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Oligo Modifications for Structure–Activity Studies (SAR)

Probe base pairing, stacking, kinetics, and repair using curated base analogs and lesions. We manufacture fluorescent base analogs (2-AP, pyrrolo-dC, BODIPY-TR-X), halogenated bases (5-Br/5-I/5-F), deaza/aza heterobases, thio/amino substitutions, oxidative/hydroxy lesions, abasic mimics, and sugar/linkage variants with full QC from RUO to GMP-like supply.

Fluorescent Base Analogs Halogenated Bases Lesion & Damage Mimics Deaza/Aza Variants Thio/Amino Substitutions

Overview

Bio-Synthesis manufactures base-analog oligonucleotides for structure–activity relationship (SAR) studies—spanning fluorescent base analogs (2-aminopurine 2-AP, pyrrolo-dC, BODIPY-TR-X), halogenated bases (5-Br/5-I/5-F), deaza/aza purines, thio/amino substitutions, site-specific DNA lesions (8-oxo-dG/dA, ε-dA, 5-hydroxymethyl-dU), and sugar/linkage variants (ψ-dU/ψ-rU, araC, 2′-5′ linkage). We deliver design-to-QC support from RUO to GMP-like supply.

Typical applications include polymerase fidelity & bypass, DNA damage & repair mapping (BER/NER), protein–DNA footprinting, base-flipping/stacking dynamics (2-AP / pyrrolo-dC), and backbone geometry tests (2′-5′ link, araC). See the full catalog under Products & Notes or jump to Technology • Design • Application for placement and control tips.

Also searched as: base-analog oligos, 2-AP oligonucleotide, pyrrolo-dC probe, 8-oxo-dG lesion, deaza adenosine, pseudouridine DNA, 2′-5′-linked DNA, SAR oligonucleotide.

Formats
Tubes • 96-well plates
Scale
µmol → multi-gram
QC
UPLC/HPLC • LC-MS
Supply
RUO → GMP-like

Products & Notes

Modification Description Typical use Code
BODIPY®-TR-X Bright reporter dye, minimal spectral overlap. Stacking/association reporter; FRET donor/acceptor. [BODIPY-TR-X]
2-Aminopurine deoxyribose Fluorescent adenine analog; sensitive to stacking. Local dynamics; base flipping; polymerase studies. [2-AP-dR]
2-Aminopurine-riboside RNA version of 2-AP. RNA folding; ribozyme mapping. [2-AP-r]
Pyrrolo-2′-dC Environment-sensitive C analog. Microenvironment polarity; duplex vs mismatch. [Pyrrolo-dC]
5′-Pyrene Cap Hydrophobic intercalator at 5′ end. π-stacking/helix geometry; supramolecular assembly. [5′-Pyrene]
Technical Notes
  • Place 2-AP/pyrrolo-dC internally; avoid terminal quenching and G-clamps directly adjacent.
  • Use short TEG/PEG spacers near pyrene caps to reduce sterics at surfaces.

Modification Description Typical use Code
8-Bromo-2′-deoxyadenosine Halogen at C8 of purine ring. Stacking/photochemistry; polymerase effects. [8-Br-dA]
8-Bromo-2′-deoxyguanosine As above for guanine. Helix perturbation; electron effects. [8-Br-dG]
5-Bromo-dU 5-brominated uracil. Photocrosslink; Tm modulation. [5-Br-dU]
5-Bromo-dC 5-brominated cytidine. Stacking/electron effects. [5-Br-dC]
5-Iodo-dU 5-iodo uracil; heavy-atom effect. Photochemistry; cleavage mapping. [5-I-dU]
5-Iodo-dC 5-iodo cytidine. Stacking/cleavage mapping. [5-I-dC]
5-Fluoro dU Subtle electronegativity change. H-bond/stacking shifts; Tm profiling. [5-F-dU]
5-Fluoro-2′-O-Methyluridine Ribo + 2′-OMe + 5-F. RNA-like stability mapping. [5-F-2′-OMe-U]
5-Fluoro-4-O-TMP-2′-O-Methyluridine Protected 5-F-2′-OMe-U. Synthetic intermediate/control. [5-F-4-O(TMP)-2′-OMe-U]
6-O-(TMP)-5-F-2′-dU Protected 5-F-dU analog. Synthetic route; SAR variant. [6-O(TMP)-5-F-dU]
Technical Notes
  • Halogens can decrease/increase Tm depending on context—benchmark vs native base at same position.
  • Use UV control when employing 5-Br/5-I due to photolability.

