Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator

We report the 1.1-Å resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5'-(dCGGAAATTCCCG)2-3'. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches

Metallo-intercalators and metallo-insertors

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical attributes and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that target single base mismatches in duplex DNA through metallo-insertion

Experimental phase-space-based optical amplification of scar modes

Waves billiard which are chaotic in the geometrical limit are known to support non-generic spatially localized modes called scar modes. The interaction of the scar modes with gain has been recently investigated in optics in micro-cavity lasers and vertically-cavity surface-emitting lasers. Exploiting the localization properties of scar modes in their wave analogous phase space representation, we report experimental results of scar modes selection by gain in a doped D-shaped optical fiber

Finiteness properties for Pisot SS-adic tilings

International audienceIn this paper, we will first formulate and prove some equivalent sufficient conditions to obtain the tiling property for a Pisot unimodular substitution. We will then apply these condition to the more general framework of adic systems, to extend to this more general (and non algebraic) case results already known for the substitutive case

Generalized Substitutions and Stepped Surfaces

A substitution is a non-erasing morphism of the free monoid. The notion of multidimensional substitution of non-constant length acting on multidimensional words introduced in [AI01,ABS04] is proved to be sell-defined on the set of two-dimensional words related to discrete approximations of irrational planes. Such a multidimensional substitution can be associated to any usual Pisot unimodular substitution. The aim of this paper is to try to extend the domain of definition of such multidimensional substitutions. In particular, we study an example of a multidimensional substitution which acts on a stepped surface in the sense of [Jam04,JP04]

Fractal representation of the attractive lamination of an automorphism of the free group

N°RR 05066 (2005)International audienceIn this paper, we extend to automorphisms of free groups some results and constructions that classically hold for morphisms of the free monoid, i.e., so-called substitutions. A geometric representation of the attractive lamination of a class of automorphisms of the free group (irreducible with irreducible powers ({\it iwip}) automorphisms) is given in the case where the dilation coefficient of the automorphism is a unit Pisot number. The shift map associated with the attractive symbolic lamination is, in this case, proved to be measure-theoretically isomorphic to a domain exchange on a self-similar Euclidean compact set. This set is called the central tile of the automorphism, and is inspired by Rauzy fractals associated with Pisot primitive substitutions. The central tile admits some specific symmetries, and is conjectured under the Pisot hypothesis to be a fundamental domain for a toral translation