Primers palindromic sequences

Another mechanism, which is utilized by some single-stranded parvoviruses,416,443 obviates the need for an RNA primer by use of a palindromic sequence to form a hairpin loop (Eq. 27-8). 

Primers can be custom synthesized commercially at a fairly reasonable rate. Primer sequences are selected so that they are typically 21 to 24 nucleotides in length with an average G + C content of 40 to 60%. The primers should not be part of repetitive-sequence DNA, nor should the DNA have palindromic sequences. There are computer programs to help select oligonucleotide primers for PCR, such as PRIMER (from White Head Institute www-genome. wi. mit. echi/ftp //distribution/software/primer. 0.5/manual. asc). In addition, commercial sources exist for software (National Biosciences) that includes the OLIGO program. 

New England Biolabs, Inc. catalogue 1982-83 contains up to date restriction endonuclease maps of pBR322, M13mp8, phage A and SV40 DNA updated lists of restriction endonucleases, M13 primers, linkers and adapters as well as cross indexes of palindromic recognition sequences and much other useful data. A valuable up to date compendium obtainable from ... 

Runs of nucleotides should be avoided because they can pair with runs of nucleotides outside of the target sequence or complementary runs within the same primer. Avoid palindromic base sequences which could cause the primer to fold and pair with itself. Secondary structure in the template can also interfere with priming. Substitution of 7-deaza-2 -deoxyGTP for dGTP can help solve this problem (Innis and Gelfand 1990). ... 

The choice of the arbitrary primer to be used for amplification is of great importance. Primers should not form secondary structures with themselves. Therefore, internal hybridization sequences and palindromes should be avoided. The length of the primer for which the protocol below is designed should be 17-20 bases. For a trial experiment, either the M13 universal or reverse primers could be used. 

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