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Spacer Modifications

Conveniently introduce spacer modifications into your oligonucleotide during synthesis with our high-quality spacer phosphoramidites and solid supports.

Adding a spacer adds distance between your sequence and a modifier to reduce the possibility of adverse interactions (e.g., unwanted quenching) and to bolster conjugation efficiency, as well as the efficiency of an oligo in its intended application.

LGC, Biosearch Technologies offers spacer phosphoramidites and solid supports to introduce hydrophilic, hydrophobic, or photocleavable spacers, available in varying lengths, into your oligo.

Hydrophilic and Hydrophobic Spacers

Whether you need a hydrophilic or hydrophobic spacer depends on the application of the modified oligonucleotide. Incorporating multiple hydrophilic or hydrophobic spacers of varying lengths allows you to control the precise length of the spacer arm—which can be important in DNA hairpin loop and duplex studies.

Several spacers have specific uses

Spacer C3 phosphoramidite (NACM1-017) mimics the three carbon spacing between the 3’ and 5’ hydroxyls of sugar units. This spacer is useful when the base at a specific site is unknown; however, the flexibility of the alkyl chain distorts the sugar-phosphate backbone.

dSpacer (NACM1-013) mimics abasic sites and is useful for studying mutations resulting from depurination. dSpacer sits directly into the natural sugar-phosphate backbone with no adverse effects.

It can be advantageous to remove the modifier from the oligonucleotide using a photocleavable spacer.

An appropriate use of a photocleavable spacer includes when you are using biotin as a means of capture, and the target is bound to the biotin labelled probe. The target-bound biotin labelled probe can be captured using a streptavidin affinity column and the target-probe duplex can be eluted by applying light to trigger the photocleavable spacer (NACK1-003).

Although less common than terminal spacing, spacers can be incorporated within an oligonucleotide to add distance between sections of the sequence.

Cytocell’s SMART detection assay uses spacer 18 or Hexadecyl-Glyc (HEG) in the template probe, adding flexibility to facilitate one section of the the oligo acting as an anchor for binding to a target and leaving the other section free for hybridisation to an extension probe.

Scorpions™ Primers use HEG to separate the probe and primer section of an oligo, allowing the probe to flip back to hybridise to the amplicon as well as block PCR to prevent read through to the probe.

3’-Spacers are often used as an alternative to 3’-phosphate as blockers.

Incorporating spacers at the 3’-end generates oligonucleotides with nuclease and polymerase resistance. Spacer C3 is often incorporated at the 3’-end of an oligonucleotide for use with restriction enzymes rather than phosphate since the latter is thought to partially cleave during the assay.