You could run a gel under non-denaturating conditions or you could use immobilised catching probes complementary to part of the SS-sequence or maybe better to the sequence that you want to remove (the reason is that if you try to fish out the single stranded, you might get some double stranded DNA with also). There are several options for catching probes. You can for example either purchase an oligo labelled with biotin and couple to Streptavidin coated beads or simply purchase an oligonucleotide make on an non-cleavable CPG support. Please email me directly, if you need further help here.

Separate the product on low gelling agarose 2 -3percent with a control ds DNA product as a control. Sequence the excised ss DNA  with shorter sequencing primers in excess to get sequence closer to the primers

Thank you

Purchase a hybridization probe, e.g. an EasyBeacon which hybridises to the target strand that you want to amplify. You can use the probe both in real-time, where you will first see an exponential (sharp increase of fluorescence) amplification followed by a linear amplification (less steep increase of fluorescence). You can also do an affinity/melt study after the amplification. Only if you have fine asymmetric amplification you get fine TM curves.

Thank you

Are there any simple procedures or kits to seperate  ssDNA from the PCTR product

You could run a gel under non-denaturating conditions or you could use immobilised catching probes complementary to part of the SS-sequence or maybe better to the sequence that you want to remove (the reason is that if you try to fish out the single stranded, you might get some double stranded DNA with also). There are several options for catching probes. You can for example either purchase an oligo labelled with biotin and couple to Streptavidin coated beads or simply purchase an oligonucleotide make on an non-cleavable CPG support. Please email me directly, if you need further help here.

one effective way to purify ss dna  product is to add a 5' biotin tag to one of te primers and run a pc with many cycles to use up all of the biotinylated primerr. then bind the product to streptavidin beads as i pyrosequencing method. Then chemically elute the single strand dna leaving the biotinylated strand attached to the streptavidin column

Thank you Ulf and Paul will give you feed back after completing the procedure

thank you Vinod I would be interested in how it goes. A thought on costs..as beads and primers are expensive once you have fully bound the biotin strand to the beads if you kept the beads after elution of the non-bio strand they could be reused to bind one strand of a non-biotinylated pcr product (denatured of course) washed and re-eluted off the bead

good luck

paul