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Amino-Modified Oligonucleotides

Reactive amino modifications for site-specific labeling, conjugation and bioconjugation of DNA, RNA, PNA and modified oligonucleotides.

5′ Amino 3′ Amino Internal NH2 PEG Amino Base-Specific Amino Custom Conjugation
Request a Quote View Amino Modifier Codes
Overview Selection Codes Reactions Payloads Matrix Design Related Contact
Overview

Reactive NH2 Handles for Oligonucleotide Conjugation

Amino-modified oligonucleotides contain a reactive primary amino group introduced at the 5′ end, 3′ end, or internal position of the sequence. The amino group provides a versatile handle for post-synthetic conjugation with dyes, affinity tags, peptides, proteins, polymers, nanoparticles and therapeutic research payloads.

Bio-Synthesis supports a broad range of amino modifiers, including terminal amino linkers, base-specific amino monomers, PEG amino spacers, branched amino structures and custom amino designs. The best choice depends on payload size, attachment position, steric accessibility, solubility, purification strategy and final application.

Customer-friendly design note: You do not need to know the exact modifier code before requesting a quote. Send the sequence, attachment position and desired payload; Bio-Synthesis can recommend the most appropriate amino modifier and conjugation route.

NH2
FluorophoreBiotinPeptideAntibodyPEG
Quick Selection Guide

What Do You Want to Attach?

Start with the payload. The table and matrix below help guide whether a short alkyl, longer alkyl, PEG, base-specific or branched amino modifier is most appropriate.

DYE

Fluorophore

Use [NH2-C6], [dT-NH2-C6] or PEG amino for dyes and imaging probes.
BIO

Biotin / DIG

Use [NH2-C6] for common affinity labels and capture tags.
PEP

Peptide

Use [NH2-C6], [NH2-C12] or PEG spacers depending on peptide size.
AB

Antibody

se PEG amino spacers to reduce steric hindrance and improve accessibility.
NP

Nanoparticle

Use longer alkyl or PEG spacers such as [NH2-C12] or [NH2-PEG12].
Complete Amino Modifier Tables

Amino Modifier Codes and Design Notes

The shorthand codes below can be used as customer-facing order notation, while the full modification names provide clarity for technical review. Every tab contains a populated table using the same structure: code, position, reaction, applications, notes and purification guidance.

Design insight: The optimal amino modifier depends on conjugation chemistry, desired position, linker length, steric accessibility, nucleic acid type, and the size of the intended labeling partner or immobilization surface.

Purification and review note: HPLC purification is generally recommended for amino-modified oligonucleotides, especially when the oligo will be used for post-synthetic conjugation. Highly modified, branched, PEGylated, reverse-polarity or multi-amino designs may require technical review before quote confirmation.

Click a tab below to explore amino modifier families, applications and conjugation recommendations.

Tables are grouped to keep the page easy to scan while preserving the full modifier list.

Terminal Amino Linkers (5′ and 3′)

Terminal amino handles for dye labeling, affinity tags, surface attachment and general bioconjugation.

