Selective Duplex Stabilization

Etheno-dA is a fluorescent nucleoside which is especially useful in observing the transition between DNA structural types. It is quite base labile and should be deprotected with ammonium hydroxide at room temperature for 24 hours. Alternatively, UltraMild chemistry can be used. 2-Aminopurine and AP-dC (G-Clamp) are also useful fluorescent nucleosides.

Pyrrolo-dC is a fluorescent deoxycytidine analog that is an ideal probe of DNA structure and dynamics.1,2 It base-pairs as a normal dC nucleotide. An oligo fully substituted with pyrrolo-dC has the same Tm as the control dC oligo with the same specificity for dG. Its small size does not perturb the structure of the DNA helix and it is well tolerated by a number of DNA and RNA polymerases. It is highly fluorescent and its excitation and emission are well to the red of most fluorescent nucleotide analogs, which eliminates or reduces background fluorescence from proteins. Pyrrolo-dCTP has potential uses in biological assay development.


1. D.A. Berry, et al., Tetrahedron Lett, 2004, 45, 2457-2461.
2. The Glen Report, 2007, 19, 8-9.
3. P. Sandin, et al., Nucleic Acids Res., 2008, 36, 157-167.
4. P. Sandin, et al., Nucleic Acids Res., 2005, 33, 5019-5025.
5. K.C. Engman, et al., Nucleic Acids Res., 2004, 32, 5087-5095.

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