Key featuresShow Hide
- Used as a universal base to alleviate degeneracy in sequencing applications.
- The overall preferential order of base-pairing is: dI-dC > dI-dA > dI-dG = dI-dT.
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In sequencing applications, the design of primers can be complicated by the degeneracy of the genetic code (there are 64 possible 3-base codon configurations and only 21 amino acids, and therefore the third base in a sequence codon is often unknown). The problem of degeneracy can also be tackled by the use of universal bases.(1) Deoxyinosine is often used as a degenerate base in an oligonucleotide to alleviate this problem.(2) This is possible since its structure allows it to base pair with all four bases in various ‘wobble’ structures. However, the base-pairing is not equivalent with each of the 4 naturally occurring bases. The overall preferential order of base-pairing is: dI-dC > dI-dA > dI-dG = dI-dT. We provide both dI phosphoramidite and CPGs. 2'-Deoxynebularine(3) is another example.
In a true universal nucleoside, the base analogue 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'-deoxynucleosides were 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 applications of universal DNA base analogues, D. Loakes, Nucleic Acids Research, 29, 2437-2447, 2001.
- (a) Base pairing involving deoxyinosine: implications for probe design, F.H. Martin, M.M. Castro, F. Aboul- ela and I. Tinoco, Jr, Nucleic Acids Research, 13, 8927-8938, 1985; (b) Studies on the base pairing properties of deoxyinosine by solid phase hybridisation to oligonucleotides, S.C. Case-Green, E.M. Southern, Nucleic Acids Research, 22, 131-136, 1994.
- (a) Synthesis and properties of oligonucleotides containing 2'-deoxynebularine and 2'-deoxyxanthosine, R. Eritja, D.M. Horowitz, P.A. Walker, J.P. Ziehler-Martin, M.S. Boosalis, M.F. Goodman, K. Itakura and B.E. Kaplan, Nucleic Acids Research, 14, 8135-8153, 1986; (b) As a custom item we have prepared the phosphoramidite, see: A convenient synthesis of deoxynebularine phosphoramidite, D. Picken and V. Gault, Nucleosides, Nucleotides and Nucleic Acids, 16, 937-939, 1997. Please enquire regarding availability.
|LK2287||dU SynBase™ CPG 1000/110|
|LK2293||dI SynBase™ CPG 1000/110|
|LK2323||5-Me-dC SynBase™ CPG 1000/110|
Physical & Dilution Data
Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile (LK4050). Adjust accordingly for other concentrations. For µmol pack sizes, products should be diluted as 100µmol/ml to achieve 0.1M, regardless of molecular weight.
Couple the phosphoramidites LK2013, LK2016 and LK2017 using the standard method as recommended by synthesiser manufacturer with coupling times as per standard bases. 90s is recommended for 2529. A coupling time of 15min is recommended for LK2145. A coupling time of 3min is recommended for LK2164. The solid supports are used as per standard nucleoside supports.
For LK2013, LK2016, LK2017 and LK2529 standard oligonucleotide deprotection conditions can be applied when deprotecting an oligo containing these modifications, however LK2013, LK2016 and LK2529 are also compatible with AMA deprotection; typically 10min at 55oC.
LK2145 - Use AMA deprotection in conjunction with Ac-dC, rather than Bz-dC, or transamidation will occur. The supports are cleaved and deprotection carried out using the protocols required by the nucleobases.
LK2164 - Cleavage from support and primary deprotection is accomplished by treatment with ammonium hydroxide solution at room temperature for 24h.
After removing the solution1, the NPE groups are removed by treatment with 0.3M tetramethylguanidinium 2-nitrobenzaldoximate solution in water/dioxan (1:1) at 70°C for 48h. We find that this extended treatment is necessary to ensure complete removal of both of the NPE protecting groups.
It should be noted that this treatment generates a variety of low molecular weight by-products which are observed in the HPLC. Satisfactory results are obtained by de-salting the deprotection mixture into water using a NAP or G25 column before HPLC, from which the final oligonucleotide product can then be isolated.
Storage & Stability
Refrigerate dry compounds. Stability of phosphoramidites in solution is similar to standard dA, dC, dG and dT monomers.
- This is best achieved by removing the deprotection solution by G25 then freeze drying to remove the water. Heat cannot be used or the NPE groups would cleave.