MiRNA detection and info - An research on MiRNA detection (Sep/13/2010 )

Hi,

I am a undergraduate who is working a detection of miRNA using carbon nanontubes. I have limited biological background (basically just high-school biology + some courses on biomedical engineering). So, i was hoping to seek some help here on the basics and some other stuff.

I will explain the basics of what i am trying to do.I am using a carbon nanotube that will have a probe (Peptide Nucliec Acid (PNA)) which will used to detect the miRNA sequences in the sample. the detection is done using a transistor like device that measures changes in the electrical conductance.

What i am trying to do now, is to obtain a couple of miRNA sequences that have important research use for cancer. Through my research i have narrowed it down to two different sequences.

1) MIR-21
2) MIR-24-1

I am having problems find their sequence as well the complementary sequence for the PNA probe. I hope i can get some assistance on that matter. Also, are there other miRNA sequences of greater importance in cancer research. I will pleased with whatever help i can get. Thank you.

Regards
Vajid

-vajid-

vajid on Mon Sep 13 05:49:31 2010 said:

Hi,
if want miRNA sequences just go to http://www.mirbase.org/ and you'll find whatever you want. If you want to know which miRNAs are important in cancer you can go to http://www.ncbi.nlm.nih.gov/sites/entrez and type microrna cance, you'll find a lot of articles. even if you have basic biology background you can read some abstracts and see which miRNAs are more frequently cited. if you need some review/article in particular and do not have access to the journal ask here or send a PM to me, i'll se if i can help (cancer is not my field)
good luck
Fiz

-Fizban-

Thanks for the quick reply. If you dont mind, i will like to ask a couple more question.

1) Do you know what is the charge of a PNA and what happens to its charge if the PNA binds with a miRNA?

-vajid-

vajid on Mon Sep 13 13:21:45 2010 said:

Thanks for the quick reply. If you dont mind, i will like to ask a couple more question.

1) Do you know what is the charge of a PNA and what happens to its charge if the PNA binds with a miRNA?

PNA are uncharged. When an miRNA binds to a PNA, the heteroduplex will have negative charges due to the anionic phosphates of the miRNA. While binding of the miRNA will not change the charge state of the PNA component, it will create a charged complex by virtue of the RNA backbone.

-Jon Moulton-

Thanks for the help.

1) How useful do u think it would be that a specific miRNA sequenes could be detected, in terms of its diagnostic ability?

2) is there any article/ reference i can refer to udnerstand better about the bonding between PNA miRNA?

-vajid-

Usefulness of the technique will depend on its fidelity, dynamic range and detection limit. With good fidelity, wide dynamic range and low detection limit I expect many applications would appear.

I follow Morpholinos, another uncharged antisense structural type. I expect the diagnostic behavior of Morpholinos and PNAs to be fairly similar, though PNAs have higher affinity per-base and lower water solubility. These citations might be useful, as they report investigation into some of the physical chemistry of DNA interactions with uncharged probes.

***Tercero N, Wang K, Levicky R. Capacitive Monitoring of Morpholino-DNA Surface Hybridization: Experimental and Theoretical Analysis. Langmuir. 2010 Aug 9.

***Tercero N, Wang K, Gong P, Levicky R. Morpholino Monolayers: Preparation and Label-free DNA Analysis by Surface Hybridization. J Am Chem Soc. 2009 Mar 18.

There are a few more on this page: http://www.gene-tools.com/node/10

-Jon Moulton-