Indole as an Artificial DNA Base Incorporated via an Acyclic 2′-Deoxyriboside Substitute

Abstract

Indole was synthetically incorporated into DNA as an artificial base at specific sites of duplex DNA. An acyclic substitute for the 2′-deoxyribose was applied in order to obtain a chemically stable nucleoside analogue that can be synthesized by a fast and facile procedure. Studies by methods of optical spectroscopy revealed that the indole base surrogate is intercalated into the DNA base stack and behaves as a universal base analogue with only little influence of the counterbase.

DNA - indole - oligonucleotide - base analogue

References and Notes

See, for example:

1a Yokoyama M. Nomura M. Togo H. Seki H. J. Chem. Soc., Perkin Trans. 1  1996,  2145 

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2 Zhang X. Lee I. Berdis AJ. Org. Biomol. Chem.  2004,  2:  1703 

3a Dinh TH. Bayard M.-J. Igolen J. C. R. Seances Acad. Sci., Ser. C  1976,  283:  227 

3b Girgis NS. Cottam HB. Robins RK. J. Heterocycl. Chem.  1988,  25:  361 

3c Cornia M. Casiraghi G. Zetta L. J. Org. Chem.  1991,  56:  5466 

4 Lai JS. Kool ET. J. Am. Chem. Soc.  2004,  126:  3040 

5a Wagenknecht H.-A. Stemp EDA. Barton JK. J. Am. Chem. Soc.  2000,  122:  1 

5b Wagenknecht H.-A. Stemp EDA. Barton JK. Biochemistry  2000,  39:  5483 

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8 See for ethidium nucleoside, for example: Amann N. Wagenknecht H.-A. Tetrahedron Lett.  2003,  44:  1685 

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10

Wagner, C.; Wagenknecht, H.-A. manuscript submitted for publication.

11

Compound 3 was purified by flash chromatography with CH₂Cl₂:MeOH:Et₃N = 100:3:0.1. Spectroscopic data of 3: ¹H NMR (300 MHz, DMSO-d ₆): δ = 2.99 (m, 6 H, OCH ₂, CHOH, CH ₂NH), 3.34 (m, 2 H, CH₂-indole, masked under residual water in the sample), 3.73 (m, 8 H, OCH ₃, NHCH ₂CH2-indole), 6.87 (d, 4 H, arom. linker), 6.99 (m, 1 H, arom. indole), 7.08 (m, 1 H, arom. indole), 7.24 (m, 7 H, arom. linker), 7.39 (m, 2 H, arom. linker, 1 H arom. indole), 7.53 (m, 1 H, arom. indole), 10.95 (br s, 1 H, NH-indole).
¹³C NMR (75,4 MHz, DMSO-d ₆): δ = 45.03 (CH₂NH), 55.25 (OCH₃), 66.06 (CH₂O), 73.47 (CHOH), 111.68, 113.37, 118.43, 118.56, 121.29, 123.20, 124.13, 127.12, 127.92, 128.03, 129.95, 135.78, 135.83, 136.36, 145.13, 149.82, 158.26. HRMS (ESI): m/z calcd: 537.2753 [MH⁺]; found: 537.2761 [MH⁺].

12

Interestingly, the trifluoroacetylated derivative of 3 shows two sets of NMR signals (due to cis/trans isomers of the immonium structure): ¹H NMR (300 MHz, DMSO-d ₆): δ = 2.90 (m, 3 H, OCH ₂, CHOH), 3.35 (m, 2 H, NCH ₂ linker), 3.64 (m, 2 H, NCH ₂CH₂-indole), 3.71 (m, 6 H, OCH ₃), 4.01 (m, 2 H, NCH₂CH ₂-indole), 6.85 (m, 4 H, arom. linker), 6.93-7.17 (m, 2 H, arom. indole), 7.22 (m, 7 H, arom. linker), 7.45 (m, 3 H, arom.), 7.55 (d, 1 H, arom. indol), 10.86 (br s, 0.5 H, NH-indole, cis-isomer), 10.91 (br s, 0.5 H, NH-indole, trans-isomer).

13 For the extinction coefficients of the oligonucleotides, see: Puglisi JD. Tinoco I. Methods Enzymol.  1989,  180:  304 

14

Indole extinction coefficient: ε₂₆₀ = 4000 M^-1cm^-1 in MeOH.

15

ESI ms data (negative mode): ssDNA1: m/z calcd: 5157.9 [M - H⁺]^-; found: 1719.6 [M - 3 H⁺]^3-; ssDNA2: m/z calcd: 5139.9 [M - H⁺]^-; found: 1713.6 [M - 3 H⁺]^3-; ssDNA3: m/z calcd: 5189.9 [M - H⁺]^-; found: 1730,3 [M - 3 H⁺]^3-; ssDNA4: m/z calcd: 5009.9 [M - H⁺]^-; found: 1703.7 [M - 3 H⁺]^3-.

A universal base analogue does not discriminate between the four natural DNA bases as the counterpart in the complementary strand; see for example:

16a Loakes D. Brown DM. Nucleic Acids Res.  1994,  22:  4039 

16b Loakes D. Hill F. Brown DM. Salisbury SA. J. Mol. Biol.  1997,  270:  426