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*****Glen Research Glen Report*****
New Products - 8-Oxo-G Clamp and 5’-Amino-Modifier TEG CE Phosphoramidites
8-oxo-dG is a key mutagenic base lesion that is linked to oxidative stress in cells and UV irradiation. Recently, the lab of Shigeki Sasaki from Kyushu University in Japan developed a novel means of detecting this lesion in DNA.1 It is based upon a very simple change in the structure of AP-dC (1), commonly known as ‘G-Clamp’, which is known for its large stabilizing effect upon duplex DNA when base-paired with guanosine.2
When a benzylcarbamoyl analogue (2) was synthesized, the Sasaki lab found that when incorporated into an oligo, it exhibited similar fluorescence to AP-dC. However, when base-paired against the 8-oxo-dG, its fluorescence was severely quenched. Rather remarkably, however, when base paired with dG or any of the other bases, A, C or T, there was no change in fluorescence – making it a specific probe for 8-oxo-dG.
While it is doubtful that the 8-Oxo-G Clamp could be sensitive enough to probe genomic DNA where the percentage of the 8-oxo-dG lesions is very small, we envisage that the 8-Oxo-G Clamp will find application in the study of DNA repair enzyme kinetics and may be very helpful in developing high-throughput fluorescence-based screening assays in the search for small-molecule inhibitors of DNA repair enzymes.
1. T. Nasr, et al., Bioorg Med Chem Lett, 2009, 19, 727-30.
2. K.Y. Lin, and M.D. Matteucci, J Amer Chem Soc, 1998, 120, 8531-8532.
The use of amino-modified oligos is ubiquitous in the field of DNA and RNA research. They provide a facile means to spot oligos on microarrays and label oligos with a variety of haptens, fluorophores and proteins, such as HRP, for enzymatic detection methodologies. A critical feature of these amino-modified oligos is the linker used to couple the amine to the oligonucleotide. The linker should be long enough to allow efficient conjugation of more bulky, sterically hindered labels and yet remain hydrophilic. The hydrophilicity is an important factor for two reasons – first, it limits non-specific interactions with hydrophobic surfaces, protein pockets or haptens, and second, it will remain well solvated in water, thereby remaining, on average, further extended into the surrounding aqueous solution. Toward this end, we are pleased to introduce a new hydrophilic amino-modifier, 5’-Amino-Modifier TEG CE Phosphoramidite (3). This amino-modifier, a triethylene glycol ethylamine derivative, is 12 atoms in length and fully soluble in aqueous media. The trifluoroacetyl protecting group on the amine is completely removed under standard deprotection procedures. We are happy to add this new product to our growing line of 5’-amino modifiers.
Please contact Glen Research if you have any questions or comments!