Targeting of an interrupted polypurine:polypyrimidine sequence in mammalian cells by a triplex-forming oligonucleotide containing a novel base analogue.

The DNA triple helix consists of a third strand of nucleic acid lying in the major groove of an intact DNA duplex. The most stable triplexes form on polypurine:polypyrimidine sequences, and pyrimidine interruptions in the purine strand are destabilizing. Sequence stringency is imparted by specific Hoogsteen hydrogen bonds between third strand bases and the purine bases in the duplex. Appropriate base and sugar modifications of triple helix-forming oligonucleotides (TFOs) confer chromosome targeting activity in living cells. However, broad utilization of TFOs as gene targeting reagents in mammalian cells has been limited by the requirement for homopurine target sequences. Although there have been a number of base analogues described that appear to be promising as candidates for triplex target expansion, none has been examined in a biological system. We have employed a postsynthetic strategy to prepare a collection of TFOs with base analogues at a defined position. Following assessment of affinity for a triplex target with a single C:G inversion, TFOs with a second generation of analogues were synthesized. One of these, TFO-5a, with 2'-OMe-guanidinylethyl-5-methylcytosine at the position corresponding to the C:G interruption in the target sequence, was further modified to confer bioactivity. The activity of this TFO, linked to psoralen, was measured in a mammalian cell line that was engineered by directed sequence conversion to carry a triplex target with a single C:G interruption. TFO-5a was active against this target and inactive against the corresponding target with an uninterrupted polypurine:polypyrimidine sequence.

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.

Activation of AP-1 through the MAP kinase pathway: a potential mechanism of the carcinogenic effect of arenediazonium ions.

Arenediazonium ions such as those found in the common mushroom Agaricus bisporus have been convincingly demonstrated to be tumorigenic. The specific mechanism of their tumorigenicity remains unclear. It has been shown that arenediazonium ions can be metabolized to aryl radicals, and that reaction of these aryl radicals with DNA produces aryl adducts. These metabolic processes also produce the reactive oxygen species superoxide and hydroxyl radicals which have been implicated in AP-1 activation. To further investigate the mechanism of tumorigenesis by arenediazonium ions, we studied the effect of a representative arenediazonium ion on AP-1 activation and phosphorylation of the signal transduction proteins ERK1, ERK2, JNK, and p38 kinase, both in vitro and in vivo. We also identified the specific radicals produced by spin trapping and ESR analysis. Here, it was found that p-methylbenzenediazonium ion (2a) induced a 16-fold increase in the extent of AP-1 activation at micromolar concentrations, and that this increase coincided with phosphorylation of the signaling kinases ERK1 and -2 and p38 kinase, but not JNK, in JB6 mouse epithelial cells. In vivo studies using AP-1 luciferase reporter-bearing transgenic mice supported the increase in the extent of AP-1 activation in 2a-treated mice over controls, and showed that this effect was different in different tissue types. The antioxidant N-acetylcysteine (NAC), a general antioxidant, showed an inhibitory effect on 2a-mediated AP-1 induction, while aspirin, a hydroxyl radical scavenger, had no effect. Spin trapping studies showed that while NAC suppressed radical formation from 2a, aspirin did not alter radical production from 2a. It appears that 3a, a carbon-centered radical formed from 2a, is responsible for AP-1-induced activation, and therefore, radical species that are not oxygen-centered are also capable of inducing AP-1. These results represent a step toward understanding the mechanism of tumorigenicity of arenediazonium ions.