Custom synthesis overview

Custom Synthesis Overview

Custom Single-strand RNA  
Single-strand RNA Synthesis Order
Multiple Single-strand RNA Synthesis Order
Custom siRNA  
siRNA Synthesis Order
Modified siRNA Synthesis Order
Multiple siRNA Syntheses Order
Custom SMARTpool Design & Synthesis Order
Custom microRNA  
Custom microRNA Request Quote
siDESIGN Center  
siRNA Design Tool Design Now

Single-strand RNA

Design a single-strand RNA molecule with a wide variety of chemical modifications, learn about our capabilities for long RNA oligos, dye labeling, custom amidites and more.

siRNA

Learn about customizing your siRNA with proprietary modification patterns or other chemical modifications, investigate your options for in vivo RNAi, design your own siRNA using the siDESIGN Center, learn about custom SMARTpool options and more.

microRNA

Customize a miRIDIAN Mimic or Hairpin Inhibitor, or design your own microRNA reagent with specialized chemical modifications, in vivo processing, gram quantities and more.

2'-ACE Chemistry

RNA applications can be executed with greater ease and confidence by utilizing the powerful advantages of the 2'-ACE technology.

  • Greater reproducibility than any other chemistry
  • Crude yields of unmatched purity without additional purification time and expense
  • Maximum sequence fidelity and integrity due to enhanced coupling efficiency

Download the Tech Note 2'-ACE RNA Synthesis Chemistry for more information on the details of the RNA synthesis platform.

All synthetic RNA oligos must be chemically protected at multiple sites during synthesis, regardless of the chemistry platform used. However, 2'-ACE synthesis chemistry allows for the quickest and mildest deprotection conditions compared to other chemistries like 2'-tBDMS and 2'-TOM. Short deprotection times and a mild chemical environment promote the highest level of purity for synthetic RNA in the marketplace today.

For unmodified, unpurified RNA, the following approximate percentages of full-length material can be expected:

  2'-ACE 2'-tBDMS 2'-TOM
ASCE* >99% >98% 95%
21-mer ** 81% 65% 34%
50-mer ** 61% 36% 8%
Coupling reaction Fast Slow Slow
Deprotection conditions Aqueous Organic Organic
Product can be delivered in 2'-protected or deprotected state Yes No No

2'-ACE chemistry features superior RNA synthesis quality.

custom rna synthesis image

Sequence fidelity and high yields are the hallmarks of 2'-ACE chemical synthesis

Unlike other synthesis chemistries, unmodified siRNA or RNA oligos >35 nt synthesized using 2'-ACE chemistry do not require purification prior to in vitro  applications.

sequence frequency 

Comparison of an unmodified, unpurified 36 nt RNA oligo synthesized using 2'-ACE, 2'-tBDMS, and 2'-TOM chemistry platforms. Anion exchange-HPLC traces for (A) 2'-ACE, (B) 2'-tBDMS, and (C) 2'-TOM illustrate a superior level of purity achieved with 2'-ACE chemistry. Smaller peaks eluting earlier than the full-length oligo (shaded area) are indicative of incomplete, non full-length, n-x products. Results are typical, but may vary slightly depending on oligo sequence.

*The average stepwise coupling efficiencies (ASCE) for each method.
**Percent full-length material listed above are approximate; exact yields will depend on sequence composition.

What is the difference between scale and yield?

SCALE

  • Relative amount of starting material packed into an RNA synthesis column
  • Typically expressed as micromole (µmol) increments

YIELD

  • Final amount of material delivered
  • Typically expressed as nanomole (nmol), micromole (µmol), milligram (mg), or gram (g) amounts

SCALE ≠ YIELD

Actual yields obtained for the final product may range from 10%-90% of the scale, depending on the oligo specifications (i.e. modification type, length, purification process, etc.).

If you have a minimum yield requirement for your experiments, please contact Technical Support for recommendations on which scale to select for your online order.

Available synthesis scales can accommodate microgram to multi-gram quantities

  Synthesis scales available online Synthesis scales available by request
siRNA 0.025 µmol - 10 µmol 20 µmol - 2 mmol
Single-strand RNA 0.05 µmol - 1 µmol 2 µmol - 2 mmol

For unmodified siRNA, the following approximate yields can be expected

  Standard (A4)** Purified in vivo in vivo HPLC
nmol mg nmol mg nmol mg nmol mg
0.025 µmol scale 20 0.25 - - - - - -
0.05 µmol scale 40 0.5 20 0.25 - - - -
0.2 µmol scale 150 2 80 1 100 1.3 50 0.65
0.4 µmol scale 300 4 160 2 200 2.6 100 1.3
1.0 µmol scale 750 10 320 4 500 6.6 200 2.6
2.0 µmol scale 1500 20 640 8.5 1000 13 500 6.6
5.0 µmol scale 3750 50 1600 21 2505 33 1000 13
10.0 µmol scale 7500 100 3200 42 5000 66 2500 33

For single-strand RNA, yields may vary greatly depending on the specifications of your request (oligo length, sequence, modifications, purification, ect.). Please contact Technical Support for RNA yield estimates.

*Yields reported above should be considered estimates, and are not guaranteed amounts. Please inquire within if a minimum guaranteed amount is required.
"**Standard processing includes 2'-ACE deprotection, desalting, and annealing.

Quality Control

We pride ourselves on our reputation for high quality RNA synthesis.

As part of our long-standing commitment to quality, we employ the following standards for quality assurance:

  • All RNA synthesis products (including siRNAs) are analyzed by mass spectrometry and quantified by UV spectroscopy
  • ESI MS for all modified siRNAs and all longer or highly modified RNAs
  • HPLC or PAGE for purification of RNA products
  • UPLC or CGE for quality analysis when appropriate
  • Custom QC methods and documentation are available upon request

See below for definitions

Quality control documentation available upon request includes:

  • Mass spectrometry traces
  • UPLC or CGE analysis
  • Duplex or individual strand purity analysis
  • Certificate of Analysis
  • Endotoxin certification
  • Custom QC documentation

For all mid-scale synthesis projects (200 mg - 10 g), a stringent manufacturing process is adhered to

  • HPLC purification highly recommended to achieve optimal purity
  • Batch records maintained on all synthesis projects (we follow GMP guidelines, but are not GMP certified)
  • Endotoxin testing included on all mid-scale orders
  • Data deliverables include MS, UPLC, endotoxin results, and a Certificate of Analysis

Definitions:

ESI MS: Electrospray ionization mass spectrometry
HPLC: High performance liquid chrmatography
PAGE: Polyacrylamide gel electrophoresis
UPLC: Ultra performance liquid chromatography
CGE: Capillary gel electrophoresis