxidase catalyzes the bromination of tyrosine, thyroglobulin and bovine serum albumin380, and myeloperoxidase brominates nucleic acids and related compounds381. 

Base analogs such as 5-bromouracil and 2-aminopurine can be incorporated into DNA and are even more likely than normal nucleic acid bases to form transient tautomers that lead to transition mutations. 5-Bromouracil, an analog of thymine, normally pairs with adenine. However, the proportion of 5-bromouracil in the enol tautomer is higher than that of thymine because the bromine atom is more electronegative than is a methyl group on the C-5 atom. Thus, the incorporation of 5-bromouracil is especially likely to cause altered base-pairing in a subsequent round of DNA replication (Figure 27.42). 

The substitution of a bromine atom on a nucleic acid base (e.g. 8Br-adenosine) provides the base with significant absorption in the 300 nm region. The RR spectrum of the brominated species can then be specifically excited by 300 nm irradiation [59]. The brominated bases are in effect RR labels but there are rare naturally occurring bases with significant absorption in the near UV, these are sulfur substituted analogs absorbing from 300-360 nm. For example Nishimura, Tsuboi and coworkers [60] obtained RR spectra of the single 4-thiouridine which occurs in a number of tRNAs. 

With a similar perspective aimed at unravelling enzymatie proeesses involving nucleic acids, Beal reported the synthesis of novel phosphoramidite for incorporation in 7-substituted-8-aza-7-deazaadenosine derivatives (36a-d) into RNA to examine the RNA-editing adenosine deaminase SAR. The 8-aza-7-deazaadenosine building block was found to be an excellent substrate while functionalisation of the C-7 hydrogen with bromine, iodine or propargyl alcohol resulted decreased rates of catalysis. 

Robins MJ, Uznanski B (1981) Nucleic acid related compounds. 34. Non-aqueous diazotiza-tion with tert-butyl nitrite. Introduction of fluorine, chlorine, and bromine at C-2 of purine nucleosides. Can J Chem 59 2608-2611... 

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