2'-Fluoro-Pyrimidine-Modified RNA Aptamers Specific for Lipopolysaccharide Binding Protein (LBP).

Lipopolysaccaride binding protein (LBP), a glycosylated acute phase protein, plays an important role in the pathophysiology of sepsis. LBP binds with high affinity to the lipid part of bacterial lipopolysaccaride (LPS). Inhibition of the LPS-LBP interaction or blockage of LBP-mediated transfer of LPS monomers to CD14 may be therapeutical strategies to prevent septic shock. LBP is also of interest as a biomarker to identify septic patients at high risk for death, as LBP levels are elevated during early stages of severe sepsis. As a first step toward such potential applications, we isolated aptamers specific for murine LBP (mLBP) by in vitro selection from a library containing a 60-nucleotide randomized region. Modified RNA pools were transcribed in the presence of 2'-fluoro-modified pyrimidine nucleotides to stabilize transcripts against nuclease degradation. As verified for one aptamer experimentally, the selected aptamers adopt a "three-helix junction" architecture, presenting single-stranded 7-nt (5'-YGCTTCY) or 6-nt (5'-RTTTCY) consensus sequences in their core. The best binder (aptamer A011; Kd of 270 nM for binding to mLBP), characterized in more detail by structure probing and boundary analysis, was demonstrated to bind with high specificity to murine LBP.

In vitro selection of RNA aptamers against a conserved region of the Plasmodium falciparum erythrocyte membrane protein 1.

The var-gene encoding Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is known to play a major role in the pathogenicity of the P. falciparum parasite. The protein enables the parasite to adhere to the endothelial linings of small blood vessels (cytoadherence) as well as to non-infected erythrocytes (rosetting), thus preventing clearance from the bloodstream. The development and spread of resistance towards most anti-malarial drugs used for treatment and prevention of the most severe form of malaria truly emphasise the importance of a continuous research and development of new drugs. In this study we use Systematic Evolution of Ligands by EXponential enrichment (SELEX) methodology to isolate high-affinity ligands (aptamers). To validate the results from the SELEX in vitro selection, different aptamers have been selected against PfEMP1 in a live cell assay of P. falciparum strain FCR3S1.2, a highly rosetting strain. We have been able to show the rosette disrupting capacity of these SELEX-aptamers at concentrations of 33 nM and with 100% disruption at 387 nM. The described results show that RNA aptamers are promising candidates for adjunct therapy in severe malaria.

Construction of polyamine-modified uridine and adenosine derivatives--evaluation of DNA binding capacity and cytotoxicity in vitro.

We here report the synthesis of the two polyamine-based nucleoside derivatives 5-{[bis-(3-aminopropyl)amino]acetamido-1-propynyl}uridine and 2-{[bis-(3-aminopropyl)amino]-acetamido-1-propynyl}adenosine. The various polyamine derivatives have been used in thermal melting analysis using DNA from herring testes, and in cellular studies using four different cell lines. The compounds were all found to be non-toxic, thus holding good promise for future use as siRNA building blocks.

{1-[1-(3-Carboxy-propanamido)eth-yl]-1',2-bis-(diphenyl-phosphino)ferrocene-κP,P'}dichloridoplatinum(II) dichloro-methane 1.25-solvate.

The dinuclear title compound, [FePtCl(2)(C(17)H(14)P)(C(23)H(23)NO(3)P)]·1.25CH(2)Cl(2), has a slightly distorted cis-PtCl(2)P(2) square-planar geometry around the Pt atom, and the ferrocenylphosphine ligands are staggered at an angle of 29.4 (2)° about Pt. In the crystal structure, the complex forms centrosymmetric dimers via two strong inter-molecular O-H⋯O bonds resulting in R(2) (2)(8) rings. A weak intra-molecular N-H⋯Cl bond leads to an S(8) motif. The solvent is highly disordered and has not been modelled with discrete atoms.

Kinetic preference for interaction of cisplatin with the G-C-rich wobble basepair region in both tRNAAla and MhAla.

The anticancer active complex cisplatin interacts preferentially with the common, G-C rich, wobble base pair region of both tRNA(Ala) and Mh(Ala) in a reaction that at pH 6.3 is rate limited by the acid hydrolysis of the metal complex.

A comparative kinetic study of modified Pt(dppf)Cl2 complexes and their interactions with L-cys and L-met.

With the success of cisplatin (cis-diamminedichloroplatinum(II)), strong interest has developed in the application of inorganic metal complexes to the treatment of cancer. Research has focused on platinum(II) complexes with a variety of spectator ligands that provide novel physicochemical properties. In this paper we report a kinetic study of 1',1'-bis(diphenylphosphino)ferrocenedichloroplatinum(II) and two related compounds with either an acetate or amide ester substituent attached to the cyclopentadienyl ring. For all compounds the reactivity towards L-cysteine and L-methionine in aqueous solution has been investigated (25 degrees C, I= 0.010 M and pseudo-first-order conditions). For the reactions with l-cysteine and l-methionine the reactions proceeded via a steady-state aquated intermediate to form mono (0.92(2)-3.25(4)) x 10(-3) s(-1)) and bis adducts (0.97(2)-3.67(4)) x 10(-4) s(-1)). For reactions with l-cysteine, direct reactions with the starting complex also contributed (mono adduct: 0.36(2)-1.41(4) M(-1) s(-1), bis adduct: 0.080(1)-0.96(1) M(-1) s(-1)). The attached substituents were found to have a significant effect upon the reaction kinetics, with the substituted complexes found to have increased reactivity. It is proposed that the increased reactivity stems from hydrogen bonding between the substituent and the entering ligand and subsequent outer-sphere complex stabilisation. Evidence in support of this theory was obtained form measurements in dichloromethane with 1-propanethiol as the entering ligand. The reactivity of the dppf containing complexes was also compared to that of cisplatin (mono adduct: (0.170(1)-0.175(1)) x 10(-3) s(-1), bis adduct: (0.183(1)-0.397(1)) x 10(-4) s(-1)) and found to be significantly enhanced.

