Aptamer for ires

[Aayush Aggarwal]

 
Can anyone help in finding an Aptamer(may be DNA or peptide aptamer) that would specifically bind to viral IRES..
Also,any open source library where we can find sequence for aptamers....


Thanks

Regards:-
aayush aggarwal

[Cathal Garvey]

Hi Aayush,
IRES = "Internal Ribosomal Entry Site", right? If so, aren't you
talking about an RNA sequence? The "Aptamer" to bind that would just be
the reverse complement, if I'm not mistaken.

What are you looking to achieve? To merely detect the sequence, or to
block it, or something else?

Best,
Cathal

[Aayush Aggarwal]

Hello Cathal,

Actually, we are trying to block IRES(Internal Ribosomal Entry Site), so that  it silences the viral infection.

Also,we  are looking  for DNA or peptide based aptamers as RNA aptamers are difficult to handle because of their stability and structure.

Yes it's the reverse complementary to IRES sequence,but designing an aptamer for particular sequence is different and it is done using SELEX.

Any library or software which are specifically for aptamers helps in finding in our motive.

Thanks

Regards:

aayush aggarwal

[Cathal Garvey]

Hi Aayush,
I'm familiar with SELEX, but aptamers are generally applied to things
like carbohydrate polymers, or surfaces, or the like. For RNA, the best
"aptamer", especially if your goal is to block IRES, is simply the
reverse complement.

That may be my opinion, but you'll notice that few people use SELEX for
RNA or DNA targeting unless they are building peptide aptamers for
conjugation to another protein. If the goal is merely to bind and
obscure a target site, use RNA or DNA reverse complement.

May I suggest looking into the use of trans-acting ribozymes
targeted at IRES? IIRC, there are some in the literature (derived from
hammerhead ribozyme I think?) which act as one-shot "restriction
ribozymes", and can cleave another RNA molecule according to their
affinity to it, base-pairing-wise. If I'm not mistaken you could apply
these to create a trivial anti-IRES that permanently cleaves viral RNA.

On Thu, 8 Aug 2013 00:07:32 -0700 (PDT)
Aayush Aggarwal <aggar...@gmail.com> wrote:

> Hello Cathal,
>
> Actually, we are trying to block IRES(Internal Ribosomal Entry Site),
> so that it silences the viral infection.
> Also,we are looking for DNA or peptide based aptamers as RNA
> aptamers are difficult to handle because of their stability and
> structure. Yes it's the reverse complementary to IRES sequence,but
> designing an aptamer for particular sequence is different and it is
> done using

> SELEX<http://en.wikipedia.org/wiki/Systematic_evolution_of_ligands_by_exponential_enrichment> .

[Aayush Aggarwal]

Hello Cathal,

Sorry for replying late.

ThankYou for your wonderfull suggestion.It would mean a lot.

[Aayush Aggarwal]

Hello,

We have found the RNA aptamers that binds to IRES of HCV virus.But we are struck in integrating these aptamers inside the nano-structure for delivery because both aptamers and nanostructure repel each other due negative charges on it.Can anyone hepls in finding the solution to this problem?

Regards

aayush aggarwal