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rC (Ac) CPG

rC (Ac) CPG

CPG for incorporation of unmodified ribo-C at 3' end of an oligonucleotide.
  • CPG has long-chain alkylamino succinyl linker
  • Available in different pore sizes
  • Available in smaller pack sizes suitable for research use
Option 1: Select a Pore Size
Option 2: Select a Functional Loading
Option 3: Select a Size
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Product information

Controlled Pore Glass (CPG) has been widely used as a solid support for oligo synthesis for several decades. LGC, Biosearch Technologies’ has perfected CPG manufacture for maximum oligo purity and yield. Our advanced CPG production techniques improve control of particle size and shape, pore size, pore volume, and specific surface area. These physical parameters influence solution exchange behaviour, ligand loading and distribution, and reaction kinetics to increase the efficiency, purity, and reproducibility of syntheses.

We have developed proprietary chemical attachment procedures to further optimise ligand distributions, providing increased accessibility to synthesis reagents and washing solutions and facilitating even better oligo yields and purities. Furthermore, process refinements and proprietary assays have been developed to minimise the troublesome “N-1” impurity levels in an oligo synthesis.

LGC, Biosearch Technologies’ Prime CPG is considered to be the gold-standard solid support used in all sectors of the market. Our collaborative process has resulted in solid supports that are optimised for the synthesis of the latest therapeutic oligo classes including LNA, delivery enhancing lipid ligands, siRNA and Spiegelmers.

Our CPG RNA solid supports are available in a variety of pore sizes and functionalised nucleoside loadings. Which pore size and loading required is dependent on the length, complexity and application of the oligo.

In general, large scale oligo synthesis for therapeutic applications requires high loaded 500-600 Å and small to medium scale synthesis for diagnostic or research use require higher pores sizes.

Pore size Optimal oligo length Capabilities
500 Å and 600 Å ≤ 30mers
  • Suitable for high yield applications such as therapeutic oligos
  • 500 Å CPG can load up to ~100 μmol/g
1000 Å > 20mers
  • Suitable for highly modified oligonucleotides
  • modifier CPGs are functionalised onto this pore size as standard
2000 Å > 80mers
  • Can be used for CRISPR applications
  • Retains higher loading (yield) possibilities of lower pore sizes
3000 Å > 80mers
  • Can be used for CRISPR applications
  • Performs well for very long sequences > 120mers

Aside from Prime CPG, many research-use CPG products are also available which originated from the legacy portfolios, including SynBase™ CPGs. These CPGs are manufactured from the same glass as the Prime products, using similar processes, but generally offered in smaller pack sizes for research purposes.

SynBase RNA CPG loading options

Product Average Pore Size (Å) Nominal Particle Size (µm) Nucleoside Loading (µmol/g)
SynBase™ CPG 1000/110 1000 110 25-40
SynBase™ CPG 3000/110 3000 110 10-25

Linkers

In our RNA CPG products, the long-chain alkyl amino succinyl linker (CNA) is the most common (denoted by “CNA” in Prime CPG product names and also used in SynBase products), although the aminopropyl (AMP)-succinyl combination allows for smaller pore sizes (denoted by “AMP” in Prime CPG product names and is the standard linker combination in the non-Prime/SynBase products).

Protection strategies

Nucleobase protection options are similar to those of the RNA Phosphoramidites, i.e. classic (Bz-A, Bz-C and iBu-dG), UltraMILD (phenoxyacetyl (Pac)-A, acetyl (Ac)-C, and iso-propylphenoxyacetyl (iPr-Pac)-G), or Fast utilising Ac-C, Bz-A and dimethylformamidine (dmf)-G.

There are some differences in 2’-OH protection options:

Products 2’-OH Protection Notes
Prime CPG TBDMS Classic RNA chemistry
2’-OAc Prime CPG O-Acetyl Cleaves to give 2,3’-diol avoiding possibility of 2’ to 3’ migration sometimes seen with TBDMS
SynBase CPG Bis-succinate Cleaves to give 2,3’-diol avoiding possibility of 2’ to 3’ migration sometimes seen with TBDMS
Others TBDMS as standard Classic RNA chemistry

Isomers

The standard stereochemistry is the D-diastereoisomer.

Applicable Products

LK2033 dmf-G-CE Phosphoramidite
LK2036 Bz-A-CE Phosphoramidite
LK2037 Pac-A-CE Phosphoramidite
LK2038 Ac-C-CE Phosphoramidite
LK2039 iPr-Pac-G-CE Phosphoramidite
LK2040 U-CE Phosphoramidite
LK2053 Ac-G-CE Phosphoramidite
LK2091 5-Me-U-CE Phosphoramidite (ribo-T)
LK2295 U-SynBase™ CPG 1000/110
LK2309 Ac-C-SynBase™ CPG 1000/110
LK2318 dmf-G-SynBase™ CPG 1000/110
LK2319 Pac-A-SynBase™ CPG 1000/110
LK2320 iPr-Pac-G-SynBase™ CPG 1000/110
LK2321 Bz-A-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.

Item

Mol. Formula

Mol. Wt.

Unit Wt.

