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Keck
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Oligo Synthesis >
Mixed Base Oligos: Equimolar and Non-equimolar
Mixed Base Oligos: Equimolar (degenerate)
and Non-Equimolar (doped)
Equimolar (Degenerate) Oligos:
Equimolar (degenerate) oligos can be ordered via the
Order DNA or RNA
link as long as the single-letter codes for the mixtures are used:
The codes are:
| M = (AC) |
V = (AGC) |
N = (AGCT) |
| R = (AG) |
H = (ACT) |
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| W = (AT) |
D = (AGT) |
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| S = (GC) |
B = (GCT) |
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| Y = (CT) |
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| K = (GT) |
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Note that AN OLIGO WITH A MIXED BASE AT THE
3' END CANNOT BE MADE AT THE 40 NANOMOLE SCALE, ONLY AT THE 0.2 OR 1.0 SCALE. IF
YOU PLACE AN ORDER FOR SUCH AN OLIGO AT THE 40 NANOMOLE SCALE, WE WILL CHANGE
THE SCALE TO 0.2 MICROMOLES. Oligo orders with a mixed base at the 3' end
may be delayed a day or two because they require special columns which we may
need to order - but there is no extra charge for these columns.
There is no extra charge for incorporating
equimolar mixtures of 2,3, or all 4 bases. Unless you specify otherwise,
equimolar incorporations are done by having the synthesizer simultaneously
deliver two or more monomers. Chemical analysis of mixed-base oligos made in
this way has shown that the differences in reactivity of the monomers [T>(C,G)>A]
are compensated for by the relative positions of the monomers on the
synthesizer.
However, if you request a manually prepared, equimolar "N" mix in a single
bottle, be advised that this will result in a non-random incorporation of 20% A
: 26%G : 24%C : 30%T at each position. A surcharge of $46 ($52.90 for non-Yale
orders) per 0.25gram (3mls) of this mixture will be applied. Please see our
reagent
usage table to determine how many additions can be made from each 0.25g
bottle.
Non-equimolar (Doped) Oligos:
Oligos containing non-equimolar mixtures must
be ordered via Order Modified Oligos. Please indicate the percentages of each
base that you want us to use for the synthesis and express them in the order of
A : G : C : T. Assign a code to each mixture: 5, 6, 7, 8, 9, etc. and use that
code in the sequence. Do NOT use upper- or lower-case A, G, C, or T to code for
mixtures.
Non-equimolar mixtures are not possible at the 3’ end. Either use a single base,
one of the equimolar doped bases listed above or some other structure. In either
of the latter two cases the scale must be either 0.2 or 1.0 micromole.
There is a $46 ($52.90 for non-Yale orders) charge for every 3ml bottle of
a doped mixture. In order to calculate the volume needed for your order, please
see our
reagent
usage table.
In order to achieve your desired final percentages, you may need to adjust your
calculations to compensate for the varying reactivities of the different
phosphoramidites (see above).
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