Re: [DIYbio] Re: restriction digest confirmation

http://www.nano.uoguelph.ca/manderville/secure/Lecture_3.pdf

On Wed, Jul 17, 2013 at 2:15 AM, Nathan McCorkle <nmz787@gmail.com> wrote:
> 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



--
-Nathan

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