Cy3 & CG bp

dNTP derivatives for "single molecule" & Polony Fluorescent In Situ Sequencing (FISSeq)

7SS3Cy5 jpg jpg, cdx, pdb jpg jpg
jpg jpg
7SS9Cy3 jpg, c3d, pdb jpg
3NB10Bodipy jpg
4NB3Rox jpg

Notes: The first column numerals indicate spacer lengths in atoms. SS=disulfide cleavable by TCEP. NB=Nitrobenzyl (photo-cleavable). Cy=Cyanine dye. Bodipy= boron dipyrromethene difluoride. c3d=Chem3D format. pdb=Protein Data Bank format.
* = Not yet synthesized.

Wish list for dNTPs and this page.
a. Some of these compounds are to some extent "reversible terminators", possibly intramolecular competitive inhibition by the fluorophores (see Fig at top, comparing Cy3 & GC bp). So we would like dNTPs with more complete termination and more complete reversal.
b. We would like for this page to include data on the properties of these compounds with various polymerases (Bst, Klenow, T7, TdT, etc.)

References and related chemistry

1. Mitra,RD, Shendure,J, Olejnik,J, Olejnik,EK, and Church,GM (2003) Analyt. Biochem. 320:55-65. Fluorescent in situ Sequencing on Polymerase Colonies.

2. Seo TS, Bai X, Ruparel H, Li Z, Turro NJ, Ju J. (2004) Proc Natl Acad Sci U S A 101(15):5488-93. Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry.

3. Blanc A, Bochet CG. J Org Chem. 2002 Aug 9;67(16):5567-77. Wavelength-controlled orthogonal photolysis of protecting groups. 2-nitroveratryl (420 nm) and 3",5"-dimethoxybenzoin (254 nm).

4. Beier, M & Hoheisel, JD (2000) Nucleic Acids Research, 28, No. 4 E11. Production by quantitative photolithographic synthesis of individually quality checked DNA microarrays.

5. Short, JM (2004) Modified nucleotides and methods useful for nucleic acid sequencing.

6. He,B, Riggs, DL, & Hanna, MM(1995) Nucleic Acids Res. 7: 1231-8. Preparation of probe-modified RNA with 5-mercapto-UTP for analysis of protein-RNA interactions.

Biorad fluorophores.
Molecular Probes Fluorophores.
Photochemical Proteolysis

Updated by GMC on 20-May-2004.