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Deuterated Base Oligos

Deuterated Base Modified Oligonucleotides

Stable‑isotope labeling for LC‑MS quantitation, kinetic isotope effects, and NMR tracing. Example product: 8‑D‑dmf‑dG phosphoramidite for site‑specific incorporation of C8‑deuterated guanine under standard DNA synthesis workflows.

Overview Technology & Methods Applications Products Technical Notes FAQ References Speak

Overview

Deuterated base oligonucleotides incorporate one or more heavy‑isotope (²H/D) substitutions at defined positions (e.g., C8 of purines). At a chosen site, these isotopes provide a mass offset for precise LC‑MS quantitation, enable kinetic isotope effect (KIE) measurements, and support NMR/IR tracing, all while preserving canonical base‑pairing.

8‑D‑dmf‑dG 8‑D‑dA 5,6‑D2‑dU 5‑D‑dC QC: HPLC • LC‑MS • %D
Why deuterate?
  • Internal standards with known mass shift
  • Probe enzyme mechanisms via KIE
  • Track molecules in complex matrices
Example: 8‑D‑dmf‑dG
  • C8‑deuterated dG, dmf‑protected, phosphoramidite‑ready
  • Compatible with standard DNA synthesis
  • Supplied with isotopic enrichment report & LC‑MS
Desalt → HPLC/UPLC
  • Desalt → HPLC/UPLC
  • LC‑MS identity; isotopic %D & expected mass shift
  • RUO → GMP‑like documentation

Technology & Methods

Isotopic Positioning

Common sites: C8 purines (G/A), 5/6 pyrimidines (U/T/C). Choose a site that balances synthetic stability and analytical resolution.

Synthesis Compatibility

Amidites such as 8‑D‑dmf‑dG run under standard phosphoramidite chemistry (0.1 M ACN). Use typical detritylation/coupling times.

Deprotection Guidance

Use time‑limited base (NH4OH or AMA). Avoid prolonged high‑temperature deprotection to minimize H/D exchange risk.

Design tip: For quantitative LC‑MS assays, place D‑labels away from known fragmentation hot‑spots or validate fragment maps with a pilot duplex.

Applications

LC‑MS Internal Standards

Isotope‑dilution workflows with D‑labeled oligos provide accurate, matrix‑tolerant quantitation.

Kinetic Isotope Effects

Measure KIEs in polymerase, glycosylase, or nuclease reactions to interrogate transition states and rate‑limiting steps.

NMR/IR Tracing

Deuterium labeling aids assignment and signal tracking in complex systems.

Products & Ordering

Product / Modification Description Function Application Code
8‑D‑dmf‑dG Phosphoramidite C8‑deuterated 2′‑deoxyguanosine (dmf‑protected), DNA synthesis compatible. Stable‑isotope mass shift LC‑MS internal standard; KIE studies [8D‑dG]
8‑D‑dA Phosphoramidite C8‑deuterated 2′‑deoxyadenosine analog for purine labeling. Isotopic labeling KIE / MS tracing / NMR [8D‑dA]
5,6‑D2‑dU Phosphoramidite Pyrimidine with two deuteriums at 5/6 positions. Mass offset / spectral simplification LC‑MS quantitation; IR/NMR assignments [D2‑dU]
5‑D‑dC Phosphoramidite 5‑position deuterated cytidine analog. Isotopic label Quantitation / mechanistic studies [5D‑dC]
Deuterated Control Oligo (Custom) Short duplex or assay control with 1–3 labeled sites; isotopic %D report included. Internal standard Assay validation / calibration [D‑IS]
Customizations: multiple labeled sites, internal placements, mixed backbones (2′‑OMe/LNA), PEG/hexa‑EG spacers, HPLC/UPLC, aliquots & kitting, RUO→GMP‑like documentation.

Technical Notes

  • Hybridization & Tm. Isotopic substitution generally preserves base‑pairing; Tm shifts are minimal. Validate when placing multiple D‑labels.
  • H/D exchange risk. Limit base/heat during deprotection (NH4OH or AMA) to reduce exchange at C8 or labile positions.
  • Analytics. Confirm mass shift by ESI‑LC‑MS. For quantitative assays, include unlabeled/labeled controls to assess ionization parity and recovery.
  • Storage & handling. Store dried at −20 °C in the dark; avoid repeated freeze–thaw; limit time in protic solvents.

Ready to specify 8‑D‑dmf‑dG or another D‑label?

Send sequence, labeled position(s), assay (MS/KIE/NMR), and purification level. We’ll return a tuned design and QC plan.

Start a design consult

Ordering Checklist

Sequence & position
Target sequence and specific labeled position(s) (e.g., C8‑D at G13).
Intended use
LC‑MS internal standard, KIE study, or NMR/IR tracing.
Scale & purification
Requested scale (µmol → multi‑gram) and purification (Desalt vs HPLC/UPLC).
QC & documentation
LC‑MS report, isotopic %D, (optional) NMR; CoA & method summary; RUO→GMP‑like docs.

FAQ

Do you support RNA labeling?

Selected positions are feasible for RNA. Share your sequence and we’ll confirm chemistry and stability.

Does deuteration change duplex stability?

Typically the effect on Tm is very small; hydrogen bonding patterns remain the same. We can model/measure if your assay needs tight thermal windows.

Will the D‑label scramble during deprotection?

Under standard, time‑limited deprotection the label is stable. Avoid unnecessary heat/base to minimize H/D exchange.

Can you provide isotopic enrichment data?

Yes—each lot can include isotopic %D and the expected mass shift; NMR data available on request.

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References

  1. Stable‑isotope labeling strategies for nucleic acids (reviews).
  2. Kinetic isotope effects in enzymatic DNA/RNA processing.
  3. LC‑MS quantitation using isotopically labeled internal standards.

We can align specific literature protocols to your design upon request.

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