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Linkers play a vital role in oligo synthesis, specifically in two main applications:

 

Solid Phase Attachment: During oligonucleotide synthesis, a linker molecule covalently attaches the growing oligonucleotide chain to a solid support. This solid support is typically a controlled-pore glass (CPG) bead. The linker offers a stable bond to the solid phase, allowing for the stepwise addition of nucleotides to create the desired oligonucleotide sequence. After synthesis is complete, the linker is cleaved under specific conditions, releasing the purified oligonucleotide from the solid support.

 

Bioconjugation: Linkers can also be incorporated at either the 5' or 3' terminus of the oligonucleotide to facilitate conjugation with various biomolecules. These biomolecules can include fluorophores, quenchers, antibodies, nanoparticles, or other functional groups. Bioconjugation allows researchers to attach functionalities to the oligonucleotide, enabling diverse applications such as:
• Fluorescence in situ hybridization (FISH) for cellular imaging
• Detection of specific nucleic acid sequences
• Immunoassays
• Drug delivery

 

There are various types of linkers available for oligo synthesis, each with unique properties and functionalities. Some common linker types include:


• Cleavable Linkers: These linkers are designed to be cleaved from the solid support under specific conditions, such as exposure to acid or base. This allows for the release of the purified oligonucleotide.
• Non-Cleavable Linkers: These linkers form a permanent bond with the solid support. While the oligonucleotide remains tethered to the solid phase, non-cleavable linkers are useful for applications like microarrays where the oligos stay attached to the surface.
• Biotinylated Linkers: These linkers contain biotin, a small molecule that can bind to streptavidin with high affinity. This property allows for easy purification of the oligonucleotide using streptavidin-coated magnetic beads.
• Fluorescent Linkers: These linkers incorporate a fluorescent moiety, enabling the direct detection of the labeled oligonucleotide.

 


The choice of linker in oligo synthesis depends on the desired application and the downstream processes involved.

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ON-093.svg

6-MMT-NH-Hexanol

Catalog No. ON-093
Molecular Formula: C26H31NO2
ON-152.svg

N6-Tr-6-amino-hexanol

Catalog No. ON-152
Molecular Formula: C25H29NO
ON-130.svg

DMT-hydroxymethyl-hexyl-phthalimide

Catalog No. ON-130
Molecular Formula: C36H37NO6
ON-153.svg

TEG linker

Catalog No. ON-153
Molecular Formula: C36H37NO6
ON-154.svg

TEG Linker2

Catalog No. ON-154
Molecular Formula: C33H45NO8
ON-155.svg

6-N3-1-hexanol

Catalog No. ON-155
Molecular Formula: C6H13N3O
CAS No. 146292-90-2
ON-156.svg

6-amino(Fmoc)-2-hydroxymethylhexan-1-ol

Catalog No. ON-156
Molecular Formula: C22H27NO4
ON-214.svg

DMT-Hexylamine-linker Phosphoramidite

Catalog No. ON-214
Molecular Formula: C36H50N3O4P
OP-065.svg

1-O-DMTr-Glycerol-TEG-Cholesterol-2-CE-Phosphoramidite

Catalog No. OP-065
Molecular Formula: C68H103N2O10P
ON-224.svg

Fmoc-aminopropyloxy-3-DMTr-glycerol

Catalog No. ON-224
Molecular Formula: C42H43NO7
ON-283.svg

TFA-EO Linker

Catalog No. ON-283
Molecular Formula: C7H8F3NO2
ON-267.svg

1, 3-Di-DMT Glycerol succinate, TEA salt

Catalog No. ON-267
Molecular Formula: C49H48O10
OP-020.svg

DMTr-Cholesteryl-TEG Phosphoramidite (plant source)

Remarks: Plant Source
Catalog No. OP-020
Molecular Formula: C70H106N3O11P
ON-371.svg

