NdeI versus NcoI... which is best?

[Bob Steinberg]

Stuart Rison wrote:
> 
> Dear All,
> 
> I am curently developing a cloning scheme in which I want to use a RE that
> incorporates a start (ATG) codon.
> 
> I've narrowed down my RE list to NdeI or NcoI (although this purely through
> hearsay/gut-feeling so please do tell me if you think I've missed out a good
> RE).
> 
> Does anybody have any experience using these REs?  Which one works best?
> Have you ever had any trouble with them?
> 
> Looking forward to hearing any suggestions.
> 
> Cheers,
> 
> Stuart.
> 
> +-------------------------+--------------------------------------+
> | Stuart Rison            | Ludwig Institute for Cancer Research |
> | Tel. (0171) 878 4127    | Courtauld Building                   |
> | Fax. (0171) 878 4040    | 91 Riding House Street               |
> +-------------------------+ London, W1P 8BT                      |
> | stuart at ludwig.ucl.ac.uk | UNITED KINGDOM.                      |
> +-------------------------+--------------------------------------+
> - and there is a NO_JUNK bit to remove in my return address !!!! -
Stuart,

We've used both successfully-- NcoI cuts more reliably in our hands and
generates a 4-base overhang, which may be an advantage in ligation. On
the other hand, the use of an NcoI site constrains the first position of
the second codon to a "G", so you can only have Val, Ala, Gly, Asp, or
Glu as the 2nd amino acid in your protein sequence.

Good luck.

Bob