Deasr Roger,

Yes, Propidium iodide binds well to ssDNA and RNA, including oligonucleotides. This is because it is a cationic dye and thus can interacts with anionic phosphates which are present in any form of nucleic acids, and this ionic binding mechanism is independent of intercalation efficiency. Just few references:

Cosa G., Focsaneanu K.S., McLean J.R., McNamee J.P., Scaiano JC. Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution // Photochem. Photobiol. 2001, V. 73, No. 6, P. 585-599.

DOI: 10.1562/0031-8655(2001)0730585PPOFDD2.0.CO2

Przybylo M., Borowik T., Okruszek A., Langner M. A method to evaluate a propidium iodide association with oligonucleotides and oligonucleotide-cationic lipid interactions // Curr. Drug Discov. Technol. 2008, V. 5, No. 2, P. 162-167.

DOI: 10.2174/157016308784746300

I'd say the brief answer is "yes" - it always baffled me why, though!

You can definitely visualise single stranded oligonucleotides with negligible self complementarity, even on a denaturing gel, using Ethidium bromide or SYBR dye derivatives. I have no feel for how much less efficient it is.

BTW, SYBR Gold is supposedly better for single stranded nucleic acid. It is not cheap and requires a different filter, but it is VERY efficient and used at near homeopathic concentrations, so one pot goes a very long way.

Good luck!

Deasr Roger,

Yes, Propidium iodide binds well to ssDNA and RNA, including oligonucleotides. This is because it is a cationic dye and thus can interacts with anionic phosphates which are present in any form of nucleic acids, and this ionic binding mechanism is independent of intercalation efficiency. Just few references:

Cosa G., Focsaneanu K.S., McLean J.R., McNamee J.P., Scaiano JC. Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution // Photochem. Photobiol. 2001, V. 73, No. 6, P. 585-599.

DOI: 10.1562/0031-8655(2001)0730585PPOFDD2.0.CO2

Przybylo M., Borowik T., Okruszek A., Langner M. A method to evaluate a propidium iodide association with oligonucleotides and oligonucleotide-cationic lipid interactions // Curr. Drug Discov. Technol. 2008, V. 5, No. 2, P. 162-167.

DOI: 10.2174/157016308784746300

Thank you both for your answers!

I did some tests in the meantime which showed that PI can bind ssDNA, but it's always nice also to know why.