Re: [DIYbio] Re: restriction digest confirmation

On Wed, Jul 17, 2013 at 12:29 AM, Cathal Garvey (Tablet)
<cathalgarvey@cathalgarvey.me> wrote:
> How big, basepair wise, is gelred, or EtBr for that matter? At 6bp I'd be
> wary that normal intercalating dyes might interrupt your DNA duplex?

EtBr looks like it needs a minimum of 2bp
http://en.wikipedia.org/wiki/File:DNA_intercalation2.jpg

and in ssDNA many comments online lead to this general idea:
"According to Sambrook et al, ethidium bromide binds to regions having
an helical character that is mainly caused by intramolecular
interactions. This is not far-fetched since it is known that
single-stranded nucleic acids often form various helical regions, and
this is where ethidium bromide could preferentially bind."

gelGreen and gelRed are much larger molecules, and they look like they
might need mor like 3 or 4 bases (or basepairs). sybr green is pretty
different from them, smaller like EtBr:
http://en.wikipedia.org/wiki/GelGreen
http://en.wikipedia.org/wiki/SYBR_Green_I

"GelRed is structurally closely related to ethidium bromide and
consists of two ethidium subunits that are bridged by a linear spacer"
http://en.wikipedia.org/wiki/GelRed

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