250mg

500mg

1g

LK2033 C49H67N8O8PSi 955.18 345.21 2.62 5.23 10.47
LK2036 C53H66N7O8PSi 988.21 329.21 2.53 5.06 10.12
LK2037 C54H68N7O9PSi 1018.23 329.21 2.46 4.91 9.82
LK2038 C47H64N5O9PSi 902.11 305.18 2.77 5.54 11.09
LK2039 C57H74N7O10PSi 1076.31 345.21 2.32 4.65 9.29
LK2040 C45H61N4O9PSi 861.06 306.17 2.90 5.81 11.61
LK2053 C48H64N7O9PSi 942.14 345.21 2.65 5.31 10.61
LK2091 C46H63N4O9PSi 875.09 320.19 2.86 5.71 11.43
LK2295 - - 306.17 - - -
LK2309 - - 305.18 - - -
LK2318 - - 345.21 - - -
LK2319 - - 329.21 - - -
LK2320 - - 345.21 - - -
LK2321 - - 329.21 - - -

Coupling

The steric hindrance introduced by the additional 2’-protecting group reduces the coupling efficiency of the phosphoramidite, and is limited to >97% using tetrazole activator even with extended reaction times. When using 0.25M ETT (LK3140/LK3142), to optimise efficiency a 12min coupling time is recommended. It has been shown that this coupling time can be reduced to 3min when using 0.3M BTT as the activator (LK0234/LK3160/LK3162).

Cleavage & Deprotection

Removal of the base protecting groups, cleavage of the linkage to the support and removal of the ß-cyanoethyl groups are all achieved routinely with aqueous 20% NH3/methylamine (1:1). The cleavage is fast (10-30min) at 65°C. (Heating can be continued up to 1h, however prolonged treatment will cause gradual loss of TBDMS groups resulting in degradation.) The deprotection strategies used are dependent on the base-protection utilised. Bz-A (LK2036), dmf-G (LK2033), Ac-C (LK2038) and Ac-G (LK2053) can also be deprotected using AMA (1:1 ammonium hydroxide solution in aqueous methylamine) at 65°C for 10min, however it should be noted that the use of ethanol in the deprotection solution aids solubility for full RNA sequences. When synthesising RNA chimera, e.g. RNA/DNA or RNA/2’-OMe RNA, the C amidite cannot be Bz protected otherwise deprotection with AMA will result in transamidation.

Pac-A (LK2037), iPr-Pac-G (LK2039) and Ac-C (LK2038) can be deprotected using UltraMILD conditions such as 0.05M potassium carbonate in methanol at room temperature for 4h.

Desilylation

The desilylation procedure is the same for DMT ON and DMT OFF oligos. Suspend the residue in dry N-methyl pyrrolidone/Et3N/Et3N.3HF (6:3:4 v/v/v) and deprotect silyl groups for 2.5h at 65°C in a sealed sterile tube. Alternatively, DMSO (or DMF)/Et3N.3HF (3:1 v/v) can be used.

Detritylation & Purification

Retaining the DMTr group after oligonucleotide synthesis is advantageous to the purification of RNA. This allows failures with no 5’-DMTr protection to be easily removed from the crude mixture. Traditionally this was carried out by RP-HPLC where the full-length DMTr-protected oligonucleotide was collected then detritylated using 10% acetic acid at pH 3.5 (30-45min) then quenched with ammonium bicarbonate followed by desalting.

Today it is possible to carry out the purification by RP-HPLC which includes the detritylation step and the full-length detritylated product is collected. Also, cartridge purification - e.g. TOPS, PolyPak or GlenPak - allow fast processing of oligonucleotides where DMTr-oligos are loaded onto the column and the full-length detritylated product eluted. This is particularly useful in preventing cross contamination since a new column is used for each oligo. DMT-ON purification, although useful, does not remove the N-1 sequences where the DMTr protection is retained. In this case cartridge purification can be useful to remove all other failures prior to purification by IE-HPLC. The latter is also the recommended method for purification of RNA where the DMTr group has been removed, or where the sequence is longer (≥40 bases). The most commonly used IE columns for purifying RNA are Dionex DNA-PAC (100 or 200) columns although there are alternatives from Phenomenex and other suppliers.

Typical buffers are:

Anion-exchange HPLC—A: 20mM aqueous Tris-HCl pH 7.6 + 1mM EDTA + 10mM sodium perchlorate; B: As A with 600mM sodium perchlorate. This system may require alteration for longer oligos.

RP-HPLC—A: 95% 0.1M triethylammonium acetate (TEAA) + 5% acetonitrile; B: 95% acetonitrile + 5% water (or 5% 0.1M TEAA). Gradient of 0-50% B during 20min.

Much longer oligos are best synthesised DMT-OFF and purified by PAGE.

Storage & Stability

All solid phosphoramidites and RNA supports are stored dry in a freezer at –10 to –30°C. The phosphoramidites are stable in anhydrous acetonitrile solution for 24h (LK2091 can be stored for 2-3 days).

Unlike DNA, RNA is highly unstable in basic media and must not be exposed to high pH. Traces of heavy metal ions present in various salts used also lead to degradation. Buffers containing 1mM EDTA are used to prevent this.

RNA is very sensitive to degradation by nucleases. All glass (and plastic) used must be rinsed in water containing diethylpyrocarbonate (DEPC) (2%) and autoclaved before re-use. All reagents, water and consumables used in subsequent handling must be sterile and certified RNAse free. Anion-exchange and desalting columns should be stored in sterile water/acetonitrile (1:1), except Q-res type which should be stored in water/ethanol (4:1).

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