Current Organic Chemistry - Volume 8, Issue 3, 2004

In this issue of Current Organic Chemistry there are papers describing different aspects of nucleic acid chemistry and metabolism. Histones, the building blocks of nucleosomes and a major component of chromatin, play essential roles in the eukaryotic cell. One of their roles is to regulate transcription by participating in forming repressive chromatin structures. In the last several years it has become apparent that histones undergo a large number of post-translational modifications prior to heterochromatin (transcriptionally repressed) formation. The first contribution, by David Donze (Louisiana State University, Louisiana, USA), describes many of the histone modifications and their roles in transcription. The second contribution is by David Frick (New York Medical College, New York, USA), and describes the enzymes needed for Hepatitis C Virus (HCV) replication. HCV is a cause of contagious hepatitis and presents a major threat to human health. To date, however, no vaccine or effective treatment is available. Recent studies on viral replication machinery and the structure and function of the replication proteins may provide clues for future therapeutic targets. One of the emerging approaches to study the thermodynamic properties of protein-nucleic acid and protein-nucleotide interactions is the use of isothermal titration microcalorimetry (ITC). The third paper, by Magnus Stödeman (Center for Chemistry and Chemical Engineering, Lund, Sweden), describes the technique and summarizes many recent studies. The last contribution is by Hans-Achim Wagenknecht (Technical University Munich, Garching, Germany) and provides an overview of synthesis methods for the production of labeled systems used in the study of charge transfer and migration process in DNA, drawing from published techniques spanning over the past decade. A consensus opinion of the reductive electron transfer mechanism is also offered, summarizing current and accepted mechanistic details of the charge transfer process. I would like to thank all the authors for their efforts in making this issue interesting and informative. As the field is rapidly expanding, we welcome your suggestions for topics to be covered in future issues.

Eukaryotic chromosomes consist of blocks of transcriptionally active and inactive regions. Heterochromatic regions of chromatin are generally transcriptionally repressed, and this repressive structure can be propagated along the chromatin fiber. Here I review recent insights on the role of histone modifications in the propagation of repressive chromatin structure, focusing on the creation of heterochromatin protein binding sites by the deacetylation and methylation of nucleosomes, and molecular models detailing the mechanism of propagation. The role of chromatin boundary elements in halting this propagation is discussed in relation to the model systems described. The results suggest that specific combinations of histone modifications constitute a histone code that promotes the propagation of heterochromatin, and by breaking this code along a nucleosomal array, propagation can be stopped to allow expression of downstream genes.

The enzymes involved in the replication of the Hepatitis C Virus (HCV) have been some of the most intensely studied proteins in recent history because they are targets for rational drug design. HCV is an established and growing menace to human health that is without a current vaccine or a widely affordable and effective treatment. Traditional antiviral screening is difficult with HCV because of the lack of a convenient animal model or tissue culture system. Consequently, two viral replicative proteins have been intensely studied as drug targets: the NS3 protein, which possesses serine protease, ATPase, and helicase activities, and the NS5B RNA-dependent RNA polymerase. Structural and mechanistic studies of the HCV replicative proteins have not yet led to antiviral HCV drugs. However, new insights have been gained into the mechanisms of actions of the enzymes comprising the viral replicase. This review discusses recent advances in understanding the HCV NS5B RNA-dependent RNA polymerase and the NS3 helicase mechanisms and suggests how this new information could be exploited for the potential development of future antiviral agents.

The area of isothermal titration microcalorimetric (ITC) studies on solution systems involving nucleotides is reviewed. 62 references are cited. About 25 ITC studies on nucleotide systems have been published during the last two decades. The main part (ca 95%) of these papers deal with nucleotide-protein interactions and one paper involves nucleotide-nucleotide binding studies. The results of such studies include stoichiometry, the (concentration) binding constant, Kb, the enthalpy of binding, ΔHb° , the standard Gibbs free energy of binding, ΔGb° , the entropy of binding, ΔSb° , and the heat capacity of binding at constant pressure, ΔCp° . Information on proton uptake / release upon complex formation, modeling on binding cooperativity and conformational change can also be derived. In binding studies, calorimetric ΔCp° and ΔHb° data have been used to model the change in apolar and polar solvent accessible surface areas, ΔASAnpol and ΔASApol, respectively.

With respect to the biological role during DNA damaging and to potential applications in DNA chip and nanotechnology, the DNA-mediated charge transfer phenomena attracted a lot of attention in the scientific community during the last 15 years. Most research groups have focused their work on the photochemically or photophysically induced oxidation or reduction of DNA using different charge donors. Organic and inorganic intercalators which were covalently attached to oligonucleotides have been employed. Using these DNA systems, a systematic measurement of the distance dependence and the base sequence dependence of the charge transfer processes became possible. This review gives a short overview about the existing photochemical donor-acceptor assays, and, more importantly, focuses on the preparative aspects of the different synthetic oligonucleotide modifications which were developed and applied by the different research groups in order to prepare suitable DNA assays for the studies of charge transfer chemistry. In many cases, DNA base or sugar modifications were introduced via automated solid-phase synthetic methods using the corresponding phosphoramidites as DNA building blocks. Alternatively, DNA modifications can be introduced by solid-phase methods which are applied during or after the automated solid-phase synthesis. It is shown that both methods are suitable for the design and preparation of interesting DNA assays.