Current Organic Chemistry, Volume 8, No. 3, 2004
Contents
DNA
Chemistry
Guest
Editor: Zvi Kelman
Breaking the Histone Code of Silence: The Propagation and
Blocking of Heterochromatin
Pp.211-221
David
Donze
The Hepatitis C Virus Replicase: Insights into
RNA-dependent RNA Replication and Prospects for Rational Drug Design Pp.223-241
David
N. Frick
Scope of Nucleotide Chemistry as Studied by Isothermal
Titration Microcalorimetry
Pp.243-250
Magnus Stodeman
Synthetic Oligonucleotide Modifications for the
Investigation of Charge Transfer and Migration Processes in DNA Pp.251-266
Hans-Achim
Wagenknecht
Abstracts
[Back to top] Breaking the Histone Code of Silence: The
Propagation and Blocking of Heterochromatin
David Donze
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.
[Back to top] The Hepatitis C Virus Replicase: Insights into
RNA-dependent RNA Replication and Prospects for Rational Drug Design
David
N. Frick
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.
[Back to top] Scope of Nucleotide Chemistry as Studied by Isothermal
Titration Microcalorimetry
Magnus Stodeman
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, ∆Hb°, the standard Gibbs free energy of binding, ∆Gb°, the entropy of binding, ∆Sb°, and the heat capacity of binding at constant pressure, ∆Cp°. Information on proton uptake/release upon complex formation, modeling on binding cooperativity and conformational change can also be derived. In binding studies, calorimetric ∆Cp° and ∆Hb° data have been used to model the change in apolar and polar solvent accessible surface areas, ∆ASAnpol and ∆ASApol, respectively.
[Back to top] Synthetic Oligonucleotide Modifications for the
Investigation of Charge Transfer and Migration Processes in DNA
Hans-Achim
Wagenknech
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.