What are Spacer Phosphoramidites?

BOC RNA provides different spacer phosphoramidites and has been working closely with global partners in the field of nucleic acid chemistry to ensure efficient and accurate synthesis of DNA and RNA oligonucleotides.

Application of spacer phosphoramidites

Spacer phosphoramidites can be used to change the oligonucleotide conformation and/or reduce steric hindrance for applications such as aptamer and label/tag analysis detection.

Interval phosphoramidites with different atomic numbers are usually used to bridge oligonucleotide fragments
The spacer can be used in combination with 3'and 5'-amino modifiers and/or other spacers to place tags at greater distances from the oligonucleotide and reduce the gap between the oligonucleotide and the fluorescent dye interaction
The hybridization of oligonucleotides bound to the support can be increased by reducing the spatial interaction between the support and the bound oligonucleotides
The C3 spacer can be used to simulate the three-carbon gap between the 3'- and 5'-hydroxyl groups of oligonucleotides or to replace bases in the sequence when the base is unknown.

Main characteristics of spacer phosphoramidite

Spacer phosphoramidites C3, 9, C12, and 18 are used to insert spacer arms in oligonucleotides, and multiple additions can meet the needs of longer spacers.
The 3'-spacer C3 CPG can act as a blocker of exonuclease and polymerase activity at the 3'-end.
dSpacer is used to introduce stable abasic sites in oligonucleotides.
PC Spacer is a photocleavable C3 spacer modifier.

Our ability

We provide a flexible ordering model to quickly meet your order requirements, whether it is a large number of standard products or customized products. With a GLP laboratory and unique technology development, we can help you meet the ever-changing market needs.

Quality control

All products are of no animal origin, and no TSE/BSE risk.
The entire process is monitored from material procurement to final quality control and product release, providing repeatability and security between batches.
C3 spacer phosphoramidite is combined with three carbon spacers or added sequentially to form longer spacer arms.
The C18 spacer is phosphoramidite to reduce possible steric hindrance and/or to prevent exonuclease digestion.
Assess the ty of each RNA phosphoramidite batch by HPLC and ³¹P NMR.
The tightly controlled manufacturing process ensures minimal levels of impurities.

Custom services

Custom manufacturing services are available to help develop or expand phosphoramidite compounds.

If you have any questions or requirements, please feel free to contact us.

Related Products

Catalog	CAS Number	Product Name	Molecular Formula	Molecular Weight	Price
BRP-00231	125607-09-2	Spacer Phosphoramidite 18	C42H61N2O10P	784.93	Inquiry
BRP-02121	83379-46-8	D-Glucose-[2-13C,2-d1]	C5[13C]H11DO6	182.15	Inquiry
BRP-02204	129821-76-7	dSpacer-CEP	C35H45N2O6P	620.71	Inquiry
BRP-02205	158665-27-1	Spacer C12 CE Phosphoramidite	C42H61N2O5P	704.93	Inquiry
BRP-02211	146668-73-7	Spacer Phosphoramidite 9	C36H49N2O7P	652.77	Inquiry
BRP-02212	653575-45-2	PC Spacer Phosphoramidite	C43H53N4O8P	784.88	Inquiry
BRP-02213	110894-23-0	C3-Spacer-CEP	C33H43N2O5P	578.68	Inquiry
BRP-02241		3'-Spacer C3 CPG			Inquiry

Frequently Asked Questions (FAQ)

What are spacer phosphoramidites used for in oligonucleotide synthesis?

Spacer phosphoramidites introduce flexible arms into DNA or RNA sequences, altering conformation, reducing steric hindrance, and improving aptamer or label/tag accessibility.

How do different spacer lengths, such as C3, C12, or C18, affect oligonucleotide function?

Shorter spacers like C3 simulate small gaps between nucleotides, while longer spacers (C12, C18) reduce steric hindrance, increase hybridization efficiency, or protect ends from exonuclease activity.

Can spacer phosphoramidites be combined with other modifiers?

Yes, they can be used with 3' or 5'-amino modifiers, fluorescent dyes, or multiple spacers sequentially to achieve precise spatial positioning of functional groups or reporter tags.

What is the role of photocleavable (PC) spacers in oligonucleotide design?

Photocleavable spacers allow controlled release of oligonucleotides or tags under light exposure, enabling temporal or spatial regulation in molecular assays.

How is quality controlled in spacer phosphoramidite production?

Each batch undergoes HPLC and 31P NMR analysis to ensure high purity, minimal impurities, and reproducibility, with tightly monitored processes from material procurement to product release.

Are custom spacer phosphoramidites available for specialized applications?

Yes, BOC RNA provides flexible custom manufacturing to develop novel spacers or tailor spacer length and chemistry to specific oligonucleotide synthesis requirements.

* Only for research. Not suitable for any diagnostic or therapeutic use.