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DNA Cross-Linking & Ligation Modified Oligonucleotides

Photo-reactive and chemically reactive base analogs for interstrand cross-links, protein–DNA capture, and non-enzymatic ligation. End-to-end design, synthesis, purification, and QC—from RUO to GMP-like supply.

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Overview

Bio-Synthesis designs and manufactures DNA cross-linking and ligation-ready oligonucleotides for structural biology, repair pathway mapping, proximity capture, and NGS adapter workflows. Choose from intercalator cross-linkers (psoralen), halogenated bases (UV-activatable), and photo-crosslinkers (benzophenone, diazirine), plus enzymatic ligation prerequisites (5′-phosphate, 5′-App) and bioorthogonal pairs for chemical ligation (CuAAC/SPAAC/IEDDA with azide/alkyne, DBCO/TCO/Tetrazine).

Services & Strengths
  • Design & placement: internal vs 5′/3′ positioning, spacer length (C2/C6/TEG), duplex context for yield, and dye/handle spacing.
  • Matched chemistry: psoralen/CNVK for ICLs; benzophenone/diazirine for protein–DNA capture; 5′-P/5′-App for ligases; CuAAC/SPAAC/IEDDA click ligation.
  • Manufacturing & QC: custom synthesis with HPLC/UPLC, LC-MS, PAGE, ICL % verification, optional endotoxin/residuals, detailed CoAs.
  • Scale & logistics: discovery µmol → bench-to-kilo; tubes/vials/plates with labels/barcodes; ISO 9001/13485, RUO→GMP-like documentation.
45+ Years ISO 9001 / 13485 RUO → GMP‑like Bench → Kilo
Explore related chemistries: Intercalators  •   Halogenated Bases  •   Reactive Handles  •   Spacers & Linkers

Services at a Glance

Design & Conjugation

Placement (internal vs 5′/3′), linker length (C2/C6/TEG), light chemistry (psoralen/CNVK/diazirine), click handles (alkyne/azide), maleimide/thiol strategies.

Analytics & QC

HPLC/UPLC, LC-MS, PAGE, OD260; ICL yield checks; mass-shift verification for conjugates; custom method development as needed.

Scale & Docs

µmol → multi-gram; vials/plates with barcodes; ISO 9001/13485; certificates (CoA, sequence, purity, MS), RUO→GMP-like documentation.

Formats & Logistics

Dry, lyophilized, or TE; custom buffers; pooled or plated libraries; batch records aligned to your LIMS conventions.

Cross-Linking & Ligation Categories

Product / Modification Description Application Code Available Scales/th>
Psoralen C6 Psoralen via hexyl linker UVA-induced ICLs [Pso-C6] RUO: µmol–100 µmol; Dev: 0.5–5 g
Psoralen C2 Psoralen via short C2 linker UVA-ICLs; tighter geometry [Pso-C2] RUO: µmol–50 µmol
3-Cyanovinylcarbazole (CNVK) Ultra-fast 365 nm photocrosslinker Interstrand cross-linking [CNVK] RUO: 0.2–50 µmol
4-Thio-dU Thione uracil; photo-reactive UVA cross-linking; damage models [4S-dU] RUO: 0.2–50 µmol
4-Thio-dT Thione thymidine; photo-reactive UVA cross-linking [4S-dT] RUO: 0.2–50 µmol
2-Thio-dT Photoactive 2-thio thymidine Photochemical probes [2S-dT] RUO: 0.2–50 µmol
6-Thio-dG Thione guanine analog Photo-crosslinking; oxidative damage [6S-dG] RUO: 0.2–25 µmol
Benzophenone-dU / dC UV aryl-ketone crosslinker Protein–DNA photocapture [Bp-dU] RUO: 0.2–25 µmol
Azido-dU / 4-Azidophenacyl-dT Nitrene photo-insertion Photo-crosslinking [N3-dU] RUO: 0.2–25 µmol
Diazirine-dU / dC Carbene photo-crosslinker Protein–DNA mapping [Diaz-dU] RUO: 0.2–25 µmol
Technical Notes
  • Light: 350–365 nm (BP/Diazirine/CNVK) or 320–400 nm (Psoralen) to minimize 254 nm damage.
  • Placement: TA/AT steps and flexible spacers (C6/TEG) often maximize ICL yield.

