Re: [ccp4bb] ssDNA self-aneal

[Bart Hazes]

Has anyone looked at the kinetics of DNA annealing. Especially for such short fragments I expect hairpin formation times to be on the order of pico to nano seconds. Of course it doesn't hurt to slow-cool but I wouldn't be too paranoid about it. Moreover, in this particular case the hairpin is probably sufficiently unstable to release and refold at a high rate at room temp so even less need to slow cool. A bigger concern may be the relative affinity of the intra-molecular hairpin versus the inter-molecular "primer dimer". The former benefits from lower entropy loss, but the latter would not need such a tight loop and possibly would form one additional G-C basepair. Bart On 11-03-17 12:06 PM, Kevin Jude wrote: I would bring up the DNA in TM buffer (10 mM Tris, 5 mM MgCl2) or similar and anneal under dilute conditions to favor hairpin formation over dsDNA.  Fast cooling will also favor hairpin formation, so you may try heating to 95° and then cooling on ice, or using a short gradient on a thermocycler.  You can check your work on native PAGE (including appropriate controls, like oligos annealed under dsDNA-favoring conditions) On Thu, Mar 17, 2011 at 4:23 AM, dengzq1987 <dengzq1...@gmail.com> wrote: Dear all,   Recently,i purchase Oligonucleotide from company.the sequence  is TTTTTTTTTTGCGTAC GCAC GTACGC .i want to perform self-annealing process to form the following second structure . 5' TTTTTTTTTTGCGTACGC                       ||| |||    ] 3'                   CGCATGCA   i hope that most of the Oligonucleotide can form this structure,how can i achieve this?  any adivice is appreciated.       best wishes. -- ============================================================================ Bart Hazes (Associate Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================