| T* phosphoramidite || |
| A* phosphoramidite || |
| C* phosphoramidite || |
| G* phosphoramidite || |
Oligonucleotides containing SAMRS:
General rules for placement of SAMRS bases into primers used in PCR and other amplification techniques. Upper case letters indicate the standard base, lower case letters indicate the SAMRS base.
- Recommended lengths are 20-35 nts. SAMRS bases should be utilized in the first 4 to 5 positions at the 3’ end of the oligonucleotide but not in the very first 3’ base.
- Between two and four SAMRS bases should be used per oligonucleotide, with two or three SAMRS modifications being preferred.
- The SAMRS t base has not demonstrated as much reduction in primer dimer formation so it is preferable to substitute a, g or c rather than t when given a choice.
- Avoid using SAMRS bases in a string of three and four consecutive identical bases. For example: ggg, ccc, aaa, ttt, gggg, cccc, aaaa, and tttt are to be avoided.
- Separate SAMRS bases with standard bases, for example: gGg, cCc, aAa, and tTt.
- If the 3’-end of an oligo is standard A or T, the second base should also be a standard base, followed by two or three SAMRS modifications.
Firebird also prepares libraries of SAMRS oligonucleotides.
SAMRS can be combined with AEGIS in oligos to get highly multiplexed and highly clean PCR, and isothermal amplification. Please inquire.
As with all primer designs, Firebird makes no guarantee as to the performance of oligonucleotides made by following these rules.
Benner et al., 2015; Glushakova et al., 2015a, 2015b; Hoshika et al., 2010; Sharma et al., 2014; Yang et al., 2015 and unpublished data