Biomod/2013/Aarhus/Materials And Methods/Chemical Modification: Difference between revisions

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===Photosensitizer===
===Photosensitizer===
===Synthesis of 5-propargylamino-ddUTP===
===5-propargylamino-ddUTP===


====1-[2,6-Dioxa-bicyclo [3.2.0]hept-3-yl]-1H-pyrimidine-2,4-dione (8). ====
====1-[2,6-Dioxa-bicyclo [3.2.0]hept-3-yl]-1H-pyrimidine-2,4-dione (8). ====

Revision as of 11:40, 20 October 2013

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Chemical Modification

Cholesterol derivative

Tert-butyl cholesteroxy acetate (3).

Cholesterol (2) (0.310 g, 0.802 mmol) was added to a flame-dried round-bottomed flask and dissolved in dry THF (2 mL) under an argon atmosphere. The solution was cooled to 0 °C and NaH (60% in mineral oil, 0.065 g, 1.63 mmol, 2 equiv.) was added. The resulting mixture was stirred for 1 h before the electrophile tert-butyl bromoacetate (0.30 mL, 2.0 mmol, 2.5 equiv.) was added. This solution was heated to room temperature and left for 20 h. The solution obtained a slightly yellow color. The reaction was cooled to 0 °C and quenched with a small amount of MeOH. The solvent was evaporated and the residue dissolved in DCM (15 mL). The organic phase was washed with H2O (2x15 mL), brine (10 mL), dried over Na2SO4, filtered by suction and evaporated to dryness in vacuo. The product was purified by flash column chromatography (EtOAc/pentane 3:97). This afforded compound 3 (0.031 g, 0.062 mmol, 8%) as a white solid.

Rf 0.29 (EtOAc/pentane 3:97). mp (uncorr.) 144.1-146.3 °C (lit.34 148-149 °C). 1H NMR (400 MHz, CDCl3): δ 5.35 (d, J = 5.1 Hz, 1H), 4.00 (s, 2H), 3.28-3.18 (m, 1H), 2.42-2.20 (m, 2H) 2.05-1.75 (m, 5H), 1.64-0.80 (m, 42H), 0.67 (s, 3H). 13C NMR (100 MHz, CDCl3): δ 170.1, 140.7, 121.8, 81.4, 79.8, 66.1, 56.8, 56.2, 50.2, 42.3, 39.8, 39.5, 38.8, 37.1, 36.8, 36.2, 35.8, 31.9, 31.9, 28.2, 28.1, 28.0, 24.3, 23.8, 22.8, 22.6, 21.1, 19.4, 18.7, 11.9. HRMS (ESI) m/z [M + Na]+ calcd for C33H56O3Na, 523.4127; found, 523.4127. IR (neat) νmax (cm-1): 2953, 2933, 2866, 1745, 1127. 〖[α]〗_D^26 -31.6 (c 0.56, CHCl3).

Cholesteroxy-acetic acid (4).

To a 25 mL round-bottomed flask containing 3 (0.091 g, 0.18 mmol) was added formic acid (9 mL) and the reaction was left to react for 20 h at rt. The solvent was co-evaporated with DCM. The residue was dissolved in Et2O (25 mL) and extracted with sat. aq. NaHCO3 (8x25 mL). The combined water phases were made acidic with 2 M HCl and extracted with DCM (6x20 mL). The combined organic phases were washed with H2O (25 mL), brine (25 mL), dried over MgSO4, filtered under suction and evaporated to dryness in vacuo, affording 4 (0.061 g, 0.14 mmol, 76%) as a white solid.