20 modifiers
Modification Code Position / Scaffold Reaction Applications Notes
5′-Amino-Modifier C2 [5NH2-C2] 5′ terminal NHS ester, isothiocyanate Compact dye or small-ligand labeling Short terminal spacer when minimal distance is desired.
3′-Amino-Modifier C2 [3NH2-C2] 3′ terminal NHS ester Compact 3′ conjugation, surfaces Useful when 5′ end must remain unmodified.
5′-Amino-Modifier C3 [5NH2-C3] 5′ terminal NHS ester, EDC/NHS Small ligands, compact probes Short flexible terminal linker.
3′-Amino-Modifier C3 CPG [3NH2-C3] 3′ terminal NHS ester, surface coupling Surface immobilization, capture probes Common 3′ amino support format.
5′-Amino-Modifier C6 / Aminohexyl [5NH2-C6] 5′ terminal NHS ester, isothiocyanate, EDC/NHS Fluorophores, biotin, peptides, haptens Most widely used terminal amino linker; also called Ahex.
3′-Amino-Modifier C6 CPG [3NH2-C6] 3′ terminal NHS ester, EDC/NHS 3′ dyes, biotin, affinity labels Balanced spacer for 3′ conjugation.
Amino-Modifier C6 family [NH2-C6] 5′ / 3′ / format-dependent NHS ester, isothiocyanate General-purpose conjugation Use shorthand when terminal orientation is specified elsewhere.
5′-Amino-Modifier C7 [5NH2-C7] 5′ terminal NHS ester, EDC/NHS Proteins, larger labels Slightly longer than C6 for more accessibility.
3′-Amino Spacer 7-C6 [3NH2-Sp7-C6] 3′ terminal amino spacer NHS ester, surface coupling 3′ labeling, immobilization Terminal 3′ amino linker; should be grouped with terminal amino linkers, not internal spacers.
5′-Amino-Modifier C12 [5NH2-C12] 5′ terminal NHS ester, EDC/NHS Proteins, enzymes, nanoparticles Longer alkyl spacer reduces steric crowding.
3′-Amino-Modifier C12 [3NH2-C12] 3′ terminal NHS ester, EDC/NHS Surfaces, beads, macromolecules Long terminal spacer for crowded conjugation systems.
5′-Amino-Modifier C18 [5NH2-C18] 5′ terminal / custom NHS ester Specialty hydrophobic spacing Extended alkyl chain for custom designs.
5′-Amino-TEG [5NH2-TEG] 5′ terminal NHS ester, EDC/NHS Flexible terminal conjugation Triethylene glycol spacer improves flexibility.
3′-Amino-TEG CPG [3NH2-TEG] 3′ terminal NHS ester, surface coupling Protein and surface conjugation Hydrophilic terminal 3′ spacer.
Amino-Modifier Serinol [NH2-Ser] 5′ / 3′ terminal design-dependent NHS ester Long oligos, flexible amino handle Serinol-based amino strategy; useful for selected supports.
Aminoethyl Linker [NH2-C2] Terminal / custom NHS ester Very compact ligand attachment Shortest practical alkyl amino spacer.
Aminopropyl Linker [NH2-C3] Terminal / custom NHS ester Compact surface chemistry C3 spacer for short-distance attachment.
Aminobutyl Linker [NH2-C4] Terminal / custom NHS ester Specialty ligand attachment Intermediate short alkyl spacer.
Aminohexyl Linker [Ahex] Terminal / internal format-dependent NHS ester, isothiocyanate General amino linker notation Common synonym for C6 amino modifier.
3′ Amino Serinol CPG [3NH2-Ser] 3′ terminal amino support NHS ester, isothiocyanate Long oligos, flexible terminal amino attachment Serinol-based 3′ amino support; useful when alternative 3′ amino installation is preferred.

Typical choice: Use [5NH2-C6] / [NH2-C6] for most terminal dye, biotin, peptide and small-molecule conjugations. Use C12, TEG or PEG when extra distance or flexibility is needed.

Base-Specific / Internal Amino Modifiers

Base-specific, ribose/purine analog, aminoallyl and internal amino-functionalized nucleosides in one focused table.

