• Chemical structure of 3′,5′-Bis-O-(tert-butyldimethylsilyl)thymidine, CAS 40733-26-4, ≥98% — silyl-protected thymidine building block used in oligonucleotide synthesis, nucleoside chemistry, and as a protected intermediate for selective functionalization at the nucleobase. Supplied by NorrChemica with DDP shipping. CoA and SDS provided.​​​​​​​​​​​​​​​​
  • ¹H NMR spectrum of 3′,5′-Bis-O-(tert-butyldimethylsilyl)thymidine (CAS 40733-26-4) in DMSO-d₆ at 298.1 K, Bruker Avance 400.15 MHz, 20 s relaxation delay, 8 scans. Thymine N–H at ~11.3 ppm (1.04); C6–H at ~7.5 ppm (1.04); anomeric C1′–H at ~6.1 ppm (1.04); sugar C–H, CH and CH₂ between ~3.5–4.5 ppm (1.03 + 3.02 + 1.03 + 1.04); thymine 5-CH₃ at ~1.8 ppm (3.04); diagnostic Si–C(CH₃)₃ at ~0.9 ppm (18.00) and Si–CH₃ at ~0.1 ppm (11.96). Confirms structure and ≥98% purity. Batch NOR40733264-25-1, NorrChemica.
  • ¹³C NMR spectrum of 3′,5′-Bis-O-(tert-butyldimethylsilyl)thymidine (CAS 40733-26-4) in DMSO-d₆ at 298.1 K, Bruker Avance 100.63 MHz, 4096 scans. Carbonyl C=O at 163.6 and 150.4 ppm; thymine C6 at 135.5 ppm; quaternary CH₃–C (C5) at 109.5 ppm; sugar C1′/C4′ at 86.7/83.7 ppm, C5′ at 72.0, C2′ at 62.7 ppm; Si–C(CH₃)₃ at 25.7–12.2 ppm; Si–CH₃ at 4.8 to –5.5 ppm. Confirms structure and ≥98% purity. Batch NOR40733264-25-1, NorrChemica.
  • gHSQC 2D NMR spectrum of 3′,5′-Bis-O-(tert-butyldimethylsilyl)thymidine (CAS 40733-26-4) in DMSO-d₆, Bruker Avance, correlating ¹H (F2, ~0–7.5 ppm) with ¹³C (F1, ~0–140 ppm) one-bond couplings. Cross-peaks confirm thymine C6–H at ~7.5/135 ppm; anomeric C1′–H at ~6.1/85 ppm; sugar C3′/C4′/C5′ at ~3.5–4.5/62–86 ppm; thymine 5-CH₃ at ~1.8/12 ppm; Si–C(CH₃)₃ at ~0.9/18–25 ppm; Si–CH₃ at ~0.1/–5 ppm. Confirms structure of bis-TBS-protected thymidine. NorrChemica.
  • gHMBC 2D NMR spectrum of 3′,5′-Bis-O-(tert-butyldimethylsilyl)thymidine (CAS 40733-26-4) in DMSO-d₆, Bruker Avance, correlating ¹H (F2, ~–0.5 to 11.5 ppm) with ¹³C (F1, ~0–160 ppm) through long-range (²J, ³J) couplings. Cross-peaks from N–H at ~11.4 ppm and C6–H at ~7.5 ppm to thymine C2/C4 carbonyls (~150–165 ppm) and C5 (~110 ppm) confirm the nucleobase framework; correlations from the silyl Si–CH₃ and t-Bu signals (~0.1–0.9 ppm) to sugar O–C carbons confirm bis-TBS protection. NorrChemica.
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NorrChemica™

3′,5′-Bis-O-(tert-butyldimethylsilyl)thymidine

CAS 40733-26-4 ≥98%

3′,5′-Bis-O-(tert-butyldimethylsilyl)thymidine | CAS 40733-26-4 | ≥98%

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Technical Specifications

CAS Number 40733-26-4
MDL Number MFCD01631042
SMILES CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C
InChI InChI=1S/C22H42N2O5Si2/c1-15-13-24(20(26)23-19(15)25)18-12-16(29-31(10,11)22(5,6)7)17(28-18)14-27-30(8,9)21(2,3)4/h13,16-18H,12,14H2,1-11H3,(H,23,25,26)/t16-,17+,18+/m0/s1
InChIKey DDLOCFSZSYGOPG-RCCFBDPRSA-N
PubChem CID 10459624
Molecular Formula C₂₂H₄₂N₂O₅Si₂
Molecular Weight 470.75 g/mol
Solubility Soluble in dichloromethane, chloroform, ethyl acetate, and THF; practically insoluble in water
Purity ≥98%
Physical Form White to off-white crystalline solid
HS Code 2934.99
Shelf Life Retest period: 24 months from date of manufacture
Storage Conditions Store at 2-8°C in a tightly sealed container, protected from moisture

Product Description & Scientific Applications

3′,5′-Bis-O-(tert-butyldimethylsilyl)thymidine (3′,5′-bis-O-TBDMS-thymidine) is a fully sugar-protected thymidine derivative in which both the 3′- and 5′-hydroxyls of the 2′-deoxyribose are masked as TBDMS ethers. The protection holds through neutral, basic, and acylating conditions, while retaining the acid- and fluoride-lability of TBDMS ethers. Fluoride (TBAF or triethylamine trihydrofluoride) removes both silyl groups; controlled acidic hydrolysis removes the more accessible primary 5′-TBDMS ether selectively, giving 3′-O-TBDMS-thymidine with a free 5′-OH.

Nucleobase modification. With both sugar hydroxyls masked, base-directed chemistry proceeds without competing reaction at the 3′- or 5′-OH. The thymine ring is functionalised through N3-alkylation or temporary N3 acyl/carbamate protection. The C5-methyl group is an entry point for side-chain chemistry: radical bromination gives the bromomethyl intermediate, which displaces with O-, N-, S-, or C-nucleophiles to install ether, amine, thioether, or carbon-linked substituents. Fluoride deprotection then gives the base-modified thymidine.

Sugar modification. Selective 5′-desilylation gives a mono-protected intermediate for stepwise sugar work. The free 5′-OH is phosphorylated, tritylated, acylated, or tagged while the 3′-OH stays protected. In the free-3′ regiochemistry the 3′-OH is activated by mesylation, tosylation, oxidation-reduction, or fluorination, and sugar-modification chemistry delivers 3′-azido, 3′-fluoro, 3′-amino, 3′-deoxy, and 2′,3′-didehydro analogues. Fluoride desilylation releases the free analogue.

Monomer preparation. The compound is a modular intermediate for modified thymidine monomers, not the ordinary dT phosphoramidite precursor. After 5′-deprotection and installation of a 5′ handle, the 3′-TBDMS is removed and the 3′-OH converted into a phosphoramidite, H-phosphonate, phosphotriester, phosphorothioate, phosphorodithioate, or phosphoramidate precursor, including for sugar- or base-modified nucleotide analogues.

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Safety Information

Hazard Class None — not subject to transport regulations
Transport Category Not classified as dangerous goods for transport (ADR/IATA/IMDG)

Documentation

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