Rf 0.47 (EtOAc/pentane 1:1 + 1% formic acid). mp (uncorr.) 152.5-154.9 °C (lit.34 163-165 °C). 1H NMR (400 MHz, CDCl3): δ 5.38 (d, J = 5.0 Hz, 1H), 4.13 (s, 2H), 3.38-3.26 (m, 1H), 2.41-2.23 (m, 2H), 2.05-1.76 (m, 6H), 1.62-0.81 (m, 33H), 0.68 (s, 3H). 13C NMR (100 MHz, CDCl3): δ 174.0, 140.1, 122.6, 80.6, 65.3, 56.9, 56.3, 50.3, 42.5, 39.9, 39.7, 38.8, 37.1, 36.9, 36.3, 35.9, 32.1, 32.0, 28.4, 28.2, 28.2, 24.4, 24.0, 23.0, 22.7, 21.2, 19.5, 18.9, 12.0. HRMS (ESI) m/z [M + Na]+ calcd for C29H48O3Na, 467.3501; found, 467.3498. IR (neat) νmax (cm-1): 3000 (broad), 2935, 2904, 2866, 1726, 1704, 1269, 1146. 〖[α]〗_D^26 -30.9 (c 0.91, CHCl3).

2,5-dioxopyrrolidin-1-yl cholesteroxy acetate (5).

The two reagents EDC•HCl (0.044 g, 0.23 mmol, 2.1 equiv.) and NHS (0.019 g, 0.17 mmol, 1.7 equiv.) were added to a solution of 4 (0.048 g, 0.11 mmol) in DCM (3 mL) in a 10 mL round-bottomed flask. The resulting mixture was stirred for 3 h, after which it was transferred to a separatory funnel and washed with a 2.5% aq. solution of NaHSO4 (3x5 mL). The organic phase was dried over Na2SO4, filtered by suction and evaporated to dryness in vacuo. The resulting product was not purified further, yielding 5 (0.047 g, 0.087 mmol, 80%) as a slightly yellow solid.

Rf 0.39 (EtOAc/pentane 3:7). 1H NMR (400 MHz, CDCl3): δ 5.37 (d, J = 5.0 Hz, 1H), 4.47 (s, 2H), 3.37-3.28 (m, 1H), 2.88-2.80 (m, 4H) 2.43-2.36 (m, 1H), 2.33-2.23 (m, 1H), 2.04-1.77 (m, 5H), 1.61-0.82 (m, 33H), 0.67 (s, 3H). 13C NMR (100 MHz, CDCl3): δ 168.9, 166.6, 122.5, 81.0, 63.7, 56.9, 56.3, 50.2, 42.5, 39.9, 39.7, 38.7, 37.1, 36.9, 36.3, 35.9, 32.1, 32.0, 28.4, 28.2, 25.7, 24.4, 24.0, 23.0, 22.7, 21.2, 19.5, 18.9, 12.0. HRMS (ESI) m/z [M + Na]+ calcd for C33H51NO5Na, 564.3659; found, 564.3630.

Photosensitizer

5-propargylamino-ddUTP

1-[2,6-Dioxa-bicyclo [3.2.0]hept-3-yl]-1H-pyrimidine-2,4-dione (8).

2′-Deoxyuridine (2) (1.099 g, 4.816 mmol) was added to a flame-dried 50 mL round-bottomed flask under an argon atmosphere and dissolved in anhydrous pyridine (8 mL). The solution was cooled to 0 °C before methanesulfonyl chloride (1.2 mL, 15.5 mmol, 3.2 equiv.) was added to the solution and the reaction was stirred at 0 °C for 2 h. The reaction was allowed to reach rt and left for 1.2 h. The solvent was evaporated in vacuo and the resulting brown oil was washed with ice water (10 mL) and EtOAc (10 mL). The water phase was extracted with EtOAc (100 mL) and the collected organic phases were added to the residual oil in the reaction flask. The organic solvent was evaporated to dryness before MeOH (25 mL) was added together with 6 M NaOH (5 mL, 30 mmol, 6.2 equiv.). When the mixture was heated to 80 °C the residual oil started to dissolve. The solution was left for 5 h at 80 °C before it was cooled to rt and neutralized with 1 M HCl (18 mL). The resulting mixture was transferred to a 100 mL flask and evaporated to dryness. The solid residue was refluxed in acetone (4x50 mL) for 10 min each time to extract the product. The combined organic phases were evaporated to dryness and the product purified by flash column chromatography (5% to 10% MeOH in DCM) yielding 8 as a white solid (0.483 g, 2.30 mmol, 48%).