Modification Description Typical use Code
7-Deaza-2′-deoxyadenosine Removes N7 of adenine. Hoogsteen/cation effects; protein contacts. [7-Deaza-dA]
7-Deaza-2′-deoxyguanosine Removes N7 of guanine. Binding to metals/cations; polymerase readout. [7-Deaza-dG]
7-Deaza-8-aza-deoxyadenosine Dual ring electronics change. Stacking/Hoogsteen tuning. [7-Deaza-8-aza-dA]
7-Deaza-8-aza-deoxyguanosine As above for G. Electronics/stacking. [7-Deaza-8-aza-dG]
3-Deaza-deoxyadenosine N3 removal in adenine. H-bond network perturbation. [3-Deaza-dA]
O6-Phenyl-2′-deoxyinosine Bulky O6 adduct mimic. Hydrophobic stacking; damage adduct model. [O6-Ph-dI]

Modification Description Typical use Code
6-Thio-dG Thiocarbonyl at C6. Photoreactivity; H-bond changes. [6-S-dG]
4-Thio-dT Sulfur at C4 of thymidine. Triplet sensitization; UV probes. [4-S-dT]
4-Thio-dU Thio uracil. UV reactivity; base pairing shifts. [4-S-dU]
2-Thio-dT Sulfur at C2. Wobble/stacking modulation. [2-S-dT]
8-Amino-dA Exocyclic amine at C8. H-bond/stacking probe. [8-NH2-dA]
8-Amino-dG Amine at C8 of G. Electronics; pairing perturbation. [8-NH2-dG]
N4-Ethyl-dC Exocyclic amine adduct. Protein–DNA interaction mimic. [N4-Et-dC]

Modification Description Typical use Code
8-Oxo-2′-dA Oxidative adenine lesion. Repair recognition; mispairing. [8-oxo-dA]
8-Oxo-2′-dG Classic oxidative G lesion. BER pathways; fidelity studies. [8-oxo-dG]
5,6-Dihydrothymidine Reduced thymine (loss of aromaticity). Stacking/ΔG perturbation. [5,6-DH-dT]
5,6-Dihydro-2′-dU Reduced uracil. Conformational probe. [5,6-DH-dU]
5-Hydroxymethyl-2′-dU Hydroxymethyl adduct. H-bond tuning; polymerase impact. [5-hme-dU]
5-Hydroxy-2′-deoxycytidine Oxidative cytidine lesion. Repair mapping; stability. [5-OH-dC]
2′-Deoxyxanthosine Deamination/oxidation product. Mispairing; enzyme specificity. [dX]
Etheno-2′-dA Exocyclic adduct. Polymerase bypass; adduct recognition. [ε-dA]
C4-(1,2,4-Triazol-1-yl)-2′-dU Heteroaryl adduct at C4. H-bond/stacking perturbation. [C4-Tz-dU]

Modification Description Typical use Code
2′-Deoxypseudouridine C-linked uracil isomer (DNA). Backbone geometry; pairing. [psi-dU]
pseudoUridine-2′deoxy (alias) Synonym of the above. Use same code. [psi-dU]
pseudoUridine ribo RNA pseudouridine. RNA folding; translation effects. [psi-rU]
Aracytidine (araC) 2′-arabinosyl cytidine. Sugar pucker/geometry. [araC]
5-Methyluridine (ribo) m5U in RNA. Stacking/stability; epigenetic model. [5-Me-U]
2-Aminopurine-2′-O-methylriboside Fluorescent + 2′-OMe. RNA folding with protection. [2-AP-2′-OMe-r]
5-Methyl-2′-O-Methylthymidine Base+Sugar methyls. Hydrophobic packing probe. [5-Me-2′-OMe-dT]
2′-5′ Linked dA/dG/dC/dA Non-canonical linkage set. Backbone geometry/protein contacts. [2′-5′-Link-dN]
rZebularine Cytidine analog (RNA). Enzyme/recognition studies. [rZeb]
Zebularine-deoxy-5-methyl Deoxy zebularine + 5-Me. Stability/recognition SAR. [dZeb-5-Me]

Modification Description Typical use Code
Pyrrolidine (Pyr) Stable abasic site mimic. Backbone flexibility/stacking effects. [Pyr]
Explore related chemistries
Services at a glance
  • Custom design review (placement & controls)
  • RUO → GMP-like manufacturing
  • QC: UPLC/HPLC, LC-MS (COA included)
Need help picking the right analogs?

We’ll recommend positions, spacers, and control sets to maximize interpretability in SAR experiments.

Technology • Design • Application

A consolidated guide to choose the right analogs, place them correctly, and map outcomes in SAR experiments.

