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?
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.
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.
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.