Rf 0.63 (MeOH/DCM 1:9). mp (uncorr.) 209.5-211.3 °C (lit.32 206-210 °C). 1H NMR (400 MHz, d6-DMSO): δ 11.35 (s, 1H), 8.16 (d, J = 8.1 Hz, 1H), 6.51 (t, J = 5.3 Hz, 1H), 5.71 (dd, J = 2.3, 8.1 Hz, 1H), 5.48 (q, J = 3.3 Hz, 1H), 4.93-4.89 (m, 1H), 4.69 (dd, J = 4.1, 8.2 Hz, 1H), 4.01 (dd, J = 1.5, 8.1 Hz, 1H), 2.53-2.46 (m, 2H). 13C NMR (100 MHz, d6-DMSO): δ 163.1, 151.2, 141.1, 102.2, 88.5, 86.9, 80.1, 75.2, 37.2. HRMS (ESI) m/z [M + Na]+ calcd for C9H10N2O4Na, 233.0538; found, 233.0535. IR (neat) νmax (cm-1): 3158 (broad), 3042, 2990, 1713, 1682, 1461, 1269, 1088. 〖[α]〗_D^26 -36.9 (c 1.06, MeOH).

2′,3′-Didehydro-2′,3′-dideoxyuridine (9).

A solution of 8 (0.600 g, 2.85 mmol) in dry DMF (12 mL) placed in a flame-dried 25 mL round-bottomed flask under an argon atmosphere was cooled to 0 °C, after which NaH (60% mineral oil suspension, 0.363 g, 9.08 mmol, 3.2 equiv.) was added. The resulting mixture was heated to 100 °C and left to react for 7 h after which the reaction was quenched with H2O (8 mL) and the solvent was evaporated to dryness. The residue was dissolved in MeOH and neutralized with 1 M HCl (8 mL). The solvent was evaporated in vacuo, and the product purified by flash column chromatography (5% to 10% MeOH in DCM) affording 9 (0.351 g, 1.67 mmol, 58%) as a white solid.

Rf 0.30 (MeOH/DCM 1:9). mp (uncorr.) 152.1-153.2 °C (lit.32 150-152 °C). 1H NMR (400 MHz, d6-DMSO): δ 11.30 (s, 1H), 7.74 (d, J = 8.1 Hz, 1H), 6.82-6.80 (m, 1H), 6.40 (dt, J = 1.6, 6.0 Hz, 1H), 5.94-5.90 (m, 1H), 5.59 (d, J = 8.0 Hz, 1H), 4.97 (t, J = 5.3 Hz, 1H), 4.80-4.75 (m, 1H), 3.58 (dd, J = 3.6, 5.0 Hz, 2H). 13C NMR (100 MHz, d6-DMSO): δ 163.2, 150.8, 141.1, 135.1, 125.8, 101.6, 89.1, 87.4, 62.2. HRMS (ESI) m/z [M + Na]+ calcd for C9H10N2O4Na, 233.0538; found, 233.0536. IR (neat) νmax (cm-1): 3449, 3171, 3101, 3043, 1697, 1672, 1454, 1393, 1106. 〖[α]〗_D^26 -6.7 (c 1.01, MeOH).

2′,3′-Dideoxyuridine (10).

To a solution of 9 (0.304 g, 1.45 mmol) in dry MeOH (10 mL) placed in a flame-dried 25 mL round-bottomed flask was added palladium on carbon (10 w/w%, 0.024 g, 0.023 mmol, 0.016 equiv.) under an argon atmosphere. The resulting solution was purged with H2 before it was left with an H2 atmosphere for 4 h at rt. The catalyst was filtered off and the solvent was evaporated in vacuo, affording 10, without further purification, in a quantitative yield (0.306 g) as a white solid.