36 modifiers
Modification Code Position / Scaffold Reaction Applications Notes
Amino-Modifier C2 dT [dT-NH2-C2] Internal dT NHS ester Short internal dye or ligand labeling Short linker attached through thymidine.
Amino-Modifier C6 dT [dT-NH2-C6] Internal dT NHS ester, isothiocyanate Internal fluorophores, FRET probes, beacons Most common base-specific internal amino modifier.
Amino-Modifier C12 dT [dT-NH2-C12] Internal dT NHS ester Large internal labels, protein-like payloads Long linker separates payload from duplex.
Amino-Modifier C6 dR [dR-NH2-C6] Internal deoxyribose / abasic NHS ester Base-free internal amino insertion, multiple labeling Abasic deoxyribose scaffold with C6 amino linker; important specialty option.
Amino dU [dU-NH2] Internal dU / U analog NHS ester DNA/RNA probe designs Uridine-like placement where dU is preferred.
Amino C6 U / RNA U [rU-NH2-C6] Internal rU NHS ester RNA dye or ligand attachment RNA uridine containing C6 amino linker.
Amino dC [dC-NH2] Internal dC NHS ester Site-specific cytidine labeling Useful when amino handle must be placed at C.
Amino dC N4 PEG3 [dC-NH2-PEG3] Internal dC NHS ester Soluble internal dC-linked labeling PEG-containing amino dC improves accessibility.
Amino dA [dA-NH2] Internal dA NHS ester Specialty structural designs Useful when amino handle must be placed at A.
Amino Deoxyadenosine dA C6 [dA-NH2-C6] Internal dA NHS ester dA-linked conjugation Deoxyadenosine analog with C6 amino linker.
N2-Amino dG [N2-dG-NH2] Internal dG NHS ester / specialty Guanine-position labeling, structure studies Specialized guanine amino placement.
Amino C6 dG [dG-NH2-C6] Internal dG NHS ester Defined dG-linked amino placement Guanine-linked amino functionality.
2′-Amino-C [2NH2-C] Ribose-modified cytidine Specialty coupling / post-synthetic design Modified RNA/DNA architecture 2′-amino cytidine analog; not simply a terminal linker.
2′-Amino-U [2NH2-U] Ribose-modified uridine Specialty coupling / post-synthetic design RNA-related modification strategy 2′-amino uridine analog for modified RNA or chimeric designs.
2′-Amino-2′-deoxyuridine [2NH2-dU] 2′-modified dU Specialty Modified duplex studies 2′ amino sugar modification.
2′-Amino-2′-deoxycytidine [2NH2-dC] 2′-modified dC Specialty Modified duplex studies 2′ amino sugar modification.
2,6-Diaminopurine / 2-Amino dA [DAP] Purine analog Base analog incorporation Altered hydrogen bonding, structure studies Adenine analog with added amino functionality.
2-Amino dA [2NH2-dA] Purine analog Base analog incorporation Modified oligo design Amino-containing adenine analog.
2-Aminopurine Deoxyribose [2AP-dR] Deoxyribose purine analog Base analog incorporation DNA fluorescence or structural studies Fluorescent purine analog; application-specific.
2-Aminopurine Ribose [2AP-rR] Ribose purine analog Base analog incorporation RNA analog incorporation RNA version of 2-aminopurine analog.
8-Amino-dA [8NH2-dA] Adenine analog Specialty Structure/function studies Adenine derivative containing amino substituent.
8-Amino-dG [8NH2-dG] Guanine analog Specialty Specialized modified oligos Guanine derivative with amino substitution.
Aminoallyl dU [aa-dU] Internal dU NHS ester after synthesis Post-synthetic dye labeling, arrays, probes Widely used aminoallyl nucleobase handle.
Aminoallyl rU [aa-rU] Internal rU NHS ester after synthesis RNA probes and labeling RNA-compatible aminoallyl uridine option.
Aminoallyl C [aa-C] Internal C analog NHS ester after synthesis Sequence-defined dye labeling Aminoallyl cytidine-like placement.
Aminoallyl A [aa-A] Internal A analog NHS ester after synthesis Specialty internal labeling Aminoallyl adenine-like placement.
Aminoallyl G [aa-G] Internal G analog NHS ester after synthesis Specialty internal labeling Aminoallyl guanine-like placement.
5′-Amino dA [5NH2-dA] 5′ nucleoside-linked NHS ester Terminal adenosine-linked amino design Special terminal format when nucleoside-linked amino handle is desired.
5′-Amino C6 dC [5NH2-dC-C6] 5′ nucleoside-linked NHS ester Terminal cytidine-linked amino handle 5′ cytidine-linked format.
3′-Amino C6 dC [3NH2-dC-C6] 3′ nucleoside-linked NHS ester Terminal cytidine-linked amino handle 3′ cytidine-linked format.
5′-Amino C6 dG [5NH2-dG-C6] 5′ nucleoside-linked NHS ester Terminal guanosine-linked amino handle 5′ guanosine-linked format.
3′-Amino C6 dG [3NH2-dG-C6] 3′ nucleoside-linked NHS ester Terminal guanosine-linked amino handle 3′ guanosine-linked format.
5′-Amino C6 dT [5NH2-dT-C6] 5′ nucleoside-linked NHS ester Terminal thymidine-linked amino handle 5′ thymidine-linked amino format.
3′-Amino C6 dT [3NH2-dT-C6] 3′ nucleoside-linked NHS ester Terminal thymidine-linked amino handle 3′ thymidine-linked amino format.
Amino Modifier C3 Internal [iNH2-C3] Internal amino linker NHS ester, isothiocyanate Internal dye, ligand or surface-probe designs Compact internal amino handle when a non-base linker is acceptable.
Amino Spacer 7 C6 Internal [iNH2-Sp7-C6] Internal amino spacer NHS ester, isothiocyanate Internal dye, hapten or ligand attachment Extended internal spacer that places the amine farther from the backbone.