Product / Modification Description Application Code Available Scales
5-Br-dU 5-Bromouracil Radical cross-linking; mutagenesis [5Br-dU] RUO: 0.2–50 µmol
5-Br-dC 5-Bromocytidine Radical cross-linking [5Br-dC] RUO: 0.2–25 µmol
5′-I-dT 5-Iodinated thymidine Photo-radical cross-linking [5I-dT] RUO: 0.2–25 µmol
5-I-dU 5-Iodouracil Radical cross-linking [5I-dU] RUO: 0.2–25 µmol
5-I-dC 5-Iodocytidine Radical cross-linking [5I-dC] RUO: 0.2–25 µmol
8-Br-dG 8-Bromoguanine (deoxy) UV-induced cross-links; lesion models [8Br-dG] RUO: 0.2–10 µmol
8-Br-dA 8-Bromoadenine (deoxy) UV-induced cross-links; lesion models [8Br-dA] RUO: 0.2–10 µmol
Bromo-U (generic) Brominated uracil analog Radical cross-linking [Br-dU] RUO: 0.2–50 µmol
Technical Notes
  • Photolysis: 302 nm commonly used; oxygen scavengers can modulate radical lifetimes and adduct profiles.

Product / Modification Description Application Code Available Scales
Maleimide (e.g., Maleimide-dT / 5′-Maleimide-C6) Thiol-reactive maleimide Thiol–maleimide ligation; cross-links [Mal] RUO: 0.2–25 µmol
Thiol-dT / 5-Mercapto-dC Internal sulfhydryls Maleimide conjugation; disulfides [SH-dT] RUO: 0.2–50 µmol
3′-Amino dT Terminal primary amine NHS/EDC coupling; capture to surfaces [3Am-dT] RUO: 0.2–50 µmol
Technical Notes
  • Maleimide: pH 6.5–7.0 preferred; avoid excess amines to limit side reactions.
  • Thiol: Ship S-protected; deprotect under mild reducing conditions.

Product / Modification Description Application Code Available Scales
3′-Propargyl-5-Me-dC 3′ terminal alkyne on 5-methyl-dC CuAAC “click” ligation to azides [3Pra-5Me-dC] RUO: 0.2–25 µmol
Propargyl-dU / dC Internal alkynes CuAAC to azide-DNA/proteins [Pra-dU] RUO: 0.2–50 µmol
Vinyl-dU / Vinylbenzyl-dC Electrophilic vinyl handles Michael-type ligation; cross-linking [Vinyl-dU] RUO: 0.2–25 µmol
Formyl-dC / dU Aldehyde-bearing bases Oxime/Schiff ligation [Formyl-dC] RUO: 0.2–25 µmol
Technical Notes
  • CuAAC: Use copper-stabilizing ligands; for SPAAC, switch to DBCO/azide partners.
  • Aldehyde: Oxime formation (aminooxy) is more hydrolytically stable than imines.

Product / Modification Description Application Code Available Scales
2′-deoxy-Pseudouridine (dΨ) Isomerized uridine lacking 2′-OH Structural probes; ligase compatibility [dPsi] RUO: 0.2–50 µmol
2-Aminopurine (2-AP) Fluorescent base analog Stacking/ligation kinetics readout [2AP] RUO: 0.2–25 µmol
5-F-dU 5-Fluorouracil (deoxy) Damage mimic; reactivity handle [5F-dU] RUO: 0.2–50 µmol
Pyrene-dU / Perylene-dU π-Stacking PAH bases Templated non-enzymatic ligation [Pyr-dU] RUO: 0.2–10 µmol
Technical Notes
  • Placement: Embed in high-Tm duplex regions to maximize stacking-driven proximity.