Improved contact tracing of Chlamydia trachomatis in a Swedish county--is genotyping worthwhile?

The vast majority of genital Chlamydia trachomatis infections are non-symptomatic or mildly symptomatic. Efficient contact tracing and screening programmes are the most effective means to reveal these infections. We conducted a prospective study on the effects of contact tracing performed by specially trained midwives in a centralized municipality-based organization during one year. In order to improve the efficiency of the contact tracing, all C. trachomatis-positive isolates in the county during one year were typed by sequencing the ompA gene. Contact tracing in two municipalities the year prior to the study revealed 1.6 partners for each index case (n = 110). The corresponding figure for the whole county during the study period was 2.1 partners per index case (n = 2065). Genotyping added valuable information in mapping individual sexual networks, but was not essential for achieving satisfactory contact tracing results.

Characterization of ompA genotypes by sequence analysis of DNA from all detected cases of Chlamydia trachomatis infections during 1 year of contact tracing in a Swedish County.

In this study we aimed to characterize the ompA gene by sequencing DNA from all detected cases of Chlamydia trachomatis infection in a Swedish county during 2001, in order to improve the efficiency of contact tracing. Approximately 990 bp of the ompA gene was amplified, and sequence analysis was achieved in 678 (94%) of 725 C. trachomatis-positive cases in this unselected population. The most prevalent genotype was serotype E (39%), followed by F (21%), G (11%), D (9%), K (9%), J (7%), H (2%), B (1%), and Ia (1%). Serotype E was found in five genotype variants, with the reference sequence comprising 96% of all E cases. Serotype D was the most variable, and of seven sequence variants, three were identified as recombinants with serotype E. Altogether 29 genetic variants were detected, and mutations and recombination events are discussed. Clinical manifestations were not associated with genotypes. Sequence variation was linked to sexual networks identified by contact tracing and improved epidemiological knowledge but was of limited benefit.

Catalysis by RNase P RNA: unique features and unprecedented active site plasticity.

Metal ions are essential cofactors for precursor tRNA (ptRNA) processing by bacterial RNase P. The ribose 2'-OH at nucleotide (nt) -1 of ptRNAs is known to contribute to positioning of catalytic Me2+. To investigate the catalytic process, we used ptRNAs with single 2'-deoxy (2'-H), 2'-amino (2'-N), or 2'-fluoro (2'-F) modifications at the cleavage site (nt -1). 2' modifications had small (2.4-7.7-fold) effects on ptRNA binding to E. coli RNase P RNA in the ground state, decreasing substrate affinity in the order 2'-OH > 2'-F > 2'-N > 2'-H. Effects on the rate of the chemical step (about 10-fold for 2'-F, almost 150-fold for 2'-H and 2'-N) were much stronger, and, except for the 2'-N modification, resembled strikingly those observed in the Tetrahymena ribozyme-catalyzed reaction at corresponding position. Mn2+ rescued cleavage of the 2'-N but also the 2'-H-modified ptRNA, arguing against a direct metal ion coordination at this location. Miscleavage between nt -1 and -2 was observed for the 2'-N-ptRNA at low pH (further influenced by the base identities at nt -1 and +73), suggesting repulsion of a catalytic metal ion due to protonation of the amino group. Effects caused by the 2'-N modification at nt -1 of the substrate allowed us to substantiate a mechanistic difference in phosphodiester hydrolysis catalyzed by Escherichia coli RNase P RNA and the Tetrahymena ribozyme: a metal ion binds next to the 2' substituent at nt -1 in the reaction catalyzed by RNase P RNA, but not at the corresponding location in the Tetrahymena ribozyme reaction.

Selection of hammerhead ribozyme variants with low Mg2+ requirement: importance of stem-loop II.

Variants of the hammerhead ribozyme with high in trans (intermolecular) cleavage activity at low Mg(2+) concentrations were in vitro selected from a library with 18 nucleotides randomised in the core and in helix II. The most active hammerhead ribozyme selected had the same sequence as the consensus ribozyme in the core but only two base pairs in stem II, G(10.1)-C(11.1) and U(10.2)-A(11.2), and a tetrauridine loop II. This ribozyme (clone 34) was found to be very active in single-turnover reactions at 1 mM Mg(2+) concentration in the context of several substrates with differences in the lengths of stem I and III, including the well-characterised HH16 substrate and a derivative thereof with a GUA triplet at the cleavage site, as well as a substrate used previously in a related study. For the HH16 substrate, a change of base pair 10.2-11.2 to C-G in stem II further improved activity by about 2.5-fold to 0.8 min(-1) (at 1 mM Mg(2+) concentration, 25 degrees C, pH 7.5). Interestingly, this very active variant was not identified by the selection procedure. Changing loop II from UUUU to GCAA or extension of stem II to three or four base pairs reduced the cleavage rate by 2.0-2.5-fold. Thus, small hammerhead ribozymes carrying a tetrauridine loop with two base pairs in stem II represent the most active versions known so far at low Mg(2+) concentrations; single-turnover rates of approximately 1 min(-1) are reached at 25 degrees C and pH 7.5 in monophasic reactions, with endpoints between 75 and 90 %. Such constructs promise to be advantageous for the inhibition of gene expression in vivo.