Typical choice: Use [dT-NH2-C6] for most internal labeling. Use [dR-NH2-C6] when an amino handle is needed without preserving a natural nucleobase at that position.

PEG Amino Modifiers

Hydrophilic flexible amino spacers for proteins, antibodies, polymers, nanoparticles and sterically demanding payloads.

12 modifiers
Modification Code Position / Scaffold Reaction Applications Notes
AminoPEG2 [NH2-PEG2] 5′ / 3′ / internal format-dependent NHS ester, EDC/NHS Dyes, biotin, small ligands Short hydrophilic spacer.
AminoPEG3 [NH2-PEG3] Custom / internal format-dependent NHS ester Intermediate hydrophilic spacing Useful as a compact PEG-like spacer.
AminoPEG4 [NH2-PEG4] 5′ / 3′ / internal format-dependent NHS ester, EDC/NHS Peptides, small proteins Balances flexibility and compact design.
AminoPEG6 [NH2-PEG6] 5′ / 3′ / internal format-dependent NHS ester, EDC/NHS Peptides, proteins, antibody fragments Good balance of distance, flexibility and solubility.
AminoPEG8 [NH2-PEG8] Custom / format-dependent NHS ester, EDC/NHS Proteins, polymers Improves spacing and solubility.
AminoPEG12 [NH2-PEG12] 5′ / 3′ / internal format-dependent NHS ester, EDC/NHS Antibodies, nanoparticles, large proteins Common for bulky biomolecules.
AminoPEG18 [NH2-PEG18] Custom / format-dependent NHS ester, EDC/NHS Large biomolecules, polymers Long PEG spacer for high steric demand.
AminoPEG24 [NH2-PEG24] Custom / format-dependent NHS ester, EDC/NHS Therapeutic research conjugates, nanoparticles Very long hydrophilic spacer.
AminoPEG36 [NH2-PEG36] Custom / format-dependent NHS ester, EDC/NHS Large polymers and macromolecules Extended PEG; synthesis and purification review needed.
AminoPEG48 [NH2-PEG48] Custom / format-dependent NHS ester, EDC/NHS Maximum spacing custom designs Very long PEG spacer; custom feasibility review.
3′ AminoPEG CPG [3NH2-PEG] 3′ terminal NHS ester, surface coupling Protein or antibody conjugation Hydrophilic 3′ amino support.
Internal Amino-TEG [iNH2-TEG] Internal NHS ester Flexible internal labeling PEG-like internal amino spacer for crowded systems.

Typical choice: Choose PEG6 or PEG12 for bulky biomolecules where steric access, solubility and distance from the oligo backbone matter.

Branched and Multiple Amino Modifiers

Multivalent amino designs for dual labeling, high payload loading and dendrimeric oligo architectures.

10 designs
Modification Code Position / Scaffold Reaction Applications Notes
Diamino Linker [NH2x2] Internal / custom NHS ester Dual labeling, dual payload attachment Two amines can increase loading but complicate analysis.
Diamino C6 Linker [C6-(NH2)2] Internal / custom NHS ester Dual payload spacing C6-spaced diamino architecture.
Lysine Brancher [Lys(NH2)2] Branched NHS ester, peptide coupling Peptide-like branching, two handles Lysine scaffold for dual amino functionality.
Serinol Brancher [Ser(NH2)2] Branched NHS ester Compact branched oligos Compact scaffold for dual conjugation routes.
Tris Amino Brancher [Tris(NH2)3] Branched NHS ester Multivalent labeling Three amino handles; purification and QC important.
Dendrimer Amino Brancher [NH2x4+] Dendrimer / branched NHS ester High payload loading, nanotechnology Tree-like architecture for multiple amino groups.
Multi-amino Brancher [Multi-NH2] Branched / internal NHS ester Multivalent conjugation Custom multi-handle design; avoid uncontrolled conjugation when selectivity matters.
Branching Unit with Amino Handles [Branch-NH2] Branch point NHS ester Branched oligo construction Can combine branching and amino conjugation.
Multiple Amino-Modified Oligo [multi-NH2-oligo] Multiple defined sites NHS ester Multicolor probes, high-density labeling Multiple amines may affect hybridization and mass analysis.
Dendrimeric Oligonucleotide Amino Design [Dendrimer-NH2] Custom architecture NHS ester Drug delivery and multivalent research Custom route, purification and QC required.

