DOI: 10.1002/chem.200600050 Induced-Fit Recognition of DNA by Small Circular Oligonucleotides Nfflria Escaja, [a, c] Irene Gómez-Pinto, [b, c] Jffllia Viladoms, [a] Manuel Rico, [b] Enrique Pedroso,* [a] and Carlos Gonzµlez* [b] Introduction During the last years, the molecular recognition properties of small circular oligonucleotides have attracted consider- ACHTUNGTRENNUNGable attention. [1, 2] These molecules have emerged as promis- ing tools in research, for diagnosis and as therapeutic agents due to their increased nuclease resistance relative to their linear analogues. In addition, in many cases cyclic oligonu- cleotides exhibit higher binding affinities and greater target specificity than their lineal counterparts. Since the early 1990s, cyclic oligonucleotides have been used to target single-stranded DNA [3] and RNA, [4] by forming triplexes, and double-stranded DNA, by forming either triplexes or more complex structures, named catenanes, in which a short ssDNA chain is threaded on a large circular DNA duplex. [5] This topic has been extensively reviewed by Kool and co- workers. [1, 2] In this paper, we explore a different mechanism for recog- nition between short linear and cyclic oligonucleotides, which may have applications to target specific regions of ge- nomic DNA. We have found that cyclic octamers can recog- nize either cyclic or linear oligonucleotides with the appro- priate sequence. Recognition occurs by forming four-strand- ed structures that are stabilized by tetrads resulting from the association of four bases forming two Watson–Crick base pairs. All the previously found structures are homodimers formed by two tetrads connected by four two-nucleotide loops. Such unusual DNA structures were first observed in the crystallographic structure of the linear heptamer dACHTUNGTRENNUNG(GCATGCT) [6] and, more recently, in crystallographic [7] and solution studies of several cyclic oligonucleotides. [8, 9] This four-stranded motif is different than the classical G- quadruplex, in which four guanine residues are paired through their Watson–Crick and Hoogsteen sides. In some cases guanine quadruplexes contain unusual tetrads. For ex- ample, pure adenine-, [10] thymine-, [11, 12] and cytosine-tet- rads [13] have been found within the scaffold of parallel gua- Abstract: We have investigated the molecular interaction between cyclic and linear oligonucleotides. We have found that short cyclic oligonucleotides can induce hairpinlike structures in linear DNA fragments. By using NMR and CD spectroscopy we have studied the interaction of the cyclic oligonu- cleotide d < pCCTTCGGT > with d < pCAGTCCCT > , as well as with its two linear analogs dACHTUNGTRENNUNG(GTCCCTCA) and dACHTUNGTRENNUNG(CTCAGTCC). Here we report the NMR structural study of these complexes. Recognition between these oligonucleotides occurs through forma- tion of four intermolecular Watson– Crick base pairs. The three-dimension- al structure is stabilized by two tetrads, formed by facing the minor-groove side of the Watson–Crick base pairs. Over- all, the structure is similar to those ob- served previously in other quadruplex- es formed by minor-groove alignment of Watson–Crick base pairs. However, in this case the complexes are heterodi- meric and are formed by two different tetrads (G:C:A:T and G:C:G:C). These complexes represent a new model of DNA recognition by small cyclic oligonucleotides, increasing the number of potential applications of these interesting molecules. Keywords: DNA recognition · NMR spectroscopy · oligonucleotides [a] Dr. N. Escaja, J. Viladoms, Prof. E. Pedroso Departament de Química Orgànica Universitat de Barcelona, Martí I Franqus 1–11 08028 Barcelona (Spain) [b] Dr. I. Gómez-Pinto, Prof. M. Rico, Dr. C. Gonzµlez Instituto de Química-Física Rocasolano (C.S.I.C.) Serrano, 119, 28006 Madrid (Spain) Fax: (+ 34) 915-642-431 E-mail : cgonzalez@iqfr.csic.es [c] Dr. N. Escaja, Dr. I. Gómez-Pinto N. Escaja and I. Gómez-Pinto contributed equally to this work. Supporting information for this article is available on the WWW under http://www.chemeurj.org/ or from the author. Supporting infor- mation contains a figure showing a NOESY spectrum in D 2 O of the complex d < pCCTTCGGT > ·d < pCAGTCCCT > . Chem. Eur. J. 2006, 12, 4035 – 4042 # 2006 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim 4035 FULL PAPER