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5'-DMT-dI-Suc-CPG (5'-DMT-deoxyInosine CPG) Column

5'-DMT-dI-Suc-CPG (5'-DMT-deoxyInosine CPG) Column

CPG used to incorporate a deoxyinosine base into the 3' end of an oligonucleotide.

Key features

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  • 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.
  • CPG has aminopropyl-succinyl linker.
  • 1000 Å CPG suitable for highly modified oligonucleotides (> 20mers).
  • Available in different column formats.
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Option 2: Select a Column Type
Option 3: Select a Scale
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Product information

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. 

Ref:

  1. The applications of universal DNA base analogues, D. Loakes, Nucleic Acids Research, 29, 2437-2447, 2001.
  2. (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.
  3. (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.
Synthesizer
Column
Type/Description
Notes
MerMade 6,12
MerMade, syringe (all scales)
Pipette type column
A MerMade column is also known as a Supercolumn
MerMade 4, 48X, 96E, 192E, 192X
MerMade, Syringe (up to 1.3 mL)
Pipette type column
A MerMade column is also known as a Supercolumn
ABI 384 / 394
Luer
Barrel column with luer fitting at either end
Also known as ALL-FIT or Standard
Expedite 8909
Luer
Barrel column with luer fitting at either end
Also known as ALL-FIT or Standard
ABI3900
MerMade
Pipette type column
A MerMade column is also known as a Supercolumn
K&A H4, H8, H8SE, H2, H32, H64
Luer
Barrel column with luer fitting at either end
Also known as ALL-FIT or Standard
K&A S4CL/S8CL
Luer
  Barrel column with luer fitting at either end 
 Also known as Standard. For this instrument, we recommend the Luer (Standard) column as the ALL-FIT columns have a wider barrel.
Dr Oligo 48
MerMade
Pipette type column
A MerMade column is also known as a Supercolumn
 Dr Oligo 192XLc, 768XLc just plates 
 MerMade, Syringe (up to 1.3 mL) 
Pipette type column
A MerMade column is also known as a Supercolumn
 OligoMaker X12, 48, 192, X192, X96 
MerMade, Syringe (up to 1.3 mL)
Pipette type column
A MerMade column is also known as a Supercolumn

Properties:

  • Appearance: White powder

Product usage:

  • Cleavage conditions: Use concentrated ammonia for 90 minutes at 25 °C when using standard amidites or 1:1 ammonia:methylamine (AMA) for 25 minutes at 25 °C when using fast deprotecting amidites.
  • Deprotection conditions: When using fast deprotecting amidites (eg. C-Ac, G-DMF) use concentrated ammonia for 1 hour or AMA for 30 minutes at 60 °C. When using standard amidites (eg. C-Bz, G-iBu) use concentrated ammonia for 5 hours at 60 °C.
  • Image of cleaved and deprotected structure:
  • The mass this product adds after conjugation and work-up (the additional mass seen by mass spectrometry) is: 314.19

Storage and handling:

  • Shipping conditions: Ambient
  • Storage conditions: +2 to +8 °C in sealed container

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