DNA small molecules

At the opposite extreme of molecular size from DNA, small molecules and free atoms can be ionized and subjected to electrophoresis in the gas phase. The technique, named ion mobility spectroscopy (IMS) or plasma chromatography, would better be called gaseous electrophoresis for consistency. The uses and theory of this method can be found in the literature [31,32]. 

While some biological targets such as DNA are not protein in nature, most receptors are. It is useful to consider the properties of receptor proteins to provide a context for the interaction of small molecule drugs with them. An important property of receptors is that they have a 3D structure. Proteins usually are comprised of one or... 

For a review, see M. Casely-Hayford, M. Searcey, The azinomycins. Discovery, synthesis and DNA-binding studies. in DNA and RNA hinders. From small molecules to drugs, Wiley-VCH, Weinheim, 2002. pp. 676 696. 

You might learn about the structure of DNA at the end of your organic chemistry course. For right now, we will be focused on problems that deal primarily with small molecules and therefore, for our purposes, we should think of H-bonding as an interaction a type of intermolecular force. 

This technique provides an easy and convenient method to evaluate the association of small molecules to various polymorphic forms of nucleic acid structures from the measurement of absorbance changes in the absorption maximum of the hgand, where the nucleic acid has no absorbance. Information about overall DNA/RNA base preference and nature of binding can also... 

Electrostatic binding Groove binding Intercalative binding Fig. 5 Schematic representation of various binding modes of small molecules to DNA... 

Molecules of the simpUcity of ethane or the complexity of proteins and DNA adopt different conformations. In the case of ethane this gives rise to the notion of a staggered and eclipsed bond, whereas proteins form an array of complex structural elements and DNA - the famous double hehx. The understanding of the conformational properties of small molecules is an important factor in computational approaches contributing to drug discovery. 

There is rather a small number of functional groups or structural motifs that have the ability to carry out efficient modification of cellular DNA. ° These molecules are of chemical and biological interest because they successfully execute a difficult balancing act—they possess sufficient reactivity to make and break covalent bonds... 

Schulz, W. G. Nieman, R. A. Skibo, E. B. Evidence for DNA phosphate backbone alkylation and cleavage by pyrrolo[l,2-a] benzimidazoles, small molecules capable of causing sequence specific phosphodiester bond hydrolysis. Proc. Natl. Acad. Sci. USA 1995, 92, 11854-11858. 

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