Rf 0.28 (MeOH/DCM 1:9). mp (uncorr.) 107.7-111.4 °C (lit.32 117.5-118.5 °C). 1H NMR (400 MHz, d6-DMSO): δ 11.24 (br. s, 1H), 7.94 (d, J = 8.1 Hz, 1H), 5.95 (dd, J = 3.6, 6.8 Hz, 1H), 5.58 (d, J = 8.1 Hz, 1H), 5.03 (br. s, 1H), 4.06-3.98 (m, 1H), 3.67 (dd, J = 3.3, 11.9 Hz, 1H), 3.53 (dd, J = 3.8, 11.9 Hz, 1H), 2.34-2.21 (m, 1H), 1.99-1.77 (m, 3H). 13C NMR (100 MHz, d6-DMSO): δ 163.3, 150.5, 140.6, 101.0, 85.1, 81.5, 62.0, 31.8, 24.8. HRMS (ESI) m/z [M + Na]+ calcd for C9H12N2O4Na, 235.0695; found, 235.0690. IR (neat) νmax (cm-1): 3370, 3170, 3050, 2908, 1655, 1618, 1468, 1397, 1275, 1100. 〖[α]〗_D^26 +51.4 (c 0.89, MeOH).

2′,3′-Dideoxy-5-iodoridine (11).

Compound 10 (0.082 g, 0.39 mmol) was placed in a flame-dried 25 mL round-bottomed flask and dissolved in glacial acetic acid (3 mL) under an argon atmosphere. Iodine (0.082 g, 0.32 mmol, 0.8 equiv.) and CAN (0.104 g, 0.19 mmol, 0.5 equiv.) was added to the solution and the reaction was stirred at 80 °C. After 37 min the mixture was cooled to rt. The solvent was evaporated and co-evaporated with MeOH (2x10 mL). The product was purified by flash column chromatography (3% to 5% MeOH in DCM) yielding 11 (0.096 g, 0.28 mmol, 72%) as a slightly yellow solid.

Rf 0.57 (MeOH/DCM 1:9). mp (uncorr.) 179.0-181.5 °C. 1H NMR (400 MHz, d6-acetone): δ 10.24 (br. s, 1H), 8.71 (s, 1H), 5.99 (dd, J = 2.9, 6.5 Hz, 1H), 4.40 (t, J = 4.8 Hz, 1H), 4.23-4.15 (m, 1H), 4.00-3.93 (m, 1H), 3.77-3.71 (m, 1H), 2.45-2.31 (m, 1H), 2.22-1.88 (m, 3H). 13C NMR (100 MHz, d6-acetone): δ 160.9, 151.0, 146.6, 87.4, 83.4, 67.2, 62.8, 33.8, 24.9. HRMS (ESI) m/z [M + Na]+ calcd for C9H11IN2O4Na, 360.9656; found, 360.9658. IR (neat) νmax (cm-1): 3414 (broad), 3158, 3043, 2923, 1674, 1603, 1435, 1275, 1094, 1063. 〖[α]〗_D^30 +16.5 (c 0.71, MeOH).

5-[3-(Trifluoroacetyl amino)-prop-ynyl]-2’, 3’-dideoxyuridine (12).

To a round-bottomed flask were added compound 11 (30 mg, 0.089 mmol), CuI (2.8 mg, 0.015 mmol, 0.17 equiv.), PdCl2(PPh3)2 (9.0 mg, 0.013 mmol, 0.14 equiv.). The reagents were then dried for 30 min under high vacuum and subsequently placed under an Argon atmosphere. Dry DMF was degassed with argon and sonicated. Dry, degassed DMF (5 mL) was added to the solid reagents followed by addition of TEA (0.1 mL, 0.72 mmol, 8 equiv.) and compound XX (94.9 mg, 0.628 mmol, 7 equiv.). The reaction was left at room temperature overnight. The mixture was diluted with brine (20 mL) and extracted with EtOAc (2x25 mL). The combined organic phases were dried over MgSO4 and evaporated to dryness. The product was purified by flash column chromatography (5% MeOH in DCM) yielding 12 (13.1mg, 0.036 mmol, 41%) as a slightly yellow oil.

