RNA Modifications, Labeling & Conjugation

2'-Fluoro (2'-F) modifications provide the highest level of nuclease resistance among standard modifications. For maximum protection, we recommend combining 2'-F with phosphorothioate (PS) backbone modifications. LNA also offers excellent stability with the added benefit of increased binding affinity. For most therapeutic applications, an alternating pattern of 2'-OMe and 2'-F with terminal PS linkages provides the optimal balance of stability, potency, and cost.

Yes, multiple modifications can be combined on a single RNA molecule. In fact, this is often recommended for optimal performance. Common combinations include: 2'-OMe/2'-F alternating patterns with 3' cholesterol conjugation for in vivo siRNA; 5' phosphorothioate with internal 2'-F modifications for antisense oligonucleotides; and 5' GalNAc with 2'-MOE modifications for liver-targeted therapeutics. Our scientists can help design the optimal modification pattern for your specific application.

Choice depends on your detection method and experimental needs: FAM (green, 495/520nm) is ideal for qPCR and flow cytometry with standard FITC filters; CY3 (yellow, 550/570nm) offers good photostability for microscopy and is compatible with TRITC filters; CY5 (far-red, 649/670nm) is preferred for in vivo imaging due to reduced tissue autofluorescence and deeper penetration. For multiplexing experiments, FAM/CY5 or CY3/CY5 pairs work well. Consider spectral overlap with your existing filter sets when selecting fluorophores.

GalNAc (N-acetylgalactosamine) is a trivalent carbohydrate ligand that binds to the asialoglycoprotein receptor (ASGPR) highly expressed on hepatocytes. It enables targeted delivery of siRNA to the liver with subcutaneous administration, achieving potent gene silencing at low doses (1-5 mg/kg). Use GalNAc conjugation for liver-targeted applications such as metabolic disease, infectious disease, or liver cancer studies. It is not suitable for extrahepatic targets. The conjugation is typically placed at the 3' end of the sense strand or via a linker at the 5' end.

Chemical modifications can affect siRNA potency depending on position and type. 2'-OMe modifications generally maintain or slightly improve potency while reducing immunogenicity. 2'-F modifications may slightly increase potency due to higher binding affinity. LNA modifications significantly increase Tm but should be used sparingly (1-2 per strand) to avoid off-target effects. Phosphorothioate modifications have minimal impact on potency. The seed region (positions 2-8 of the guide strand) is most sensitive to modifications. Our design algorithms optimize modification placement to preserve silencing activity.

Standard turnaround times are: Unmodified RNA (5-7 business days), Single modification type (7-10 business days), Complex modification patterns (10-14 business days), and GMP-grade modified RNA (4-6 weeks). Rush services are available for most modification types with 50% surcharge. Large-scale synthesis (>100mg) may require additional time. Each batch includes comprehensive QC including MS verification of modification incorporation, HPLC purity analysis, and endotoxin testing. Expedited shipping options are available worldwide.