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OLIGONUCLEOTIDE SYNTHESIS
RESOURCE
Nucleic acid syntheses are run on Applied
Biosystems 394 or 3900 Synthesizers using beta-cyanoethyl chemistry.
Unless the researcher requests otherwise, normal DNA oligos are delivered in a
fully deprotected, lyophilized, unpurified form with hydroxyl groups at both the
3' and 5' ends. The sole exceptions are:
-
Trityl-On oligos which
are supplied on the support without cleavage or deprotection
-
RNA oligos which are
delivered with a 2' protecting group to prevent degradation
-
Modified oligos
requiring UltraMild deprotection (i.e.TAMRA-dT, etheno-dA, cy3, cy5 etc) which
are supplied cleaved and deprotected in 3mls potassium carbonate/MeOH/TEAA but
must be desalted before use.
Protocols for cleavage and deprotection of
these exceptions can be found on our
Protocols page.
Every effort is made to maximize the quality of the unpurified product by using high
quality reagents and optimizing the synthesizer cycles. We monitor our product by checking
trityl yields and by analyzing approximately 20% of our oligos by capillary
electrophoresis.
The quality of our unpurified oligos is high enough that most labs find they can be
used directly (or after desalting, for which we can provide a
protocol) for sequencing or PCR. We offer three scales of synthesis for DNA:
|
Scale |
Approximate Yield per base
* |
| 40/50 nanomole
|
~0.2 OD260 (6 µg)
|
| 0.2 µmole
|
~1 OD260 (30 µg)
|
| 1.0 µmole
|
~5 OD260 (150 µg)
|
*To ensure consistency, you should check the DNA concentrations of your oligos before
using or purifying them.
If you need more than 1.0 micromole of a given
sequence, we handle it as multiple 1.0 micromole syntheses. When placing these orders, you must change the name of each
micromole
slightly because the database will not accept duplicate sequence names (for obvious
reasons):
e.g., OLIGO1A, OLIGO1B, OLIGO1C, etc.
For sequences longer than 100 bases we recommend
synthesis at the 200 nanomole or 1.0 µmole scale. We will synthesize oligos
longer than 100mers at 40 nanomole if you specifically request that we do so,
but our usual guarantee does not apply in these cases.
We emphasize rapid turnaround:
- Our turnaround time for normal, unpurified,
40 nanomole DNA oligos is typically <24 hours for <60-mers. Orders of this
type placed before 5pm are usually delivered the following afternoon, although
we cannot guarantee this. Orders submitted after 5:00 PM may not be processed
until the next business day.
- Longer normal, unpurified DNA oligos may
take 1-2 days more due to longer synthesis and deprotection times.
- Turnaround times for specialty oligos vary
but we try to finish them within a week.
- Gel purification typically adds several days
to a week, depending on workload. Gel purification is now available for Yale
and non-Yale labs at all synthesis scales.
Completed Yale orders will be delivered by
courier to your P.I.'s delivery location. Deliveries will be made
once a day in the mid-afternoon. If no delivery location for your lab has been
specified, we will phone you when your order is ready and you can pick it up at
300 George St. (room 2127). Non-Yale orders are shipped via Federal Express
Priority 1. In all cases, the current status for each oligo can be monitored
using the Check
My Orders.
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