Structures of non-canonical tandem base pairs in RNA helices: review.

The structures of tandem non-canonical base pairs, a frequently recurring motif in RNA molecules, are reviewed and analysed. The tandem non-canonical base pair motifs can be roughly divided in three groups, containing seven subgroups based on their base pairing patterns and local geometries. Structural details and helical parameters that can be used to numerically distinguish between the subgroups are tabulated.

Synthesis and bioactivity of labelled germination stimulants for the isolation and identification of the strigolactone receptor.

Strigolactones are highly potent germination stimulants for seeds of the parasitic weeds Striga and Orobanche spp. The induction of seed germination is thought to proceed via a receptor-mediated mechanism. Isolation and purification of the strigolactone receptor by affinity chromatography using immobilized avidin or streptavidin requires a biotin labelled strigolactone analogue.

Structure of the pyrimidine-rich internal loop in the poliovirus 3'-UTR: the importance of maintaining pseudo-2-fold symmetry in RNA helices containing two adjacent non-canonical base-pairs.

Formation of non-canonical base-pairs in RNA often plays a very important functional role. In addition they frequently serve as factors in stabilizing the secondary structure elements that provide the frame of large compact RNA structures. Here we describe the structure of an internal loop containing a 5'CU3'/5'UU3' non-canonical tandem base-pair motif, which is conserved within the 3'-UTR of poliovirus-like enteroviruses.

X-ray absorption spectroscopic studies of zinc in the N-terminal domain of HIV-2 integrase and model compounds.

X-ray absorption spectroscopy (XAS), including extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) analysis, has been carried out at the Zn K edge of the N-terminal part of the integrase protein of the human immunodeficiency virus, type 2 (HIV-2), and of some zinc coordination compounds. In the presence of excess beta-mercaptoethanol, which was present in the NMR structure elucidation of the protein [Eijkelenboom et al. (1997), Curr.

Design, synthesis, and biological evaluation of a dual tumor-specific motive containing integrin-targeted plasmin-cleavable doxorubicin prodrug.

The design, synthesis, and initial biological evaluation of a doxorubicin prodrug that contains a dual tumor specific moiety, which allows enhanced tumor recognition potential, is reported. Both a tumor-specific recognition site and a tumor selective enzymatic activation sequence are incorporated in the prodrug. The first tumor-specific sequence is the bicyclic CDCRGDCFC (RGD-4C) peptide that selectively binds alpha v beta 3 and alpha v beta 5 integrins.

Novel 20-carbonate linked prodrugs of camptothecin and 9-aminocamptothecin designed for activation by tumour-associated plasmin.

The first prodrugs of camptothecin and 9-aminocamptothecin that are activated by the tumour-associated protease plasmin are reported. The tripartate prodrugs consist of a tripeptide sequence recognised by plasmin, which is linked to the 20-hydroxyl group of the camptothecins via a 1,6-elimination spacer. After selective N-protection of 9-aminocamptothecin with an Aloc group, the promoiety (tripeptide-spacer conjugate) was linked to camptothecin or 9-Aloc-9-aminocamptothecin via a 20-carbonate linkage by reacting parent drugs with the p-nitrophenyl carbonate activated promoiety in the presence of DMAP.

Synthesis of 1-deoxy-L-gulonojirimycin (L-guloDNJ) and 1-deoxy-D-talonojirimycin (D-taloDNJ).

Carbohydrate based syntheses of azasugars with unusual configurations viz. 1,5-dideoxy-1,5-imino-L-gulitol (L-guloDNJ) and 1,5-dideoxy-1,5-imino-L-talitol (L-taloDNJ) are reported, from D-mannose and D-fructose, respectively. The key steps in both syntheses involved reductive aminative cyclizations.

Lipase polystyrene giant amphiphiles.

A new type of giant amphiphilic molecule has been synthesized by covalently connecting a lipase enzyme headgroup to a maleimide-functionalized polystyrene tail (40 repeat units). The resulting biohybrid forms catalytic micellar rods in water.

The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1.

The human Y-box protein 1 (YB-1) is a member of the Y-box protein family, a class of proteins involved in transcriptional and translational regulation of a wide range of genes. Here, we report the solution structure of the cold-shock domain (CSD) of YB-1, which is thought to be responsible for nucleic acid binding. It is the first structure solved of a eukaryotic member of the cold-shock protein family and consists of a closed five-stranded anti-parallel beta-barrel capped by a long flexible loop.

Hierarchical self-assembly of amphiphilic metallohosts to give discrete nanostructures.

The synthesis and aggregation behavior of a new class of rigid metallohosts is described. The molecules consist of a ruthenium-bipyridine complex functionalized with a glycoluril-based receptor cavity. By specific molecular recognition processes in water, the metallohosts self-assemble to form large arrays of molecules.

Elongated multiple electronic cascade and cyclization spacer systems in activatible anticancer prodrugs for enhanced drug release.

The design and synthesis of several novel elongated self-elimination spacer systems for application in prodrugs is described. These elongated spacer systems can be incorporated between a cleavable specifier and the parent drug. Naphthalene- and biphenyl-containing spacers were synthesized but did not eliminate.