Product / Modification Description Application Code Available Scales
2′-OMe-2,6-Diaminopurine 2′-O-Me ribose + DAP base Stabilized pairing; templated ligation [2OMe-DAP] RUO: 0.2–50 µmol
2′-OMe-5-F-U 2′-O-Me-5-fluorouridine Ligation/stacking; probe design [2OMe-5F-U] RUO: 0.2–50 µmol
2′-OMe-5-Me-U 2′-O-Me-5-methyl-U Duplex stabilization [2OMe-5Me-U] RUO: 0.2–50 µmol
2′-OMe-5-Me-C 2′-O-Me-5-methyl-C Affinity tuning [2OMe-5Me-C] RUO: 0.2–50 µmol
2′-OMe-I (Inosine) Hypoxanthine base on 2′-O-Me ribose Degenerate pairing; templated ligation [2OMe-I] RUO: 0.2–25 µmol
2′-OMe-5-Br-U 2′-O-Me-5-bromouridine Photo/radical strategies with added stability [2OMe-5Br-U] RUO: 0.2–25 µmol
2′-OMe-TMP-5-F-U* Specialty 2′-O-Me U derivative (TMP/5-F) Custom ligation/cross-linking studies [2OMe-TMP-5F-U] RUO: 0.2–10 µmol
2′-OMe-2-Aminopurine Fluorescent base on 2′-O-Me ribose Real-time ligation/stacking readouts [2OMe-2AP] RUO: 0.2–10 µmol
Technical Notes
  • Design: 2′-OMe increases nuclease resistance and Tm; balance density to preserve activity.

Design & Technology

Placement Strategy
  • Photocrosslinkers: Psoralen & CNVK favor TA/AT steps; place within a stable duplex to maximize ICL yield.
  • Protein–DNA capture: Seat benzophenone/diazirine at suspected contact bases; avoid termini unless end-effects are desired.
  • Click ligation: Internal propargyl bases for proximity ligations; use 3′-propargyl-5-Me-dC for terminal joins.
Light & Activation
  • Psoralen: 320–400 nm (typ. 365 nm). Track mono-adduct → ICL conversion by denaturing PAGE/LC-MS.
  • CNVK: 365 nm; very fast—short pulses reduce non-specific background.
  • Benzophenone/Diazirine: ~350–365 nm; diazirine carbene is short-lived → prioritize exact contact sites.
  • 5-I/5-Br bases: ~302 nm for radical routes; consider oxygen scavengers to tune adduct profiles.
Spacer/Linker & Geometry
  • Use C6/TEG to relieve steric clash in protein footprints or crowded duplex regions.
  • Pyrene/perylene boost π-stacking and templated non-enzymatic ligation—embed in high-Tm segments.
Enzymatic vs Chemical Ligation
  • Enzymatic: Avoid bulky lesions at nick sites; heavy 2′-OMe can inhibit ligase/polymerase.
  • Chemical: Oxime (formyl + aminooxy) is more hydrolytically stable than imine; CuAAC needs copper-stabilizing ligands.
Purification & QC
  • ICL verification: Compare native vs denaturing traces; quantify ICL % by LC-MS deconvolution.
  • Conjugates: Maleimide adducts verified by mass shift; maintain pH 6.5–7.0 during coupling.
Controls & Readouts
  • No-UV and scrambled-site controls; duplex with matched unmodified strand; titrate light dose/time.
  • Readouts: gel shifts, LC-MS adduct mapping, fluorescence (2-AP/2′-OMe-2-AP), or qPCR blockade where appropriate.

Need help choosing the best cross-linking or ligation strategy?

We’ll recommend placement, spacers, purification, and QC to fit your assay—then scale from mg to multi-gram.

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FAQ

Which base is best to create interstrand cross-links (ICLs)?

Psoralen C6/C2 and CNVK are the most reliable ICL tools; pick TA/AT steps and confirm by denaturing PAGE/LC-MS.

When should I choose benzophenone or diazirine over psoralen?

Use benzophenone/diazirine to capture protein–DNA contacts at specific bases under 350–365 nm; psoralen is preferred for strand-to-strand ICLs.

Can I combine crosslinkers with click handles or fluorophores?

Yes—pair internal propargyl bases for CuAAC or terminal 3′-propargyl-5-Me-dC. Keep the crosslinker ≥3–5 nt away from dyes to minimize quenching.

Do 2′-OMe variants affect ligation or polymerase steps?

Moderate 2′-OMe content increases Tm and nuclease resistance; very high density can reduce ligase/polymerase efficiency—balance per assay.

What scales and QC do you support?

µmol → multi-gram, with HPLC/UPLC, LC-MS, PAGE, optional endotoxin/residuals, and RUO→GMP-like documentation.

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