oligo synthesis without an activator?

[CodeWarrior]

My apologies if I'm rehashing old topics but I have a question and I can't seem to find the answer. I've heard various references to oligo synthesis without the use of an activator. Is this in fact possible? How feasible is it in terms of the quality of the oligos and the time necessary for the reaction? Secondly is there any waste product from reaction without an activator? For that matter with an activator aside from the activator it self? Thirdly is there any compelling reason why an activator and nucleotide can't be premixed. As I said forgive my ignorance of organic chemistry but I have an idea for something and I want to quickly get an idea of whether what I'm thinking of is plausible.

[Nathan McCorkle]

I think they skip capping, not activation

On Fri, Feb 1, 2013 at 5:49 PM, CodeWarrior <code.w...@gmail.com> wrote:
> e quality of the oligos and the time necessary for the reaction? Secondly is
> there any waste product from reaction without an activator? For that matter
> with an activator aside from the activator it self? Thirdly is there any
> compelling reason why an activator and nucleotide can't be pr

--
-Nathan

[CodeWarrior]

Alow me to consentrate your atention on the 3rd question. Is there any compelling reason not to premix the activator and nucleoside in an oligo synth cycle. Will there be undesirable side reactions if they are premixed? Also regarding the by products of activated coupling. Are they chemically inert wrt the other chemicals involved or can we expect side reactions if some are present in the premixed activator and nucliocide?

[CodeWarrior]

In essence the this question is about the plausibility of recycling a premixed activator nucleoside mix.

[Cathal Garvey]

I don't know much about this besides what's available on wikipedia, but
my understanding is that you keep the activator separate from the next
nucleoside so you can wash away nucleosides before activation of the
next stage.

Assume I barely recall what I'm talking about here:

So, here's the reaction with separate activator / next-N:
~NN + Activator
-> Wash ->
~NN*
-> Wash & add G nucleoside ->
~NNG
-> Wash & add activator ->
~NNG*
-> Wash & add A nucleoside ->
~NNGA

Whereas without the intervening wash steps you could get rapid
polymerisation of new nucleosides:
~NN + Activator + G
-> Wash ->
~NNG
~NNGG
~NNGGGGGGG
-> Add Activator + A nucleoside ->
~NNGAA
~NNGGA
~NNGGGGGGGAAAA

[peter clark]

I thought the activator functioned in combination with the nucleoside
and would not function applied one after the other with a wash in
between?

[Cathal Garvey]

My ignorance, laid bare! :)
Honestly, I'm not that familiar with the chemistry. I know it's an
acetonitrile-based phosphoramitide blocking/deblocking process that runs
a risk of generating side-chains as one approaches 200bp, but that's
about it. And even that contains lots of lovely chemistry concepts that
are largely opaque to me.

[J Adams]

The Activator protonates the amine on the phosphoramidite so that it attacks the 5' hydroxyl and thus coupling occurs.

So, you need both TOGETHER for nucleoside activation and thus coupling....

J Adams

Azco Biotech, Inc.

3626 Ocean Ranch Blvd.

Oceanside, CA 92056

t. 858-525-2770

-------- Original message --------
From: peter clark <petergra...@blueyonder.co.uk>
Date: 02/02/2013 11:27 AM (GMT-08:00)
To: diy...@googlegroups.com
Subject: Re: [DIYbio] oligo synthesis without an activator?


I thought the activator functioned in combination with the nucleoside 
and would not function applied one after the other with a wash in 
between?
On 2 Feb 2013, at 16:53, Cathal Garvey wrote:

> I don't know much about this besides what's available on wikipedia, 
> but
> my understanding is that you keep the activator separate from the next
> nucleoside so you can wash away nucleosides before activation of the
> next stage.

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