Nucleosides and Nucleotides. 174. Synthesis of Oligodeoxynucleotides Containing 4‘-C-[2-[[N-(2-Aminoethyl)carbamoyl]oxy]ethyl]thymidine and Their Thermal Stability and Nuclease-Resistance Properties¹

Abstract

The synthesis and properties of oligodeoxynucleotides (ODNs) containing 4′-C- [2-[[N-(2-aminoethyl)carbamoyl]oxy]ethyl]thymidine (3) are described. 4′R-(2-Hydroxyethyl)thymidine (4), which is a precursor for phosphoramidite 5, was synthesized using a newly developed intramolecular radical cyclization reaction at the 4′-position of thymidine derivative 7. The radical reaction of 4′ -(phenylseleno)-3′-O-(dimethylvinylsilyl)thymidine derivative 7, which was prepared from thymidine in several steps, with Bu 3 SnH and AIBN, followed by Tamao oxidation, gave either 4′R-(2-hydroxyethyl) derivative 6 or 4′R-(1-hydroxyethyl) derivative 13, respectively. With a low Bu 3 -SnH concentration, the reaction gave 6, via 6-endo-radical-cyclized product 11, as a sole product in 87% yield. The reaction of 7 in the presence of excess Bu 3 SnH gave 13 in 75% yield, via 5-exocyclized product 12, as a diastereomeric mixture. The 4′R-(2-hydroxyethyl) derivative 6 was then converted into a 4′-C-[2-[[N-(2-aminoethyl)carbamoyl]oxy]ethyl]thymidine derivative 14, which was phosphitylated to give phosphoramidite 5 in 72% yield. In this study, 3 was incorporated into a nonadecamer, d[CTGGCTCAGCTCGTCTCAT]-3′, and a heptadecamer, d[CTCGTACCATTCCGCTC]-3′, instead of T at various positions. ODNs containing 3 were more resistant to nucleolytic hydrolysis by both snake venom phosphodiesterase (a 3′-exonuclease) and DNase I (an endonuclease) than unmodified parent ODNs, although ODNs containing 3 only slightly destabilized duplex formation with both complementary DNA and RNA strands. Furthermore, the duplex formed by an ODN containing 3 and its complementary RNA was a good substrate for Escherichia coli RNase H.

Synthesis and Hybridization Properties of Oligonucleotides Containing Polyamines at the C-2 Position of Purines: A Pre-synthetic Approach for the Incorporation of Spermine into Oligodeoxynucleotides Containing 2-(4,9,13-Triazatridecyl)-2′-deoxyguanosine

“…The solvent was evaporated in vacuo to give a beige foam (400 mg, 88 %). ); FAB-MS (positive mode): m/z (%): calcd for C18 H 18 FN 5 O 6 (419.12); found 420.2 (55) [MH] , 304.1 (100) [M À ribose H] .5'-O-(4,4'-Dimethoxytrityl)-6-O-[2-(4-nitrophenyl)ethyl]-2'-deoxy-2-fluoroinosine (6): 6-O-NPE-2'-deoxy-2-fluoroinosine (5) (400 mg, 0.95 mmol)was coevaporated with dry pyridine and the residue was dissolved in pyridine (10 mL). DMT chloride (520 mg, 1.53 mmol) was added and the solution was kept under argon.…”

Oligodeoxynucleotides Having a Loop Consisting of 3‘-Deoxy-4‘-C-(2-hydroxyethyl)thymidines Form Stable Hairpins

“…We have improved the previous procedure for synthesizing 3 (20). One-pot treatment of thymidine with TBSCl/imidazole/DMF and then TFA/aqueous THF provided the 3′-O-TBS-thymidine (6) on a large scale.…”

Synthesis of 4-C-modified 2-Deoxyribonucleoside Analogues and Oligonucleotides

“…Another elegant synthetic route was recently introduced, in which a 4'-C-heteroatom modification is introduced to a nucleoside derivative (Scheme 6) [34]. The aldehyde derivative 10 T which is easily available from thymidine as shown in Scheme 4 served as starting point and was converted as previously reported [35] with phenylselenyl chloride followed by reduction with diisobutylaluminiumhydride into the 4'-C-phenylseleno derivative 26 with high stereoselectivity; only one diastereomer was formed.…”

“…The aldehyde derivative 10 T which is easily available from thymidine as shown in Scheme 4 served as starting point and was converted as previously reported [35] with phenylselenyl chloride followed by reduction with diisobutylaluminiumhydride into the 4'-C-phenylseleno derivative 26 with high stereoselectivity; only one diastereomer was formed. Radical cyclization with tributyltin hydride gave stereo-and regioselectively (6-endo) the cyclic intermediate 30 which was oxidized with hydrogen peroxide to the 4'-C-hydroxyethyl-modified thymidine derivative 31 in good yield (87%) [34]. By reaction with dimethylvinylsilyl chloride the 3'-O vinylsilyl derivative 28 was prepared in 95% yield.…”

“…Reaction with sodium azide, deprotection with TBAF, azide reduction by catalytic hydrogenation, and acylation of the amino group with ethyl trifluoroacetate gave the trifluoroacetyl-protected 4'-C-aminoethyl-modified thymidine derivative 41 [36]. Reaction with ethylenediamine and acylation of the amino group with ethyl trifluoroacetate gave the trifluoroacetylprotected 4'-C-modified thymidine derivative 43 containing a urethane group [41]. The synthesis of the C 3 derivatives was performed accordingly from the 4'-C-hydroxypropyl compound 32.…”