N-(Boc-aminoethyl)-Gly-oEt

Catalog No. ON-371
Molecular Formula: C11H22N2O4
ON-373.svg

Diethyl 2-(4-chlorobutyl)malonate

Catalog No. ON-373
Molecular Formula: C11H19ClO4
ON-374.svg

(R)-2-amino-3-(bis(4-methoxyphenyl)(phenyl)methoxy) propan-1-ol

Catalog No. ON-374
Molecular Formula: C24H27NO4
OP-064.svg

DFA-AH Linker Amidite

Catalog No. OP-064
Molecular Formula: C17H32F2N3O3P
OP-055.svg

Phenylacetyl HA amidite linker

Catalog No. OP-055
Molecular Formula: C23H38N3O3P
ON-173.svg

Fmoc-AEG-OMe•HCl

Catalog No. ON-173
Molecular Formula: C20H23ClN2O4
ON-172.svg

Fmoc-AEG-OH•HCl

Catalog No. ON-172
Molecular Formula: C19H21ClN2O4
CAS No. 172405-44-6
ON-379.svg

Ethyl-γ-(N-(3-hydroxypropyl)anilino)-butyrate

Catalog No. ON-379
Molecular Formula: C15H23NO3
ON-380.svg

Propargyl-PEG2-NH2

Catalog No. ON-380
Molecular Formula: C7H13NO2
ON-381.svg

6-amino(Fmoc)-1-O-DMT-2-hydroxymethylhexan-1-ol

Catalog No. ON-381
Molecular Formula: C43H45NO6
ON-382.svg

N-Fmoc-2-(2-aminoethoxy)ethanol

Catalog No. ON-382
Molecular Formula: C19H21NO4
D4-034.svg

5'-DMT-dT-linker-NH2

Catalog No. D4-034
Molecular Formula: C39H46N4O8
ON-417.svg

Cholesteryl succinate, TEA salt (plant source)

Remarks: Plant Source
Catalog No. ON-417
Molecular Formula: C61H86O9 (free acid)
ON-418.svg

Cholesterol tetraethylene glycol (TetraEG) (plant source)

Catalog No. ON-418
Molecular Formula: C39H69NO7
ON-419.svg

Cholesterol tetraethylene glycol (TetraEG) amidite (plant source)

Remarks: Plant Source
Catalog No. ON-419
Molecular Formula: C48H86N3O8P
ON-420.svg

Cholesteryl-TEG-succinate (plant source)

Remarks: Plant Source
Catalog No. ON-420
Molecular Formula: C65H93NO13 (free acid)
CAS No. 873435-28-0
ON-422.svg

Cholesteryl amidite (plant source)

Remarks: Plant Source
Catalog No. ON-422
Molecular Formula: C68H103N2O10P
ON-423.svg

Cholesterol-TEG CPG 500Å (plant source)

Remarks: Plant Source
Catalog No. ON-423
Molecular Formula: C65H94N2O12
ON-424.svg

Cholesterol-TEG CPG 1000Å (plant source)

Remarks: Plant Source
Catalog No. ON-424
Molecular Formula: C65H94N2O12
ON-421.svg

