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Modifications
Modifications
For modified oligo pricing information see our
Modifier
Pricing Page.
See the
Modified
Oligo Order Form Instructions Page
for information on how to use this site.
We have experience performing a wide variety of
special modifications. Our goal is to provide the highest quality oligos while
preserving the integrity of the modification. We order most specialty reagents
at the time your order is placed to ensure freshness. We do not attempt to use
leftover reagents as that may result in less than optimal coupling. We will also
work with you to group your orders so as to minimize your cost by maximizing the
utilization of expensive monomers. If possible, we will work our way down a list
of oligos until a specialty reagent is exhausted.
Generally, we will
incorporate ANY commercially available modifier, not just those listed below, as
long as it is particulate-free. To avoid issues of improper storage
and handling, we recommend allowing us to order the modified phosphoramidite/column.
However, if you would like to provide us with a phosphoramidite/column that you
purchased or synthesized, a $250 surcharge for each different modification will
apply. This surcharge covers the additional labor costs of modified
phosphoramidite/column handling and storage, synthesizer programming, oligo
processing and e-mail correspondence. Also, since we are not supplying the
modified phosphoramidite/column, our usual quality guarantee does not apply and
the oligos must be accepted "as is".
Modifications can be loosely divided into several groups:
- backbone
- internal
- 5' terminal
- 3' terminal
Two backbone modifications are presently
available:phosphorothioate linkages and methyl phosphonate linkages. The
phosphorothioate modification replaces one of the ether oxygens on the phosphate
with a sulfur (giving equal amounts of the two resulting stereoisomers). This
modification can be placed at any or all positions along the backbone and will
be charged at $5.75 per linkage ($6.61 for non-Yale orders) to cover
additional labor in setting up and maintaining the synthesizer. Methyl phosphonate linkages are also available but are quite expensive because special
amidites and deprotection reagents must be used.
Obviously internal reagents can also be placed at the 5' end, since synthesis is done
in the 3' to 5' direction. Many internal reagents can also be placed at the 3' end by a
special trick which results in a 3' phosphate, if this is acceptable. Note also that 3'
modifiers are generally supplied only on 0.2 or 1.0 micromole columns, which means that we
must run the synthesis at one of these scales. Furthermore, these columns are NOT
low-volume, which means that we must use synthesis cycles which will consume much more of
any other modified monomers being incorporated into the same oligos than the low volume
cycle would.
Some modifications require the use of UltraMild
columns, phosphoramidites and reagents that allow for mild cleavage and
deprotection conditions. Some of these modifications include:
- cyanine dyes including Cy3, Cy3.5, Cy5 and
Cy5.5
- TAMRA-dT and 3'-TAMRA
- acridine
- etheno-dA
- 5,6-Dihydro-dU
- 5'-iodo-dT
- 5'-OH-dU
- 5'-OH-dC
- thymidine glycol
Please see our
UltraMild Synthesis page for further details.
The following is a partial list of the more
popular types of modifications that we offer. For other available modifications
and pricing, please see the Glen Research web page (www.glenresearch.com)
or E- mail us at oligos@yale.edu for more
details."
- Inosine and other partially selective or nonselective bases
- 5' or 3' phosphate
- Primary amines, thiols: used primarily to link other groups (such as dyes) to the oligo
post synthesis, but also used to block termini; available either for the 5' or 3' ends;
amines also available attached to the base of thymidine for internal use.
- Dyes: fluorescein and derivatives FAM, HEX,
and TET; cyanine dyes; dabcyl; TAMRA; acridine; etheno-dA (Note: Oligos that
contain cyanine dyes, TAMRA, acridine or etheno-dA are supplied
cleaved, deprotected, and dissolved in 0.025 M potassium carbonate/MeOH/1M
TEAA, and must be desalted before use. Please see our
UltraMild Synthesis page for further details).
- Halogenated deoxy and ribonucleotides
- Spacers: various lengths of hydrocarbon chains or mixed polarity (ethylene glycol)
linkers, or just plain ribose lacking a base
- Biotin: either as a 5'-only moiety which couples very well, a biotin on a mixed-polarity
linker (Biotin-TEG) which can be placed at either end or in the middle of an oligo, and
Biotin-dT (biotin attached to one of the non base-pairing positions on thymidine)
- Reverse synthesis: "Backwards" monomers enable us to synthesize in the reverse
direction: 5' to 3'. We have used them to insert a normal monomer "backwards" in
the molecule, and to block ends with a 3'-3' or a 5'-5' linkage.
- Branches (symmetric or asymmetric): these enable you to increase the number of 5' ends
(for example, to add more dye molecules to increase signal, or to have multiple oligos at
one end linked to a single oligo at the other.
- Dideoxy and other chain terminators
- Cross-linking: psoralen
For modified oligo pricing information see our
Modifier
Pricing Page.
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