Oligonucleotide Conjugates of Nile Red

Abstract

Oligonucleotides containing long chain amine on uridine‐2′‐carbamate have been covalently modified with Nile Red, a hydrophobic long wavelength fluorescent benzophenoxazine dye. The fluorescence of the dye is quenched in oligonucleotide conjugates. Thermal denaturation studies show considerable interactions of Nile Red with DNA–DNA duplexes.

^†In honor and celebration of the 70th birthday of Professor Leroy B. Townsend.

Keywords:

• Modified oligonucleotides
• Nile Red
• Interaction with ds DNA

Acknowledgments

The research was supported by RFBR grants No. 00‐03‐32701 and 03‐03‐32196. We thank Dr. Dmitry A. Stetsenko, Dr. Michael J. Gait (MRC Laboratory of Molecular Biology, Cambridge, UK), Sergei V. Gontarev (Institute of Physical Organic Chemistry, Minsk, Belarus) and Prof. Vladimir A. Efimov (Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia) for their support and fruitful discussions.

Notes

^†In honor and celebration of the 70th birthday of Professor Leroy B. Townsend.