1H NMR (400 MHz, Acetone) δ 10.19 (s, 1H), 9.03 (s, 1H), 8.47 (s, 1H), 6.00 (dd, J =3.2, 6.5 Hz, 1H), 4.38-4.28 (m, 2H), 4.23-4.14 (m, 1H), 3.93 (d, J = 11.9 Hz, 1H), 3.74 (d, J = 13.2 Hz, 1H), 2.49-2.29 (m, 1H), 2.28-1.84 (m, 4H).

5-[3-Aminoprop-1-ynyl]-2’, 3’-dideoxyuridine-5’-O-triphosphate (13).

Compound 12 (13.1mg, 0.036 mmol),salicyl phosphorochloridite (22.9 mg, 0.113 mmol, 3 equiv.) and tributylammonium pyrophosphate (85.3 mg, 0.155 mmol, 2.1 equiv.) were dried overnight in separate flasks. Tributylamine (0.6 mL, 2.5 mmol, 35 equiv.) was dried under high vacuum for 1 h. Tributylammonium pyrophosphate was dissolved in dry DMF (0.5 mL) before Tributylamine was added. Salicyl phosphorochloridite was dissolved in dry DMF (0.25 mL) followed by addition of 0.55 mL of the pyrophosphate mixture. The solution was left for 40 min before it was transferred to the flask containing the nucleoside. The reaction was left for 3 h before an iodine solution (0.6 mL, 3% in pyridine/H2O 9:1) was added. After 15 min water (2 mL) was added and the reaction was left for another 1.5 h. The product was precipitated by addition of aq. NaCl (0.5 mL,3 M) and EtOH (15mL, 96%), cooled on dry ice for 1 h and centrifuged (4 °C, 20 min, 3000 rpm). The supernatant was discarded and the residue dissolved in water (5 mL). To the dissolved product was added NH4OH (5 mL, 24%) and the mixture was left for 3 h. The resulting mixture was freeze-dried and purification was attempted using a prep. TLC (i-propanol/NH4OH/H2O 48:32:20). No product was obtained.

Propargyl trifluoroacetamide (XX).

Propargylamine (0.990 g, 18.0 mmol) was dissolved in dry DMF (12mL). To the solution was added TEA (2.5mL) before the mixture was cooled to °0 C. A solution of Trifluoroacetic anhydride (2.80 mL, 20.0 mmol, 1.1 equiv.) in dry DMF (5mL) was added dropwise. The reaction was let for 50 min before water (5 mL) was added. The resulting mixture was washed with 1 M HCl (15 mL) and sat. NaHCO3 (15 mL), dried over Na2SO4, filtered and concentrated to dryness in vacuo. Compound XX (0.7115 g, 4.7 mmol, 26%) was obtained without further purification as a yellow oil.

1H NMR (400 MHz, CDCl3) δ 6.63 (br. s, 1H), 4.24-4.09 (m, 2H), 2.34 (s, 1H).

DNA Conjugation

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</style> </head> <body> <div id="indexing"> <div id="sitemap"> <p id="sitemapTitle">SITEMAP | BIOMOD 2013 NANO CREATORS | Aarhus University</p> <div id="footer-contents"> <div class="footer-section"> <p class="footer-section-title">INTRODUCTION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus">Home, abstract, animation and video</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Introduction">Introduction</a></li </ul> </div> <div class="footer-section"> <p class="footer-section-title">RESULTS AND DISCUSSION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/System_In_Action">System in action</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">MATERIALS AND METHODS</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/System_In_Action">System in action</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Methods">Methods</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">SUPPLEMENTARY</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Team_And_Acknowledgments">Team and acknowledgments</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Optimizations">Optimizations</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Data">Supplementary data</a></li>

                                               <li><a

href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Informations">Supplementary informations</a> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/References">References</a></li> </ul> </div> </div> <div> <p id="copyright">Copyright (C) 2013 | BIOMOD Team Nano Creators @ Aarhus University | Programming by: <a href="mailto:pvskaarup@gmail.com?Subject=BIOMOD 2013:">Peter Vium Skaarup</a>.</p> </div> </div>

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