Spacer Modified Oligonucleotide, Spacer Modification Oligo Synthesis

Bio-Synthesis offers a number of different Spacer Modified Oligonucleotide Synthesis for both DNA and RNA oligonucleotide. These spacers differ in number of atoms and are typically used to create distance between a functional moiety and the hybridizing region of an oligonucleotide. Spacers are also often used when there is a concern about steric hindrance between the oligonucleotide and the desired functional group interaction or as a blocking group when oligonucleotide extension is not desired . Spacer modifiers can be incorporated into oligonucleotide during chemical synthesis using C3, C12, hydrophilic PEG spacer 18. They can be inserted in the multiple additions when a longer spacer is required especially when coupling an enzyme or antibody to an oligonucleotide, where there is a need to add a hydrophilic spacer such as spacer 18 to optimize the coupling reaction. Addition of a spacer at 3' end may also act as a blocker of exonuclease and polymerase activity at the 3'-terminus. dSpacer is used to introduce a stable abasic site within an oligonucleotide. Photocleavable PC Spacer modifier is available to be modified during oligonucleotide synthesis.

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Description Quality Services Resources How to Order

Spacers modifications impart a number of desirable benefits:

Reduce interaction by creating greater distance: : Spacers can be used in conjunction with 3' and 5'-amino-modifiers and/or additional spacers to place tags at greater distances from the oligonucleotide and reduces interaction between the oligonucleotide and the fluorescent dye¹.
Reduce steric interaction: Spacer can increase hybridization to a support bound oligonucleotide by reducing steric interaction between support and bound oligo² .
Base mimic: The C3 spacer can be used to mimic the three carbon spacing between the 3'- and 5'-hydroxyls of the oligonucleotide³ or replace a base within a sequence when the base is unknown.
Abasic mimic: dSpacer modified oligonucleotide can be used to mimic abasic sites within an oligonucleotide. It is known to undergo β-elimination reactions and lead to single strand scission of DNA^4,5

Type of Spacer Modifier

Spacers C₃, C₆ and C₁₂ spacers contain an aliphatic linker which can be added to oligos requiring long spacer arms. In general, spacers are used during oligonucleotide synthesis to introduce a longer arm into the sequence, bridging sections of an oligonucleotide.
C₆, C_16-6, C_18-6 disulfide phosphoramidites contain a disulfide linker which can be added to oligos requiring disulfide spacer arms.
Polyethylene glycol PEG 9, 12, or atom 18 spacer, commonly known as HEG can be added to oligos requiring hydrophilic spacer arms.
Abasic and dSpacers are used to introduce a stable abasic site within an oligonucleotide.
Hexadecane and octadecane phosphoramidites are hydrophobic.

Purification

Desalting or cartridge purification is acceptable for spacer modified oligonucleotide. However, additional purification by HPLC is strongly recommended.

Quality Controls:

Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD₂₆₀ In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

Reference:

1. Trawick, B. N.; Osiek, T. A.; Bashkin, J. K. (2001) Bioconjugate Chem. 12, 900.
2. Takeshita, M.; Chang, C. N.; Johnson, F.; Will, S.; Grollman, A.P. (1987) J. Biol. Chem. 262, 10171.
3. Kalnik, M.W.; Chang, C.N.; Grollman, A. P.; Patel, D.J. (1988), Biochemistry 27, 924
4. Sproat, B. S.; Beijer, B. S.; Rider, P.; Neuner, P. (1987) Nucleic Acids Research, 15, 4837.
5. Hermanson, G. T. Bioconjugate Techniques, Acedemic Press, San Diego.

Product	Code	5'	Internal	3'	Function
C3 Spacer	[SpC3]	Y	Y	Y	Introducing linker arm, prevent enzymatic degradation, a DNA abasic site, an effective chain terminator
C6 Spacer	[SpC6]	Y	Y	Y	Introducing linker arm
C12 Spacer	[SpC12]	Y	Y	Y	Introducing linker arm
Spacer 9	[Sp9]	Y	Y	Y	Introducing linker arm, hydrophilic spacer
Spacer 18 (hexaethyleneglycol)	[Sp18]	Y	Y	Y	Introducing linker arm, hydrophilic spacer
dSpacer (Abasic furan)	[dSp]	Y	Y	Y	DNA abasic site, prevent enzymatic degradation
ribospacer rSpacer	[rSp]	Y	Y	Y	RNA abasic site, prevent enzymatic degradation
Photocleavable PC Spacer	[PLC]	Y	Y	N	photocleavable spacer

Purification

Desalting or cartridge purification is acceptable for spacer modified oligonucleotide. However, additional purification by HPLC is strongly recommended.

Quality Controls

Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

Cleavage Protocol

Optimal cleavage is obtained with exposure to long-wave UV light in the 300-350 nm spectral range. Cleavage releases the oligo with a 5'-phosphate group.

Technical Resources

Ordering & Contact Information

Please contact us for additional information or send an email to info@biosyn.com.
You may also request an online quote.
To contact us by phone, please Call 972-420-8505 (USA) 800-227-0627 (INTL.) or Fax 972.420.0442
Orders may be placed using a purchase order (PO) or by credit card through our secure online ordering system.
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Spacer Modified Oligonucleotide