Cholesterol-TEG

Catalog No. ON-421
Molecular Formula: C61H89NO10
CAS No. 869354-69-8
OP-168.svg

n-Butyl-2-cyanoethyl-N, N-diisopropylphosphoramidite

Catalog No. OP-168
Molecular Formula: C13H27N2O2P
OP-171.svg

MMTr C3 linker Phosphoramidite

Catalog No. OP-171
Molecular Formula: C32H42N3O3P
OP-172.svg

NHMMTr-C4 Phosphoramidite

Catalog No. OP-172
Molecular Formula: C33H44N3O3P
OP-173.svg

NHMMTr-C5 Phosphoramidite

Catalog No. OP-173
Molecular Formula: C34H46N3O3P
OP-174.svg

NHMMTr-C7 Phosphoramidite

Catalog No. OP-174
Molecular Formula: C36H50N3O3P
OP-182.svg

Spacer C12 Phosphoramidite

Catalog No. OP-182
Molecular Formula: C42H61N2O5P
CAS No. 158665-27-1
OP-189.svg

1, 3-di-O-DMTr-glycerol-bis-(diisopropylamino)-Phosphane

Catalog No. OP-189
Molecular Formula: C57H71N2O7P
OP-190.svg

6-O-DMTr-hexane-bis-(diisopropylamino)-Phosphane

Catalog No. OP-190
Molecular Formula: C39H59N2O4P
OP-191.svg

12-O-DMTr-dodecane-bis-(diisopropylamino)-Phosphane

Catalog No. OP-191
Molecular Formula: C45H71N2O4P
OP-192.svg

1, 3-di-O-DMTr-glycerol-CE-Phosphoramidite

Catalog No. OP-192
Molecular Formula: C54H61N2O8P
ON-407.svg

β-Mannose C4 alcohol

Catalog No. ON-407
Molecular Formula: C18H28O11
ON-408.svg

α-Mannose C4 alcohol

Catalog No. ON-408
Molecular Formula: C18H28O11
ON-402.svg

Galactose C4 alcohol

Catalog No. ON-402
Molecular Formula: C18H28O11
ON-400.svg

Glucose C4 alcohol

Catalog No. ON-400
Molecular Formula: C18H28O11
ON-439.svg

benzyl 6-aminohexanoate

Catalog No. ON-439
Molecular Formula: C20H27NO5S
ON-440.svg

Methacrylate C6

Catalog No. ON-440
Molecular Formula: C10H19NO2
ON-442.svg

2-(2-nitrophenyl)propyl imidazole-1-carboxylate

Catalog No. ON-442
Molecular Formula: C13H13N3O4
ON-449.svg

3'-thio modifier 6 S-S-DMTr-linker-succinate, TEA salt

Catalog No. ON-449
Molecular Formula: C35H44O9S2(free acid)
OP-175.svg

NHMMTr-C8 Phosphoramidite

Catalog No. OP-175
Molecular Formula: C37H52N3O3P
OP-183.svg

DMTr-hydroxymethyl hexyl-Biotin Phosphoramidite

Catalog No. OP-183
Molecular Formula: C47H66N5O7PS
ON-503.svg

N-[2-[(2-Aminoethyl)amino]ethyl]-1,2-dithiolane-3-pentanamide

Catalog No. ON-503
Molecular Formula: C12H25N3OS2
CAS No. 2855082-29-8
ON-504.svg

N2-[5-(1,2-Dithiolan-3-yl)-1-oxopentyl]-L-arginine methyl ester

Catalog No. ON-504
Molecular Formula: C15H29N4O3S2+
CAS No. 1422468-18-5
ON-528.svg

3'-thio modifier 6 S-S-DMTr-linker CPG (500Å)

Catalog No. ON-528
Molecular Formula: /
ON-526.svg

3'-thio modifier 6 S-S-DMTr-linker CPG (1000Å)

Catalog No. ON-526
Molecular Formula: /
ON-529.svg

Biotin-LC-NHS Ester

Catalog No. ON-529
Molecular Formula: C20H30N4O6S
ON-453.svg

2, 5-dioxopyrrolidin-1-yl-3-(dodecyldisulfaneyl)propanoate

Catalog No. ON-453
Molecular Formula: C19H33NO4S2
ON-491.svg

Peracetylated GalNAc PEG linker-Azide

Catalog No. ON-491
Molecular Formula: C22H36N4O12
ON-530.svg

Peracetylated GalNAc PEG linker-Amino

Catalog No. ON-530
Molecular Formula: C22H38N2O12 (free acid)
ON-546

1, 3-dioxo-2-(4-dimethoxytrityloxyhex-1-yl)isoindole-5-carboxylic acid, TEA salt

Catalog No. ON-546
Molecular Formula: C33H29NO7 (free acid)
ON-781

Benzyl N-[2-(Fmoc)aminoethyl]glycinate

Catalog No. ON-781
Molecular Formula: C26H26N2O4(free base)
CAS No. 511534-93-3
ON-783

t-butylbenzoyl biotin-NHS ester

Catalog No. ON-783
Molecular Formula: C25H31N3O6S