Notes: Pyrrolo-C (PC) is a fluorescent analog of cytidine.
Description: Pyrrolo-C (PC) is a fluorescent analog of cytidine.1 It is highly fluorescent, the 2'-deoxy version exhibiting an emission maximum at 473 nm when incorporated into a 19-mer oligodeoxyribonucleotide, where it base-pairs normally with dG. Pyrrolo-C has proven to be useful for monitoring RNA secondary structure formation, where its fluorescence is reversibly quenched upon base-pairing.2 PC has been used to follow the kinetics of formation and dissociation of an RNA/DNA complex and has been used to monitor the thermal denaturation of the central segment of an RNA duplex.2 Most recently, PC has been incorporated into native and minimal hammerhead ribozymes at cleavage site position C17, where it was found to be capable of efficient photocrosslinking to G12, resulting in catalytically active RNA that was useful in structural studies.3 2'-O-TBS-Pyrrolo-C CEP should behave in oligonucleotide synthesis in a manner similar to the other modified 2'-O-TBS nucleoside CEPs, but this has not yet been proven. This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research.
1. Berry, D.A.; Jung, K.-Y.; Wise, D.S.; Sercel, A.D.; Pearson, W.H.; Mackie, H.; Randolph, J.B.; Somers, R.J. Tetrahedron Lett. 2004, 45 (11), 2457-2461).
We also offer the 2'-O-Methyl phosphoramidite of Pyrrolo-C (BA 0356) as well as the 2'-deoxyribo version, Pyrrolo-dC CEP (BA 0170). BA 0245 and BA 0170 are also available from Glen Research (Pyrrolo-C CEP as the 2'-O-TOM version), our development partner for these products. Glen Research also offers the triphosphates of Pyrrolo-C and -dC. We offer the two nucleosides (PYA 11090 and PYA 11092) as well as the simple fluorescent pyrrolocytosine heterocycle (i.e., Pyrrolo-C aglycone (HC 9060). Thompson and co-workers have studied the photophysical properties of these fluorescent pyrrolopyrimidines.4
2. Tinsley, R.A.; Walter, N.G. RNA, 2006, 12, 522-529.
3. Lambert, D.; Heckman, J. E.; Burke, J. M. Biochemistry, 2006, 45, 7140-7147.
4. Thompson, K. C.; Miyake, N., J. Phys. Chem. B, 2005, 109, 6012-6019.