Photo-reactive, radical-generating, click-ready and ligation-ready oligonucleotides for interstrand cross-links, protein–DNA capture, proximity ligation, non-enzymatic ligation, NGS adapters and structure–function studies.
Bio-Synthesis supports custom DNA cross-linking and ligation oligonucleotides for structural biology, repair pathway mapping, proximity capture, protein–DNA interaction studies, chemical ligation and adapter workflows.
Bio-Synthesis offers a broad portfolio of DNA cross-linking and ligation modifications including psoralen cross-linkers, CNVK photocrosslinkers, thio-bases, halogenated radical bases, benzophenone and diazirine photocapture chemistries, as well as 5′-phosphate, 5′-App and click-ready handles for enzymatic and chemical ligation workflows.
Our team can help evaluate placement, spacer length, duplex context, light wavelength, coupling chemistry, matched controls, purification, ICL verification, LC-MS compatibility and documentation from discovery-scale RUO supply to larger development programs.
This section reorganizes the important live-site technology details into a decision guide so customers can select the right reactive base, linker, light condition and QC approach.
tight positioning, short reach
general cross-linking and conjugation
reduced steric hindrance
bulky partners and surfaces
Short spacers help preserve positional accuracy for cross-link formation. Longer C6, TEG or PEG spacers can improve accessibility for proteins, surfaces, fluorophores, click partners and bulky conjugates.
Use C2 or direct base placement when geometry must be close and cross-link position needs high specificity.
Use C6 or TEG when protein access, click ligation or conjugation yield may be limited by steric hindrance.
Pyrene and perylene analogs can support proximity-driven interactions through π-stacking in high-Tm duplex regions.
Use the tabs to compare photoreactive cross-linkers, radical bases, conjugation handles, click ligation handles, structural reporters and 2′-OMe variants.
Technology note: Use 350–365 nm for CNVK, benzophenone and diazirine, and 320–400 nm for psoralen to reduce unwanted 254 nm damage.
Technology note: Oxygen scavengers can modulate radical lifetime and adduct profiles; include no-light and unmodified controls.
Technology note: Maleimide coupling commonly uses pH 6.5–7.0; thiols often ship protected and are deprotected under mild reducing conditions.
Technology note: CuAAC requires copper-stabilizing ligands; oxime ligation is usually more hydrolytically stable than imine formation.
Technology note: Embed stacking analogs in high-Tm duplex regions when proximity or stacking-driven ligation is the goal.
Technology note: 2′-OMe can increase nuclease resistance and Tm; balance density to preserve ligase, polymerase or hybridization function.
The same reactive base can behave differently depending on whether the goal is interstrand cross-linking, protein capture, chemical ligation or adapter/library construction.
Interstrand cross-link studies require duplex-compatible placement, controlled light activation and ICL verification.
Protein–DNA capture benefits from short-lived reactive groups placed at suspected contact positions.
Chemical ligation depends on compatible functional groups, reaction pH and partner chemistry.
Adapter and library workflows need ligation-ready termini and careful avoidance of blocking chemistry near nick sites.
Successful reactive oligo projects connect assay design with placement, activation chemistry, synthesis, purification and analytical release.
BCross-linking and ligation-ready oligos often require method-matched purification and analytical confirmation because reactive groups can alter stability, chromatography and mass interpretation.
QC packages may include HPLC/UPLC purity, LC-MS identity, PAGE, OD260 concentration, ICL conversion support, conjugate mass shift verification, custom packaging and documentation.
Purity assessment and chromatographic profile for modified oligos.
Mass identity confirmation and conjugate mass-shift verification where compatible.
Native vs denaturing comparison and ICL conversion support.
Optional endotoxin, residuals, stability points, plate formatting and barcodes.
Plan wavelength, dose/time, no-light controls and non-specific background checks.
Confirm modified oligo profile and attachment where method-compatible.
Discovery µmol to larger supply, tubes, vials, plates, labels and barcodes.
Reactive oligonucleotides require controlled synthesis, purification, handling and analytical release methods matched to photochemistry or ligation chemistry.
Bio-Synthesis supports design, synthesis, purification, analytical characterization, custom packaging and documentation for cross-linking and ligation oligonucleotide programs.
Connect cross-linking or ligation assay design with the right Bio-Synthesis synthesis, modification and QC service.
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Compare photoreactive, radical, click, enzymatic and chemical ligation strategies.
Purification, LC-MS, PAGE, analytical purity, concentration, labeling and documentation.
Use this section to support scientific credibility while keeping the page focused on cross-linking chemistry, ligation strategy, synthesis and analytical verification.
Suggested page note: References are provided for scientific background. Final reactive oligo design should be evaluated within the sequence, placement, light/chemical activation, linker geometry, purification method and QC requirements.
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