Topological Links between Duplex DNA and a Circular DNA Single Strand**

DNA is well known to adopt various topological (and pseudotopological) structures like knots, catenanes, Borromean rings, and pseudorotaxanes.[1] It has long been recognized that DNA topology plays a crucial role in such fundamental biological phenomena as DNA supercoiling and topoisomerization.[2] Another reason for the considerable interest in higher order DNA topology structures stems from the realization that DNA topological and pseudotopological forms may provide stable and sequence-specific targeting of DNA. Accordingly, highly localized DNA detection and precise spatial positioning of various ligands on the DNA scaffold become possible. This may lead to new applications in molecular biotechnology, in gene therapy, and in the emerging field of DNA nanotechnology.[1d, 3] In this connection, one of the promising DNA pseudotopological constructions is the DNA padlock, consisting of a long single-stranded (ss) DNA molecule forming a pseudorotaxane with a short cyclic oligodeoxyribonucleotide (cODN).[4] Another interesting pseudorotaxane-type structure, the sliding clamp, contains a short cODN threaded on doublestranded (ds) DNA.[1c] Notwithstanding the value of the indicated pseudotopological structures for DNA labeling, note that in these constructions the cODN tag is allowed to slide along the target for considerable distances, compromising the precision of spatial positioning of the label. We have assembled a new supramolecular structure, a linked DNA pseudorotaxane, in which part of a cODN appears to be threaded sequence specifically between complementary strands of dsDNA (see Scheme 1 and Figure 1 a). 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[16] Crystal sructures: 1a (tetragonal isomorph): C24H24N2O4, Mrˆ 404.47, yellow crystals from MeOH, m.p. 171 ± 172 8C; crystal dimensions: 0.50 0.13 0.13 mm; tetragonal, space group I41cd (No. 110), aˆ 18.831(3), bˆ 18.831(3), cˆ 11.639(2) Š, aˆ 908, Vˆ 4127.3(12) Š3, Zˆ 8, 1calcdˆ 1.302 gcmÿ3 ; F(000)ˆ 1712; mCuˆ 7.3 cmÿ1; qmaxˆ 74.978 ; 4372 determined, 2058 independent, 1918 observed reflexions with (F 2 o > 2sF 2 o ); R1ˆ 0.0260, wR2ˆ 0.0714, GOF (F 2)ˆ 1.083 for 137 parameters, residual electron density 0.026/ÿ 0.092 e Šÿ3. 1b (monoclinic isomorph): C24H24N2O4, Mrˆ 404.47, yellow crystals from MeOH, m.p. 171 ± 172 8C; crystal dimensions: 0.20 0.20 0.09 mm; monoclinic, space group P21/n (No. 14), aˆ 7.943(1), bˆ 10.499(1), cˆ 12.7930(1) Š, aˆ 90, bˆ 107.00(1)8, Vˆ 1020.24(19) Š3, Zˆ 2, 1calcdˆ 1.317 g cmÿ3; F(000)ˆ 428; mCuˆ 7.3 cmÿ1; qmaxˆ 758 ; 2200 determined, 2017 independent, 1662 observed reflections (F 2 o > 2sF 2 o ); R1ˆ 0.0358, wR2ˆ 0.1183, GOF (F 2)ˆ 1.004 for 139 parameters, residual electron density 0.215/ÿ 0.132 eŠÿ3. (1 ́ PF6)2: (C24H24N2O4F6P)2, M/2ˆ 549.43, bluish-black needles, decomp.> 250 8C; crystal dimensions: 0.25 0.08 0.03 mm; triclinic, space group P1Å (No. 2), aˆ 8.36(1), bˆ 11.220(1), cˆ 13.067(1) Š, aˆ 111.78(1), bˆ 96.23(1), gˆ 90.56(1)8 ; Vˆ 1129.8(8) Š3, Zˆ 2, 1calcdˆ 1.444 g cmÿ3; F(000)ˆ 510; mMoˆ 1.021 cmÿ1; qmaxˆ 59.99; 3304 determined 3304 independent, 1813 observed refections (F 2 o > 2sF 2 o ); R1ˆ 0.0496, wR2ˆ 0.1234, GOF (F 2)ˆ 0.908 for 339 parameters, residual electron density 0.297/ÿ 0.216 eŠÿ3. The crystallographic data (excludung structure factors for the structures reported in this paper have been deposited with the Crystallographic Data Centre as supplementary publication nos CCDC-102195 (1a), -102194 (1b), and -102196 (1 PF6)2. Copies of the data can be obtained free of charge on application to CCDC, 12 Union Road, Cambridge CB2 1EZ, UK (fax: (‡44) 1223-336-033; e-mail [email protected]. ac.uk). [17] H. J.Keller, D. Nöthe, H. Pritzkow, D. Wehe, M. Werner, P. 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