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Specialty Chemistry Forums => Biochemistry and Chemical Biology Forum => Topic started by: thedy on April 24, 2013, 02:20:22 PM

Title: palindromes in single stranded DNA
Post by: thedy on April 24, 2013, 02:20:22 PM
Hi,can anyone explain me why is for example sequence ATCTATAGAT palindrome?Because defintion of palindrome is,that word or sequence looks exactly same but in different way.For example:GTCGGCTG.I am really confused.Some articles say this,and other something other.If GTCGGCTG is palindrome it would quite strange,because this sequence can not form hairpin due incomplementarity....But on other side, sequence ATCTATAGAT is complementary,but dont obey by definition of palindrome.
Thanks very much for clarifying
Title: Re: palindromes in single stranded DNA
Post by: Babcock_Hall on April 24, 2013, 04:29:27 PM
Write out this sequence with a sequence that is complementary to it.  In other words write out the sequence of the duplex DNA.
Title: Re: palindromes in single stranded DNA
Post by: Yggdrasil on April 24, 2013, 08:50:49 PM
Biologists have a slightly different definition of palindrome than the common definition.
Title: Re: palindromes in single stranded DNA
Post by: thedy on April 25, 2013, 12:23:04 PM
Quote from: Babcock_Hall on April 24, 2013, 04:29:27 PM
Write out this sequence with a sequence that is complementary to it.  In other words write out the sequence of the duplex DNA.
Well,OK.First sequence,which I mentioned:ATCTATAGAT----this can form hairpin,but it is not readable from both side without change of sense.
                                                         TAGATATCTA

                                             second:GTCGGCTG---this have the same sense from both sides,but it is not complementary,so it can not form hairpin.
                                                        CAGCCGAC
I mean palindromes on one single strand of DNA..
But, what next?What is definition for palindrome in genetics?Palindrome have to be complementary on one strand,or have to be just mirror reflection?Or both?I am stucked...
Title: Re: palindromes in single stranded DNA
Post by: Babcock_Hall on April 25, 2013, 03:16:42 PM
Now read both sequences (ATCTATAGAT and TAGATATCTA) from the 5' end to the 3' end, remembering that DNA is antiparallel.  It may be easier to write it as a duplex.
Title: Re: palindromes in single stranded DNA
Post by: Babcock_Hall on April 25, 2013, 07:46:52 PM
Palindromes in DNA refer to sequences of duplex DNA that read the same in both directions with the understanding that one has to jump to the other strand and read in the same direction with respect to the 5' and 3' ends (for example, one can read both in the 5' to 3' sense).