Typical choice: Branched amino designs are powerful for multivalent payload attachment but should be reviewed for hybridization, purification and analytical complexity.

Custom Amino Design

Special amino designs requiring route planning, orthogonal chemistry, custom conjugation strategy or customer-supplied linker review.

16 routes
Modification Code Position / Scaffold Reaction Applications Notes
Custom Long-Chain Amino Linker [Custom-NH2] Custom terminal/internal NHS ester, EDC/NHS Large payloads, unusual spacing Custom linker length chosen by payload and application.
Reverse-Synthesis Amino Placement [5′-NH2-design] Reverse polarity / custom NHS ester Inverted or reverse-polarity constructs Useful when amino placement is tied to unusual polarity.
Multiple Internal Amino Sites [multi-iNH2] Internal multiple sites NHS ester Multicolor probes, high loading Requires careful stoichiometry and purification.
Mixed Amino/Thiol Oligo [NH2+SH] Custom NHS ester + maleimide/gold routes Orthogonal dual conjugation Requires orthogonal protecting group and reaction planning.
Mixed Amino/Azide Oligo [NH2+N3] Custom NHS ester + click chemistry Dual-payload conjugation Allows amine coupling plus CuAAC/SPAAC click chemistry.
Mixed Amino/Alkyne Oligo [NH2+Alkyne] Custom NHS ester + click chemistry Dual-payload conjugation Allows amine coupling plus azide payload click chemistry.
Amino + Fluorophore Combination [Dye+NH2] Terminal/internal NHS ester after synthesis Dual-functional probes Oligo can contain a dye and a free amino handle.
Amino + Biotin Combination [Biotin+NH2] Terminal/internal NHS ester after synthesis Capture plus second conjugation Useful for affinity capture and secondary payload attachment.
Amino + Peptide Conjugate [Peptide-NH2-oligo] Custom Amide coupling / activated peptide Peptide-oligo conjugates Can use customer-supplied peptide or Bio-Synthesis conjugation support.
Amino + GalNAc Conjugate [GalNAc-NH2-oligo] Custom Amide coupling / activated GalNAc Targeted oligonucleotide research GalNAc linker architecture must be selected carefully.
Amino + Cholesterol / Lipid Conjugate [Lipid-NH2-oligo] Custom Amide coupling / activated lipid Delivery and uptake studies Hydrophobic payloads may require HPLC method optimization.
Customer-Supplied Linker Integration [Client-NH2-linker] Custom Project-specific Customer proprietary linkers Route depends on stability, solubility and functional groups.
Aminooxy-Modifier-11 [Aminooxy-11] Specialized reactive handle Oxime ligation with aldehyde/ketone Glycan or carbonyl-bearing payloads Aminooxy is distinct from primary amine NHS chemistry.
Photocleavable Amino C6 [PC-NH2-C6] Photocleavable linker NHS ester after synthesis Light-triggered release or capture Photocleavable amino linker for specialized assays.
AP-dC G-Clamp / Aminoethyl-Phenoxazine-dC [AP-dC] Specialized base analog Specialty Affinity or structural applications Modified cytosine analog with aminoethyl-phenoxazine character.
Modified Backbone with Amino Handle [NH2-modified] ASO / siRNA / LNA / BNA / 2′-OMe NHS ester after synthesis Therapeutic-style research constructs Compatibility depends on deprotection and purification.

Technical review recommended: Custom amino designs should be evaluated for synthesis compatibility, protecting groups, deprotection, conjugation chemistry, purification and final QC.

Final design note: The tables are intended as a broad capability and ordering guide. Bio-Synthesis can evaluate the sequence, placement, scale, payload, purification target and QC requirements to recommend the best amino modifier and conjugation route.

Scope note: The codes shown are practical customer-facing shorthand for quote communication, not universal supplier product codes. Bio-Synthesis can map these requests to the appropriate synthesis route and available reagent format.

