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Synlett 2005(9): 1442-1446  
DOI: 10.1055/s-2005-868503
LETTER
© Georg Thieme Verlag Stuttgart · New York

PNA-Directed Triple-Helix Formation by N 7-Xanthine

Robert H. E. Hudson*, Mykhaylo Goncharenko, Andrew P. Wallman, Filip Wojciechowski
Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
Fax: +1(519)6613022; e-Mail: rhhudson@uwo.ca;
Further Information

Publication History

Received 16 August 2004
Publication Date:
29 April 2005 (online)

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Abstract

We report the first example of alkylation of underivatized xanthine with chloroacetic acid to yield a separable mixture of N 7- and N 9-(methylenecarboxyl)xanthine and its conversion to a peptide nucleic acid monomer compatible with Fmoc-based oligomerization chemistry. Additionally, we have simultaneously prepared the N 7 - and N 9-PNA monomers of guanine by alkylation of 2-N-isobutyrylguanine which were subsequently separated. Molecular modeling of the nucleobase base triplets indicates that N 7-xanthine and N 7-guanine form isomorphous triplets with adenine and guanine, respectively. We also show that polyamides containing N 7-xanthine are compatible with triple-helix formation.

Key words

xanthine - peptide nucleic acid - isomorphous - triplex

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N 7- and N 9-xanthine acetic acids were separated by differential solubility in water, the N 7-derivative being less soluble. N 7-isomer: white solid, mp 320 °C (dec). 1H NMR (400 MHz, DMSO): δ = 13.30 (br s, 1 H), 11.61 (s, 1 H), 10.91 (s, 1 H), 7.91 (s, 1 H), 4.99 (s, 2 H). 13C NMR (100 MHz, DMSO): δ = 169.8, 156.3, 151.9, 149.6, 143.9, 107.3, 47.7. HRMS (EI): m/z calcd for C7H6N4O4: 210.0389; found: 210.0397. N 9-isomer: white solid, mp >290 °C (dec). 1H NMR (400 MHz, DMSO): δ = 10.82 (s, 1 H), 7.60 (s, 1 H), 4.84 (s, 2 H). 13C NMR (100 MHz, DMSO): δ = 170.1, 158.9, 152.2, 142.8, 138.5, 115.7, 48.4. HRMS (EI): m/z calcd for C7H6N4O4: 210.0389; found: 210.0451. N3-isomer: see ref. [11]

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Selected data.
Allyl ester precursor to 5: white solid, mp 168-170 °C (dec). 1H NMR (400 MHz, DMSO): δ = 11.53 (br s, 1 H), 10.87 (br s, 1 H), 7.87-7.20 (m, 10 H), 5.90 (m, 1 H), 5.38-5.09 (m, 4 H), 4.66-4.19 (m) and 4.09 major (s, 7 H), 3.46 major (m, minor rotamer overlapping with H2O), 3.09 minor (m, major rotamer overlapping with H2O). HRMS (ESI-TOF): m/z calcd for sodium adduct C29H28N6O7Na: 595.1917; found: 595.1912.
Compound 5: off-white solid, mp 162-164 °C (change in appearance), 205-208 °C (dec). 1H NMR (400 MHz, DMSO): δ = 12.81 (br s, 1 H), 11.58 major and 11.56 minor (1 H), 10.86 major and 10.84 minor (1 H), 7.88-7.28 (m, 10 H), 5.27 major and 5.07 minor (s, 2 H), 4.34-4.20 (m)and 3.98 major (s, 5 H), 3.43 major (m, minor rotamer overlapping with H2O), 3.10 minor (m, major rotamer overlapping with H2O). HRMS (ESI-TOF): m/z calcd for sodium adduct C26H24N6O7Na: 555.1604; found: 555.1602.

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Data for 6 and 7.
Compound 6 (N 9-isomer): white solid, mp 310-331 °C. 1H NMR (400 MHz, DMSO): δ = 12.10 (s, 1 H), 11.66 (s, 1 H), 7.94 (s, 1 H), 4.87 (s, 2 H), 2.76 (sept, 3 J = 6.8 Hz, 1 H) 1.40 (s, 9 H), 1.09 (d, 3 J = 6.9 Hz, 6 H). 13C NMR (100 MHz, DMSO): δ = 180.9, 167.4, 155.5, 149.6, 148.8, 141.0, 120.3, 83.0, 45.5, 35.3, 28.4, 19.6. HRMS (EI): m/z calcd for C15H21N5O4: 335.15937; found: 335.15937.
Compound 7 (N 7-isomer): white solid, mp 202-204 °C. 1H NMR (400 MHz, DMSO): δ = 12.13 (s, 1 H), 11.56 (s, 1 H), 8.10 (s, 1 H), 5.06 (s, 2 H), 2.72 (sept, 3 J = 6.8 Hz, 1 H), 1.40 (s, 9 H), 1.10 (d, 3 J = 6.8 Hz, 6 H). 13C NMR (100 MHz, DMSO): δ = 180.7, 167.6, 157.5, 153.3, 147, 9, 145.5, 112.4, 82.7, 48.6, 35.4, 28.3, 19.6. HRMS (EI): m/z calcd for C15H21N5O4: 335.15937; found: 335.15937.

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Data for 13 and 14.
Compound 13 (N 9-isomer): white solid, mp 234-235 °C. 1H NMR as reported in ref. [22] ; HRMS (ESI-TOF): m/z calcd for sodium adduct C30H31N7O7Na: 624.2183; found: 624.2213.
Compound 14 (N 7-isomer): white solid, mp 188-190 °C (dec). 1H NMR (400 MHz, DMSO): δ = 12.13 (br s, 1 H), 11.59 major and 11.56 minor (s, 1 H), 8.18 minor and 8.15 major (s, 1 H), 7.87-717 (m, 10 H), 5.38 major and 5.20 minor (s, 2 H), 3.46-3.12 (m, 4 H), 2.71 (m, 1 H), 1.10 major and 1.05 minor (d, 3 J = 6.8 Hz, 6 H). HRMS (ESI-TOF): m/z calcd for sodium adduct C30H31N7O7Na: 624.2183; found: 624.2165.

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Oligomers were synthesized on Rink amide resin by an ABI 433a peptide synthesizer at the 5 µmol scale according to the manufacturer-supplied cycles and purified by RP-HPLC.
Data for -T6-lys-NH2 (15) HRMS (MALDI-TOF): m/z calcd for C74H101N27O26: 1783.7411; found: 1784.6012.
Data for Ac-X6-lys-NH2 (16) HRMS (ESI-TOF): m/z calcd for C74H89N39O26: 1940.76; found: 1940.55 [MH+]