I found a function called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of finding palindrome in DNA sequences?
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2$\begingroup$ In regards to a Matlab function, it is probably used to find Restriction Enzyme digestion sites. Many, but not all of the recognition sites of Restriction Enzymes are palindromic, and having a function that can search a sequence and find these site will give you the location where restriction enzymes will cut. Palindromes also can represent places in genomes where viral DNA has been incorporated. So the basis of Bacterial adaptive immunity are these short palindromic repeats that encode RNA template strands for an enzymes such as Cas that can identify and cleave infecting DNA. $\endgroup$– AMRSep 19, 2015 at 5:11
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3 Answers
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My knowledge of biology is extremely limited, but this is what I know of palindromic sequences:
Palindromic sequences are their own reverse complements. I have seen many restriction sites be palindromic. Also, some Transcription Factor Binding sites are palindromic. The canonical E-box site, for example, can be expressed as CANNTG.
Also, these palindromes, when occurring in pairs with a sequence between the occurrences, can double back and bind to each other (when the DNA is transcribed to RNA, say), and this would result in the RNA stem and loop structure.
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$\begingroup$ Are these the only biological significance? do you have the extensive list of all possible significances ? $\endgroup$– girl101Sep 19, 2015 at 7:36
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$\begingroup$ I wish I did. In my opinion, you learn as you go. Maybe Google+dig deep would help get a longer list of potential areas of significance, but an extensive list serves no purpose as it is not constant, and because most problem solving is done with the thought process "What are the available solutions to this problem" and not "What are the problems this individual piece of a larger solution can address" $\endgroup$– Ram RSSep 19, 2015 at 11:23
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$\begingroup$ @RamRS what must be the length of such palindromes?? $\endgroup$– girl101Oct 26, 2015 at 5:53
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$\begingroup$ I've encountered 6 and 8-mers, and I remember a colleague saying those are the typical length you see, but that statement may be specific to human TFBS sites. $\endgroup$– Ram RSOct 26, 2015 at 13:04
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Palindrome sequences are important in bioinformatics understanding, it helps us to extract patterns in the genomic sequences. I'll give an example in HIV (very important application).
HIV has a nasty requirement that the virus must keep the cell alive. It does that by inserting itself into the host's genome. We know from biology that cutting and pasting of DNA works best when the sequences at either end of the cut site are identical. In fact, we usually look for palindromes, sequences that read the same backward and forward. We know the virus prefer to integrate at a palindromic sequence.
Therefore we should look at those palindromic patterns for HIV. Once we find those regions, we might do an alignment with known HIV sequences.
Please Google "restriction sites" for more information.
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This information is mainly from my bioinfo class notes. Palindromes or inverted repeats in genome can help in
- Predicting regions in RNA that are self-complementary and that, therefore, have the potential of forming secondary structure.
- Identification of binding site of regulatory proteins involved in regulation of transcription. This is because sometimes the binding protein has a couple of monomers which bind to both sequences (orignal and inverted) resulting in stronger interaction than cases where only one monomer binds.
- Inverted repeats of small length are also present in some transposons (though I am not really aware of their function there).
I also came across a section on function of inverted repeats (palindromes) on google books that discusses the topic in more detail.
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$\begingroup$ what must be the length of such palindromes?? $\endgroup$– girl101Oct 26, 2015 at 5:53