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Length Limitation of Universal Base Homopolymer

DNA homopolymer Universal Base Degenerate Base Nucleoside

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#1 MrFreak

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Posted 25 February 2013 - 09:15 PM

Universal bases are base analogs that can act as a complement to any of the normal bases (A, G, C, or T). I know that people can order oligos that are 20 bases long containing a few (like 6) universal bases. The resulting oligo is still stable when bound to the complement.

Is it possible to have a stable oligo (lets say a 20-mer) made entirely out of universal bases? Or is it too unstable? Would it bind to normal ssDNA, or would its melting temperature be too low for any binding to occur? I cannot find any papers or info about the melting temperature of oligos with a large percentage of universal bases. (Note that there are many different universal bases, and some may be better than others in terms of stability probably.)

Any help would be muchly appreciated!





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