Conjugation Chemistry

What Reactions Work with Amino-Modified Oligos?

Primary amino groups are most often used for amide bond formation with activated esters, but they can also participate in several other useful conjugation reactions.

Compatible Reaction Chemistry

Reactive Molecule Reacts With Bond Formed Typical Products Notes
NHS ester Primary NH2 Amide Fluorophores, biotin, PEG, peptides Most common amino-oligo conjugation reaction.
Isothiocyanate Primary NH2 Thiourea FITC and related labels Classic dye-labeling chemistry.
Activated carbonate Primary NH2 Carbamate PEG, polymers, small molecules Useful for activated linker reagents.
Carboxyl + EDC/NHS Primary NH2 Amide Proteins, peptides, nanoparticles Requires activation of carboxyl group before coupling.
Squarate ester Primary NH2 Squaramide Proteins, antibodies, glycans Mild conjugation option for selected biomolecules.
Aldehyde + reducing agent Primary NH2 Secondary amine Glycans, oxidized carbohydrates Reductive amination; conditions require optimization.
Maleimide Indirect Thioether Thiol payloads Amino oligo must first be converted or paired with a suitable heterobifunctional linker.

NHS Ester Route

Oligo-NH2 + NHS-Dye ↓ Amide

Best for FAM, Cy dyes, Alexa Fluor®, ATTO dyes, biotin and many activated labels.

FITC Route

Oligo-NH2 + FITC ↓ Thiourea

Classic route for fluorescein isothiocyanate labeling.

Protein Coupling

Oligo-NH2 + Activated Protein ↓ Protein-Oligo

Used for enzyme, streptavidin, antibody and protein conjugates.

Conjugation Targets & Payload Options

What Can Amino Modifiers Be Conjugated To?

Primary amino (-NH2) groups are highly versatile conjugation handles and can be coupled to a broad range of fluorescent labels, affinity tags, proteins, antibodies, peptides, polymers, nanoparticles, targeting ligands and small molecules using well-established amine-reactive chemistries.

DYE

Fluorophores

FAM, HEX, TAMRA, Cy3, Cy5, Alexa Fluor®, ATTO, IRDye® and NIR dyes.

→

TAG

Affinity Labels

Biotin, desthiobiotin, digoxigenin, DNP and other capture tags.

→

PRO

Protein Conjugation

HRP, alkaline phosphatase, streptavidin, BSA, enzymes and antibody fragments.

→

AB

Antibody Conjugation

Antibody-oligo conjugates for detection, proximity assays and targeted systems.

→

PEP

Peptide Conjugation

CPPs, targeting peptides, epitope tags, linkers and customer-supplied peptides.

→

PEG

PEG / Polymer Conjugation

PEGylation and polymer conjugation to improve solubility, spacing or biodistribution.

→

LIG

Targeting Ligands

GalNAc, folate, mannose, cholesterol, lipids and receptor-targeting ligands.

→

NP

Nanoparticle Conjugation

Gold, iron oxide, silica, quantum dots, magnetic beads and other surfaces.

→

RX

Small Molecule Conjugation

Drug-like payloads, haptens, chelators, imaging agents and custom molecules.

→

SUR

Surface Immobilization

Plates, beads, glass, arrays and functionalized solid supports.

→

Compatibility Matrix

Which Amino Modifier Should I Choose?

Use this as a practical first-pass guide. Final selection depends on payload size, solubility, attachment position, sequence, purification and desired scale.

Payload Compatibility Rating

★★★★★ = excellent, ★★★ = usable, ★ = usually not preferred.

Payload / Application [NH2-C2] [NH2-C6] [NH2-C12] [NH2-PEG6] [NH2-PEG12] [dT-NH2-C6]
Fluorophore ★★★ ★★★★★ ★★★★ ★★★★★ ★★★★ ★★★★★
Biotin / affinity tag ★★★ ★★★★★ ★★★★ ★★★★ ★★★★ ★★★★
Peptide ★★ ★★★★ ★★★★★ ★★★★★ ★★★★★ ★★★
Protein / enzyme ★ ★★★ ★★★★★ ★★★★★ ★★★★★ ★★
Antibody ★ ★★ ★★★★ ★★★★★ ★★★★★ ★★
PEG / polymer ★★ ★★★★ ★★★★ ★★★★★ ★★★★★ ★★★
Nanoparticle / bead ★ ★★★ ★★★★★ ★★★★ ★★★★★ ★★
Internal probe labeling ★★ ★★★ ★★★ ★★★★ ★★★ ★★★★★

Simple Decision Guide

Need dye or biotin?

