Molecular dynamics simulations have been used to compare the structure and dynamics of three A-tract-containing DNA dodecamer sequences:  d(CGCAAATTTGCG)2, d(CGCAIATMTGCG)2, and d(CGCIIIMMMGCG)2, where M = 5-methylcytosine. The simulations shed light on experimental observations regarding DNA bending induced by these sequences. We find that replacing an A•T base pair by an I•M base pair does far more to the structure and particularly dynamics of the oligonucleotides than might be expected if the substitution were regarded as just exchanging a hydrogen bond donor and acceptor across the DNA major groove. The evaluation of the molecular dynamics data is greatly simplified by the application of the method of principal component analysis. This allows key differences in the structures and dynamics of the three systems to be readily discerned. Three major modes of deformation are observed, the amplitudes and/or average values of which can vary with sequence. The results allow a simple interpretation of the effects of A•T to I•M substitutions on DNA bending and point to the importance of DNA flexibility, as much as static structure, in determining macroscopic behavior.

We report the results of molecular dynamics studies on the stability of different triple helices containing the pyrimidine motif d(G‚C‚C) in aqueous solution. The stability of triplexes where the Hoogsteen cytosine is protonated is compared with that of triplexes where the same base is present as the neutral imino tautomer. Results support the hypothesis that Hoogsteen cytosines in triplexes where d(G‚C‚C) trios are contiguous are not fully protonated, but a certain percentage of neutral form exists. The results help in the understanding of the apparently contradictory experimental data on d(G‚C‚C)-containing triplexes, and encourages new studies in the field.

Molecular dynamics simulations have been used to study the structure and flexibility of a DNA‚ PNA duplex and a RNA‚PNA duplex in aqueous solution. In this study, trajectories have been generated starting from three different conformations of the PNA‚DNA and PNA‚RNA duplexes: A-like, B-like, and P A/B -like. For the DNA‚PNA duplex, the three trajectories converge within the nanosecond time scale to give structures resembling closely the P B model. The RNA‚PNA duplex trajectories started from A-and P A -forms converge to give structures resembling the P A model, but the trajectory begun from the B-like conformation leads to an unfolded duplex. Despite the similarity between P A and P B structures calculations show the existence of important differences in terms of molecular recognition between both conformations. Analysis of the trajectories shows that the PNA backbone is very flexible provided that the backbone movements do not alter the positioning of the bases. It is found that PNA is able to distort the structure of RNA and especially DNA strands during the formation of the PNA‚DNA and PNA‚RNA hybrids. The impact of these findings in antigene and antisense therapies is discussed.

The synthesis and the pharmacological activity of a series of 1,5-diarylimidazoles developed as potent and selective cyclooxygenase-2 (COX-2) inhibitors are described. The new compounds were evaluated both in vitro (COX-1 and COX-2 inhibition in human whole blood) and in vivo (carrageenan-induced paw edema, air-pouch, and hyperalgesia tests). Modification of all the positions of two regioisomeric imidazole cores led to the identification of 4-[4-chloro-5-(3-fluoro-4-methoxyphenyl)imidazol-1-yl]benzenesulfonamide (UR-8880, 51f) as the best candidate, which is now undergoing Phase I clinical trials.

The mechanism of binding of different nonsteroidal anti-inflammatory drugs to the cyclooxygenase active site of cyclooxygenase-2 (COX-2) has been studied by means of a wide range of theoretical techniques including molecular dynamics and free energy calculations. It is found that theoretical methods predict accurately the binding of different drugs based on different scaffolds. Calculations allow us to describe in detail the key recognition sites and to analyze how these recognition sites change depending on the scaffold of the drug. It is concluded that the recognition site of COX-2 is very flexible and can adapt its structure to very subtle structural changes in the drug.

A DNA-triplex stabilizing purine (8-aminoguanine) is designed based on molecular modeling and synthesized. The substitution of guanine by 8-aminoguanine largely stabilizes the triplex both at neutral and acidic pH, as suggested by molecular dynamics and thermodynamic integration calculations, and demonstrated by melting experiments. NMR experiments confirm the triplex-stabilizing properties of 8-aminoguanine and demonstrate that few changes are found in the structure of the triplex due to the presence of this modified base.

The Drosophila GAGA factor binds specifically to simple repeating d(GA⅐TC) n DNA sequences. These sequences are known to be capable of forming triple-stranded DNA as well as other non-B-DNA conformations. Here, it is shown that GAGA binds to a d[CT(GA⅐TC)] 22 intermolecular triplex with similar specificity and affinity as to a regular double-stranded B-form d(GA⅐TC) 22 sequence. The interaction of GAGA with triplex DNA cannot, however, stimulate transcription in vitro. The affinity of GAGA for triplexes of the purine motif, such as a d[AG(GA⅐TC)] 22 intermolecular triplex, is significantly lower. The DNA binding domain of GAGA is sufficient for efficient binding to triplex DNA. Based on the reported solution structure of the complex of GAGA-DNA binding domain with double-stranded DNA, a model for its interaction with triplex DNA is proposed in which most of the protein-DNA contacts observed in duplex DNA are maintained, especially those occurring through the minor groove. The higher negative charge of the triplex is likely to have also an important contribution to both the specificity and affinity of the interaction.The GAGA factor of Drosophila is a sequence-specific DNAbinding protein that participates in a variety of different chromosomal functions (for reviews see Refs. 1 and 2). GAGA has been shown to stimulate transcription of some developmentally regulated homeotic genes and heat shock genes (3, 4), and GAGA-binding sites are found at the promoters of numerous Drosophila genes (1), suggesting a general role of GAGA in transcription regulation. Although its actual mechanism of action is not yet fully understood, it is believed that, at least to some extent, GAGA functions at the level of chromatin structure, participating in nucleosome remodeling at the promoter regions (5, 6). Consistent with a role at the level of chromatin structure, GAGA is a modifier of position effect variegation (7). A link to chromatin structure is also indicated by its association with heterochromatin (8). Interestingly, GAGA is found associated with the centromeric heterochromatin in mitotic, but not in polytene, chromosomes (9); some GAGA mutants show mitotic defects (10), suggesting a role of GAGA in chromosome condensation and/or segregation.GAGA binds to repeated d(GA⅐TC) n DNA sequences. In general, GAGA-binding sites found at promoters are short, with a consensus of 3.5 dinucleotide repeats, and multiple (1). In some promoters, however, long binding sites are also observed (i.e. hsp26, hsp70, his3, and his4) (1, 11). Moreover, the association of GAGA with heterochromatin occurs mainly through its binding to the (AAGAG) n and (AAGAGAG) n satellites (8), which constitute extremely long arrays of consecutive GAGA-binding sites. Repeated d(GA⅐TC) n DNA sequences are structurally polymorphic being capable of adopting different non-B-DNA conformations (for reviews see Refs. 12 and 13). In particular, they form triple-stranded conformations which, depending on the experimental conditions, are of the d[CT(GA⅐TC)] n or the d[AG(GA⅐T...

State of the art molecular dynamic simulations show that simple modification of the sugar puckering of 2'deoxyriboses leads to a reversible change between two stable forms of DNA which resemble very closely the canonical A and B duplex forms. Analysis of the A-type and B-type structures reveals interesting, and previously unknown features of these two families of conformations of the DNA.