Synthesis of novel paclitaxel prodrugs designed for bioreductive activation in hypoxic tumour tissue.

The syntheses and preliminary evaluation of the first potential bioreductive paclitaxel prodrugs are described. These prodrugs were designed as potential candidates in more selective chemotherapy by targeting hypoxic tumour tissue. Aromatic nitro and azide groups were used as the bioreductive trigger.

Synthesis and Photophysical Properties of Porphyrin-Functionalized Molecular Clips.

Different clip-shaped receptor molecules functionalized at one side-wall with a porphyrin unit have been synthesized by a condensation involving a diamino glucoluril derivative and a porphyrin dione. A similar condensation reaction with a porphyrin tetraone resulted in porphyrin molecule with two receptor sites. The binding and photophysical properties of some of these porphyrin-receptor molecules are described.

Enantioselective Synthesis of 4-Acetylaminocyclopent-2-en-1-ols from Tricyclo[5.2.1.0(2,6)]decenyl Enaminones. Precursors for 5'-Norcarbocyclic Nucleosides and Related Antiviral Compounds.

An efficient synthesis of both (1S,4R) and (1R,4S)-4-N-acetylamino-1-benzoylcyclopent-2-enes 33 has been accomplished starting from enantiopure 5-(1'-phenylethylamino)-endo-tricyclo[5.2.1.

X-ray Absorption Spectroscopic Studies of the Copper(I) Complexes of Crown Ether Appended Bis{(2-pyridyl)ethyl}amines and Their Dioxygen Adducts.

An X-ray absorption spectroscopic study of the Cu complexes of the bis{(2-pyridyl)ethyl}-appended monoaza crown ether 1, diaza crown ether 2, and diphenylglycoluril diaza basket 3 is reported. Following detailed analysis of the spectra of the crystallographically characterized model compound tetrapyridyl Cu(II) bis(nitrato pyridine) (4), the contributions of the ring atoms of the coordinating pyridine to the EXAFS were simulated using a multiple-scattering approach and the final parameters obtained by restrained refinement. Oxygenation of the Cu(I) complexes resulted in a large increase of the intensity of the major peak in the phase-corrected Fourier transform.

Vibrational predissociation dynamics of methane-Ar: an ab initio approach.

We calculated the cross sections for vibrational predissociation of methane-Ar induced by excitation of the methane nu 3 mode with the aid of an ab initio CH4-Ar potential depending explicitly on the nu 3 and nu 1 normal coordinates of the CH4 monomer. We found that dissociation into CH4 fragments excited in the nu 1 mode, a V-->V' process with very low kinetic energy release, strongly dominates over direct dissociation into Ar and ground state CH4, and is responsible for the line broadening observed experimentally. The (observed and calculated) strong variation of the line widths for the Van der Waals levels excited in combination with the nu 3 mode (giving states of A, F and E symmetry) is related to the opening up of appropriate nu 1 dissociation channels and the occurrence of rotational resonances in the nu 1 continuum in the energy range of the quasi-bound nu 3 levels.

Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting.

RNA pseudoknots play important roles in many biological processes. In the simian retrovirus type-1 (SRV-1) a pseudoknot together with a heptanucleotide slippery sequence are responsible for programmed ribosomal frameshifting, a translational recoding mechanism used to control expression of the Gag-Pol polyprotein from overlapping gag and pol open reading frames. Here we present the three-dimensional structure of the SRV-1 pseudoknot determined by NMR.

Anticancer prodrugs for application in monotherapy: targeting hypoxia, tumor-associated enzymes, and receptors.

In order to improve current chemotherapeutic treatment and diminish severe side effects, several prodrug strategies have evolved to achieve site-specific delivery of cytotoxic anticancer agents. This review concentrates on recent developments of antitumor prodrug monotherapy with prodrugs that are designed for direct recognition of tumor-associated factors, such as hypoxia, tumor-associated enzymes and receptors. Firstly, oxygen deficiency in the core of solid tumors leads to enhanced activity of reducing enzymes, like for example nitroreductases, which can be used for site- specific conversion of prodrug to drug.

Lamellar organic thin films through self-assembly and molecular recognition.

Molecular clips possessing U-shaped cavities have been functionalized on their convex side with long aliphatic tails. These molecules form dimers which self-assemble into malleable lamellar thin films. Upon addition of a guest (methyl 3,5-dihydroxybenzoate), a 1:1 host-guest complex is formed, which prohibits clip dimerization.

Self-Assembly and Manipulation of Crown Ether Phthalocyanines at the Gel-Graphite Interface.

Two "face-on" phases and one "edge-on" lamellar phase comprised of self-assembled structures of phthalocyanines have been visualized by scanning tunneling microscopy (STM) at the gel-graphite interface. The switching between the phases can be stimulated with the microscope tip with a resolution on the molecular scale. The STM image shows the manipulated area consisting of π-π stacked phthalocyanines forming the lamellar phase, which is embedded in a hexagonally packed "face-on" phase.

Molecular clips based on propanediurea: exceptionally high binding affinities for resorcinol guests.

A series of new receptor molecules derived from 2,4,6,8-tetraazabicyclo[3.3.1]nonane-3,7-dione (propanediurea) is described.