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Murat P.,University of Cambridge | Singh Y.,Rutgers University | Defrancq E.,CNRS Molecular Chemistry Department
Chemical Society Reviews | Year: 2011

DNA is considered an important target for drug design and development. Until recently, the focus was on double-stranded (duplex) DNA structures. However, it has now been shown that single stranded DNA can fold into hairpin, triplex, i-motif and G-quadruplex structures. The more interesting G-quadruplex DNA structures comprise four strands of stacked guanine (G)-tetrads formed by the coplanar arrangement of four guanines, held together by Hoogsteen bonds. The DNA sequences with potential to form G-quadruplex structures are found at the chromosomal extremities (i.e. the telomeres) and also at the intra-chromosomal region (i.e. oncogenic promoters) in several important oncogenes. The formation of G-quadruplex structures is considered to have important consequences at the cellular level and such structures have been evoked in the control of expression of certain genes involved in carcinogenesis (c-myc, c-kit, K-ras etc.) as well as in the perturbation of telomeric organization. It has been shown that the formation of quadruplexes inhibits the telomere extension by the telomerase enzyme, which is up-regulated in cancer cells. Therefore, G-quadruplex structures are an important target for drug design and development and there is a huge interest in design and development of small molecules (ligands) to target these structures. A large number of so-called G-quadruplex ligands, displaying varying degrees of affinity and more importantly selectivity (i.e. the ability to interact only with quadruplex-DNA and not duplex-DNA), have been reported. Access to efficient and robust in vitro assays is needed to effectively monitor and quantify the G-quadruplex DNA/ligand interactions. This tutorial review provides an overview of G-quadruplex ligands and biophysical techniques available to monitor such interactions. © 2011 The Royal Society of Chemistry.

Casida M.E.,CNRS Molecular Chemistry Department | Huix-Rotllant M.,CNRS Molecular Chemistry Department
Annual Review of Physical Chemistry | Year: 2012

The classic density-functional theory (DFT) formalism introduced by Hohenberg, Kohn, and Sham in the mid-1960s is based on the idea that the complicated N-electron wave function can be replaced with the mathematically simpler 1-electron charge density in electronic structure calculations of the ground stationary state. As such, ordinary DFT cannot treat time-dependent (TD) problems nor describe excited electronic states. In 1984, Runge and Gross proved a theorem making TD-DFT formally exact. Information about electronic excited states may be obtained from this theory through the linear response (LR) theory formalism. Beginning in the mid-1990s, LR-TD-DFT became increasingly popular for calculating absorption and other spectra of medium- and large-sized molecules. Its ease of use and relatively good accuracy has now brought LR-TD-DFT to the forefront for this type of application. As the number and the diversity of applications of TD-DFT have grown, so too has our understanding of the strengths and weaknesses of the approximate functionals commonly used for TD-DFT. The objective of this article is to continue where a previous review of TD-DFT in Volume 55 of the Annual Review of Physical Chemistry left off and highlight some of the problems and solutions from the point of view of applied physical chemistry. Because doubly-excited states have a particularly important role to play in bond dissociation and formation in both thermal and photochemistry, particular emphasis is placed on the problem of going beyond or around the TD-DFT adiabatic approximation, which limits TD-DFT calculations to nominally singly-excited states. © Copyright ©2012 by Annual Reviews. All rights reserved.

Gilles P.,CNRS Molecular Chemistry Department | Py S.,CNRS Molecular Chemistry Department
Organic Letters | Year: 2012

The SmI 2-mediated cross-coupling of nitrones with β-silyl-α,β-unsaturated esters, followed by zinc reduction, allows an efficient and highly diastereoselective preparation of β-silyl lactams, which are precursors of β-hydroxy lactams through Tamao-Fleming oxidation. By applying the method to a cyclic, carbohydrate-derived nitrone, a new synthesis of (+)-australine has been realized in only 11 steps and in 21% overall yield from l-xylose. © 2012 American Chemical Society.

Cosnier S.,CNRS Molecular Chemistry Department | Holzinger M.,CNRS Molecular Chemistry Department
Chemical Society Reviews | Year: 2011

This tutorial review briefly surveys the chronological evolution of biosensor concepts based on electrogenerated polymers. The most common procedures of biomolecule immobilization are classified as direct electropolymerization, physical entrapment, covalent linkage, and anchoring by affinity interactions via electropolymerized films. These are discussed, and recent bioanalytical applications are described. The discussion emphasizes the use of templates for controlling the formation of nanowires and composite polymers. Recent advances in the design of three-dimensional biological architectures are also highlighted. © 2011 The Royal Society of Chemistry.

Singh Y.,Rutgers University | Murat P.,CNRS Molecular Chemistry Department | Defrancq E.,CNRS Molecular Chemistry Department
Chemical Society Reviews | Year: 2010

Synthetic oligonucleotides (ONs) are being investigated for various therapeutic and diagnostic applications. The interest in ONs arises because of their capability to cause selective inhibition of gene expression by binding to the target DNA/RNA sequences through mechanisms such as antigene, antisense, and RNA interference. ONs with catalytic activity (ribozymes and DNAzymes) against the target sequences, and ability to bind to the target molecules (aptamers), ranging from small molecules to proteins, are also known. Therefore ONs are considered potentially useful for the treatment of viral diseases and cancer. ONs also find use in the design of DNA microchips (a powerful bio-analytical tool) and novel materials in nanotechnology. However, the clinical success achieved so far with ONs has not been satisfactory, and the major impediments have been recognised as their instability against nucleases, lack of target specificity, and poor uptake and targeted delivery. Tremendous efforts have been made to improve the ON properties by either incorporating chemical modifications in the ON structure or covalently linking (conjugation) reporter groups, with biologically relevant properties, to ONs. Conjugation is of great interest because it can be used not only to improve the existing ON properties but also to impart entirely new properties. This tutorial review focuses on the recent developments in ON conjugation, and describes the key challenges in efficient ON conjugation and major synthetic approaches available for successful ON conjugate syntheses. In addition, an overview on major classes of ON conjugates along with their use in therapeutics, diagnostics and nanotechnology is provided. © The Royal Society of Chemistry 2010.

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