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rI CNA CPG

CPG for incorporation of unmodified inosine at 3' end of an oligonucleotide.

Structural Studies

Explore our wide-ranging phosphoramidites and solid supports for generating oligos that help stabilize DNA duplexes, elucidate 3D structures of DNA, investigate DNA damage and epigenetic processes, and more. Several oligo modifications are useful for studying the structure, activity and function of DNA in various biological processes. 

By partnering with LGC, Biosearch Technologies, you can get everything you need to synthesise modified oligos for your specific structural study. 

We offer a wide portfolio of phosphoramidites and solid supports to help you:

  • Generate nuclease-resistant aptamers
  • Create oligos for investigating DNA damage and epigenetic processes
  • Improve stabilization of DNA duplexes and triplexes
  • Incorporate halogenated modifications for probing 3D DNA structures 
  • Address the degeneracy of the wobble base by incorporating a universal base

Aptamers

We offer the Nap-dU CE-Phosphoramidite (NACN5-001) which can be used to incorporate functional diversity into oligonucleotides for aptamer research.

Figure 1: Chemical structures of sugar modified nucleotides used in the aptamer generation resulting in increased nuclease resistance : 2’-fluorouridine-5’-triphosphate, 2’-aminouridine-5’-triphosphate, 2’-methoxyuridine-5’-triphosphate and 4’-thiouridine-5’-triphosphate, These are currently not available from Biosearch Technologies as stock items. However, contact our Customer Service for a custom order (terms apply).

DNA Damage and Epigenetics Modifiers

At Biosearch Technologies, we offer several amidites to incorporate hydroxy, hydroxymethyl, carboxy, and formyl modifications into your oligo for studying oxidative damage and repair, methylation and epigenetics.

Once incorporated into an oligonucleotide, these modifiers represent the various products in the biochemical pathway of dC modification.

Duplex Modifiers

Stabilizing duplexes is challenging with natural bases, so we offer several modifications—as phosphoramidites and CPG—that can be incorporated into your oligo at your desired location and for your specific application.

Duplex Modifiers Description
C-5 Methyl pyrimidine Known to stabilise duplexes and enhance binding relative to the non- methylated bases.
  • Available either as N-Bz (NACN1-011) or N-Ac (NACN1-009)
  • The stabilisation properties make this a suitable modification for stabilisation of triplex strands
Amino phosphoramidites One of the simplest methods of improving duplex stabilisation is the use of 2-Amino-dA CE Phosphoramidite (2,6-diaminopurine) in place of dA. 
  • Forms an additional hydrogen bond with thymidine
  • Destabilises A-G wobble mismatches—increasing specificity
Deoxyinosine (dI) Often used as a degenerate base in an oligonucleotide to alleviate the problem of degeneracy of the genetic code. 
  • Base pairs with all four bases in various ‘wobble’ structures
  • Base-pairing is not equivalent with each of the 4 naturally occurring bases: dI-dC > dI-dA > dI-dG = dI-dT
Deoxyuridine base Used to induce mutagenic effects. 
  • Uracil-N-glycosylase (UNG) can specifically remove uracil to create abasic sites at the deoxyuridine positions
  • Used to generate site-specific strand breaks in the oligonucleotide 
Xanthosine (dX) Considered a ‘universal base’ that can pair equally well with all four natural nucleosides. 
  • The most effective monomer for incorporating dX is the 2-(4-nitrophenyl)ethyl (NPE) O2 /O6 doubly protected monomer
  • Use 2’-Deoxyxanthosine-CE Phosphoramidite (NACN1-012) as per standard protocols, with an extra deprotection reagent to remove the NPE groups

Halogenated Nucleoside Phosphoramidites and CPGs

We provide a wide range of halogenated nucleoside phosphoramidites and CPG supports, which can be used to synthesize oligos suitable for probing the three-dimensional structure of DNA by x-ray crystallography. 

5-Fluoro-deoxyuridine is a base analogue that has the potential to bind to A and G without destabilising duplex formation, and it is an alternative to using mixed bases A/G for degeneracy.

Structure and Activity Modifiers

2-Aminopurine-CE Phosphoramidite is useful for investigating structural changes, as the base is deficient in hydrogen bonding sites. It is also mildly fluorescent.

8-oxo-dG-CE Phosphoramidite can be sued to investigate the structure and activity of oligonucleotides containing an 8-oxo mutation. This is formed naturally when DNA is subjected to oxidative conditions or ionising radiation. The resulting 8-oxo modification is significant in mutagenesis and ultimately carcinogenesis.