Technology

  • Fluorescent base analogs (2-AP, pyrrolo-dC, BODIPY-TR-X)
    • Placement: internal ≥1 nt from termini; avoid direct G adjacent to 2-AP to reduce quench.
    • Readouts: steady-state fluorescence, stopped-flow kinetics, single-molecule or FRET (pair with dyes if needed).
  • Halogenated bases (5-Br/5-I/5-F dU/dC; 8-Br dA/dG)
    • Photochemistry & Tm tuning; heavy-atom effects enable crosslink/cleavage mapping.
    • Protect from strong UV during handling; benchmark ΔTm vs native base.
  • Deaza/aza heterobases (7-deaza, 7-deaza-8-aza, 3-deaza, O6-phenyl-dI)
    • Modulate ring nitrogens to probe Hoogsteen/cation contacts and polymerase dependence.
  • Thio/amino substitutions (2-/4-/6-thio; 8-amino)
    • Change donor/acceptor patterns and triplet sensitization; useful for photo-induced mapping.
  • Lesion & adduct mimics (8-oxo-dG/dA, 5,6-dihydro, 5-OH-dC, ε-dA, C4-triazol-dU, dX)
    • Interrogate recognition, excision, and bypass; combine with enzyme panels (BER/NER/polymerases).
  • Sugar/linkage variants (ψ-dU/ψ-rU, araC, 2′-5′ link, 5-Me-2′-OMe-dT)
    • Probe backbone geometry, pucker, and protein contacts; add LNA clamps only outside the analog window.
  • Abasic mimic (Pyrrolidine/Pyr)
    • Isolate backbone/stacking contributions without coding.

Design

  • Scanning strategy: start with a 3-position scan (−1 / 0 / +1 around motif), then refine.
  • Controls: native base control, positional swap, scrambled strand; include duplex vs single-strand control.
  • Spacing & sterics: add short TEG/PEG spacers near bulky caps (e.g., pyrene) or enzyme sites.
  • Backbone context: stabilize with LNA clamps outside the analog region; PS ends to reduce nuclease clipping.
  • Buffers/ions: set cations for Hoogsteen/G4 tests (K+/Na+); keep oxygen/light low for thio/halogen work.
  • PUR/QC: HPLC/UPLC purification; LC-MS confirmation (and intact mass for crosslinked products).
Measurement Toolkit
  • Thermodynamics: UV melt → Tm, ΔΔG; CD for global conformation.
  • Kinetics: stopped-flow fluorescence (2-AP/pyrrolo-dC), primer-extension time courses.
  • Binding: EMSA/SPR/BLI for protein–DNA contacts; footprinting with halogenated/abasic positions.
  • Processing: polymerase misincorporation spectra; enzyme excision assays; LC-MS product mapping.
Common Pitfalls
  • Terminal placement of fluorescent bases → quenching; move internal or add a spacer.
  • Halogenated bases over-irradiated → unintended photochemistry; use minimal UV during handling.
  • Excess stabilization (too much LNA) inside the analog window can mask the SAR signal.

Application

  • Polymerase fidelity & bypass: place 8-oxo-dG or ε-dA at target sites; quantify misincorporation and extension kinetics.
  • Repair enzyme mapping: embed lesions (8-oxo-dG, 5-OH-dC, dX); run excision/BER panels; verify excised bases by LC-MS.
  • Protein–DNA interfaces: use N4-Et-dC or 7-deaza at footprints; EMSA/SPR for KD, koff.
  • Base flipping/stacking dynamics: monitor 2-AP/pyrrolo-dC emission changes ± quenchers.
  • Photochemical mapping: 5-Br/5-I dU/dC under 312–365 nm; analyze crosslinks by PAGE/LC-MS.
  • Backbone geometry tests: 2′-5′ link or araC; compare Tm, CD and ligase-mediated cyclization.
Tip: for publication-grade SAR, report sequence context, ionic conditions, analog lot/QC, and complete control outcomes alongside the target analog data.

FAQ

Which analogs are best to monitor stacking or base flipping?

2-AP (A analog) and pyrrolo-dC (C analog) are classic environment-sensitive reporters. Place internally (avoid terminal quench), and use native-base controls at the same position.

Do halogenated bases increase or decrease Tm?

It’s context-dependent. 5-Br/5-I/5-F can shift Tm via electronics and sterics; benchmark vs the native strand and include a positional swap control.

Where should lesion mimics go for repair assays?

Place the lesion (e.g., 8-oxo-dG, ε-dA) within a defined sequence context near recognition motifs; include upstream/downstream positional controls and confirm by LC-MS.

Can these be combined with LNA/PS backbones?

Usually yes, but placement matters. We routinely design mixed backbones (e.g., native core with LNA clamps) to stabilize readouts without masking the analog’s effect.

What purification and QC do you recommend?

HPLC/UPLC purification with LC-MS confirmation is standard. For labile analogs (e.g., 5-I, thio), minimize light/oxidants and ship with desiccant.

Speak to a Scientist

Tell us about your SAR study. We’ll recommend analog selection, positions, control sets, spacers, and QC for clear interpretation.

Please avoid confidential details; we can arrange an NDA if needed.

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