Duplex Effects

The design of primers is frequently complicated by the degeneracy of the genetic code. Three strategies are now available to confront this problem. In the first, a mixed base addition (N) is used to form the degenerate site. This approach is best if the number of degenerate sites is small. A second option is the use of 2’-deoxyInosine or 2’-deoxyNebularine which exhibit low, but unequal, hydrogen bonding to the other four bases. The third option is the use of a universal nucleoside. In this strategy, the base analog does not hybridize significantly to the other four bases and makes up some of the duplex destabilization by acting as an intercalating agent. 3-Nitropyrrole 2’-deoxynucleoside (M) is the first example of a set of universal bases. Subsequently, 5-nitroindole was determined to be an effective universal base and to be superior to 3-nitropyrrole, based on duplex melting experiments.

The modified bases designated P and K show considerable promise as degenerate bases. The pyrimidine derivative P, when introduced into oligonucleotides, base pairs with either A or G, while the purine derivative K base pairs with either C or T. A dP+dK mix also can serve as a mixed base with much less degeneracy than dA+dC+dG+dT (N).

Mixed Base Phosphoramidites: Other pack sizes, mixed base combinations and custom doping of individual monomers are available on request.  

Also, mixed base columns are available in 0.2 and 1.0 µmole sizes on request.

15 Product Results
 
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  • dmf-isodG-CE Phosphoramidite
    dmf-isodG-CE Phosphoramidite (10-1078)
    Catalog #: 10-1078
    Formal Name: 5'-Dimethoxytrityl-O2-diphenylcarbamoyl-N6-dimethylaminomethylidene-2'-deoxyisoGuanosine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
  • dI-CPG 500
    dI-CPG 500 (20-2040)
    Catalog #: 20-2040
    Formal Name: 5'-Dimethoxytrityl-2'-deoxyInosine,3'-succinoyl-long chain alkylamino-CPG 500
  • dI-CPG 1000
    dI-CPG 1000 (20-2041)
    Catalog #: 20-2041
    Formal Name: 5'-Dimethoxytrityl-2'-deoxyInosine,3'-succinoyl-long chain alkylamino-CPG 1000
  • dU-CPG 500
    dU-CPG 500 (20-2050)
    Catalog #: 20-2050
    Formal Name: 5'-Dimethoxytrityl-2'-deoxyUridine,3'-succinoyl-long chain alkylamino-CPG 500
  • dU-CPG 1000
    dU-CPG 1000 (20-2051)
    Catalog #: 20-2051
    Formal Name: 5'-Dimethoxytrityl-2'-deoxyUridine,3'-succinoyl-long chain alkylamino-CPG 1000
 
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