parallel binding of miRNA with mRNA

[tareq07]

I have identified a miRNA which is assumed to be transcribed from the opposite of mRNA transcribing strand. Thus they are complementary as the miRNA and mRNA is transcribed from the opposite strand of each other. But the problem here is, miRNA and mRNA are parallel to each other; not anti-parallel. Now my question is there any possibility of binding this miRNA with the mRNA? Is it necessary to be anti-parallel for binding of miRNA with a mRNA?

[jonmoulton]

I have not heard of a case of parallel complementary binding.

However, you said that the miRNA and mRNA are complementary and are transcribed from opposite strands of DNA. This makes miRNA and mRNA antiparallel because their templates, the two strands of DNA, are both complementary and antiparallel.

[JackBean]

if they are transcribed from opposite strands (on the same locus of course) than they are complementary and can bind to each other just as the DNA strands do

[tareq07]

Thanks to all. I know if they transcribe from the opposite strand they would be complementary and anti-parallel. then there will have no problem to bind with each other. But here, case is not like that. Here they are complementary but not anti-parallel. I again repeat, they are complementary and parallel. As they are transcribed from the opposite strand but in same direction, they are parallel to each other. Now do they bind with each other?

[JackBean]

You cannot transcribe from both strands in the same direction. Would you mind to share your source?

[jonmoulton]

I agree with Jack. Polymerase adds bases by elongating from the 3' end of a nucleic acid strand which is bound in an antiparallel orientation with the template strand. I have not heard of priming the template backwards (parallel). I have never heard of a natural system making parallel complementary transcripts from opposite strands of an antiparallel DNA duplex. OK, there might be something new for us to learn about here. To reiterate Jack, "Source?"

[tareq07]

We are working on jute. A predicted miRNA has been identified in a gene of jute through bioinformatic tools mirabela and mir-para. It was found in the reverse orientation of our gene.Then the predicted miRNA was validated by mfold and the secondary structure fulfilled the criteria of miRNA. Later this miRNA specific primer was designed and validated through stem-loop RT PCR followed by end-point PCR. So it was confirmed that this miRNA get expressed. we have analyzed it's expression patterns under different stress conditions at different hours. Now as it expresses from the reverse orientation of our gene, it would be complementary but parallel to our gene. Do they bind with each other. If they dont bind then how can i confirm the target gene of this miRNA? For your convenience i would like to add that this predicted miRNA doesn't match with any reported miRNA in mirBase or any other sites. Any one can help?

[JackBean]

Ah, jute, sentimental reminiscences...

OK, so you know that it is expressed from the other strand, but for some reason you think it's parallel?

[tareq07]

Thank you JackBean. So you have worked on Jute. Nice to hear from you. Yes. as we get that the miRNA expresses, sequence analysis revealed it possibly transcribes from the opposite strand. sequence analysis further confirmed that it would be parallel to our desire mRNA. Now i need to know do they bind?

[JackBean]

if it's from the opposite strand, it must be antiparallel. If it's parallel, it must be transcribed either from the mRNA or from other locus.