Start with

[NH2-C6]
Need internal label?

Start with

[dT-NH2-C6]
Need antibody or protein?

Start with

[NH2-PEG6] or [NH2-PEG12]
Need nanoparticle?

Start with

[NH2-C12] or [NH2-PEG12]
Design Recommendations

Conjugation Design Considerations

Practical Recommendations

Consideration Recommendation Why It Matters
Linker length Use [NH2-C6] for most dyes, biotin and peptide conjugations. Use C12 or PEG spacers for larger proteins and nanoparticles. Longer or hydrophilic spacers reduce steric hindrance and improve payload accessibility.
Modification position 5′ amino groups are easiest to access. Internal amino groups are useful for FRET probes, molecular beacons and site-specific labeling. Position affects hybridization, conjugation efficiency and purification behavior.
Number of amino groups Multiple amino handles enable higher payload loading but require careful purification and analytical review. Multiple payloads can change solubility, mass spectrum complexity and duplex behavior.
Reaction buffer Use amine-free buffers for NHS ester reactions. Avoid Tris and other primary amine-containing buffers. Competing amines can consume activated ester reagents and reduce conjugation yield.
Purification HPLC purification is generally recommended after conjugation. Purification removes excess payload, hydrolyzed reagent and unconjugated oligo.
Storage Amino-modified oligos are usually stable lyophilized. Conjugated products should be stored based on payload stability. Dyes, proteins and nanoparticles often require different storage conditions than unmodified oligos.
Bio-Synthesis Capability

Custom Amino Oligo Synthesis and Conjugation Support

Broad Oligo Chemistry

DNA, RNA, PNA, LNA/BNA, 2′-OMe, 2′-F, ASO and siRNA-style designs.

Flexible Amino Placement

5′, 3′, internal, multiple amino positions and base-specific amino modifiers.

Custom Conjugation

Fluorophores, peptides, antibodies, PEG, GalNAc, lipids, proteins and nanoparticles.

Analytical QC

HPLC, LC-MS, MALDI-TOF, UV-Vis and project-specific QC documentation.

FAQ

What is the best general amino modifier?
For most routine dye, biotin, small molecule and peptide conjugations, [NH2-C6] is the best starting choice because it is widely used, flexible and compatible with many NHS ester reactions.
When should I use a PEG amino modifier?
PEG amino modifiers are preferred when the payload is large, hydrophobic, protein-like or sterically demanding. PEG can improve spacing, flexibility and water solubility.
Can amino modifiers be placed internally?
Yes. Internal amino modifiers such as [dT-NH2-C6] and [dR-NH2-C6] can place a reactive amino group at a specific site within the oligonucleotide sequence.
Can amino-modified oligos be conjugated to antibodies?
Yes, but the best chemistry depends on the antibody activation strategy. PEG amino spacers are often preferred to reduce steric hindrance between the antibody and oligo.
What buffer should be avoided for NHS ester conjugation?
 Avoid Tris and other buffers containing primary amines, because they can compete with the amino-modified oligo and reduce conjugation efficiency.
Is HPLC purification recommended?
 HPLC purification is commonly recommended after conjugation to separate conjugated oligo from unconjugated oligo and excess payload.
More FAQ'sAll FAQ's
Contact & Quote Request

Need help choosing the right amino modifier?

Send your sequence, desired amino position, target payload, scale, purification preference and QC requirements. Bio-Synthesis can recommend the appropriate amino modifier, linker length and conjugation chemistry for your application.
Request a Quote Speak to a Scientist

Need help before quoting?

Email: info@biosyn.com
Phone: 800-227-0627 (US/CAN)
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What to Send

  • Oligo sequence and orientation
  • NH2 position: 5′, 3′, internal or multiple
  • Payload to attach and preferred chemistry
  • Scale, purity target and buffer needs
  • QC requirements such as HPLC, LC-MS or MALDI

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