3′-Modified Nucleotides for DNA Sequencing Without Gel Electrophoresis

Abstract

Dibenzyl-3′-O-[(6-azido-2,3,6-trideoxy-4,5-di-O-benzyl) hexanoyl] thymidine 5′-yl phosphate 8a was prepared. Catalytic hydrogenolysis removed only the benzyl esters and reduced the azido group. When the benzyl ethers were replaced by p-phenylbenzyl or allyl ethers, their deprotection also failed.

Notes

¹H NMR (CDCl₃) δ: 1.85 (d, 3H, Me-T, J₆ Me = 0.79 Hz); 2.17 (dd, 1H, H′2, J2′-1′ = 5.52 Hz, J2′,2″ = 13.97 Hz); 2.34 (t, 2H, CH₂); 3.49 (m, 2H, 2xCHOBn); 3.62 (m, 2H, CH₂N₃); 3.98 (m, 1H, H4′); 4.16 (m, 2H, H′5, H5″); 4.70 (d, 2H, CH₂Ph); 4.57 (d, 2H, CH₂Ph); 5.06 (m, 5H, H′3, 2xCH₂Ph); 6.31 (dd, 1H, H′1, J1′,2′ = 5.35 Hz, J1′,2″ = 9.28 Hz); 7.35 (m, 21H, NH, 4xPh); 8.82 (d, 1H, H6). ¹³C NMR (CDCl₃) δ: 12.19 (Me-T); 25.24 (C″2); 25.46 (C″3); 36.84 (C′2); 50.71 (C″6); 66.92 (C′5); 69.66 (2xCH₂Ph); 72.40 (2xCH₂Ph); 74.48 (C′3); 77.07 (C″5); 79.08 (C″4); 82.55 (d, C′4); 84.82 ((C′1); 111.62 (C5); 127.48–137.67 (C aromatics); 134.63 (C6); 150.20 (C2); 163.31 (C4); 172.76 (C=O). ³¹P NMR (CDCl₃) δ: -2.50 (m, 1P)

¹H NMR (D₂O) δ: 1.86 (s, 3H, Me-T); 3.22 (m, 2H, CH₂NH₂); 3.94 (m, 2H, H′5, H5″); 4.05 (m, 1H, H4′); 4.64 (m, 4H, 2xCH₂Ph); 5.13 (m, IH, H′3); 6.11 (dd, 1H, H′1); 7.33 (s, 10H, 2xPh); 7.65 (s, 1H, H6). ³¹P NMR (D₂O) δ: 0.78 (s, 1P)