Bent oligonucleotide duplexes as HMGB1 inhibitors: a comparative study

In this work we explore the ability of a chimeric LNA/DNA bent duplex, in which the kink is induced by 2 unpaired adenines in the middle of one strand, to bind HMGB1, a protein involved in many inflammatory processes. The LNA/DNA duplex was compared with the corresponding full DNA and PNA/DNA chimera duplexes from a thermodynamic and spectroscopic point of view.     

Condensation of oligonucleotides assembled into nicked and gapped duplexes: potential structures for oligonucleotide delivery

The condensation of nucleic acids into well-defined particles is an integral part of several approaches to artificial cellular delivery. Improvements in the efficiency of nucleic acid delivery in vivo are important for the development of DNA- and RNA-based therapeutics. Presently, most efforts to improve the condensation and delivery of nucleic acids have focused on the synthesis of novel condensing agents. However, short oligonucleotides are not as easy to condense into well-defined particles as gene-length DNA polymers and present particular challenges for discrete particle formation. We describe a novel strategy for improving the condensation and packaging of oligonucleotides that is based on the self-organization of half-sliding complementary oligonucleotides into long duplexes (ca. 2 kb). These non-covalent assemblies possess single-stranded nicks or single-stranded gaps at regular intervals along the duplex backbones. The condensation behavior of nicked- and gapped-DNA duplexes was investigated using several cationic condensing agents. Transmission electron microscopy and light-scattering studies reveal that these DNA duplexes condense much more readily than short duplex oligonucleotides (i.e. 21 bp), and more easily than a 3 kb plasmid DNA. The polymeric condensing agents, poly-l-lysine and polyethylenimine, form condensates with nicked- and gapped-DNA that are significantly smaller than condensates formed by the 3 kb plasmid DNA. These results demonstrate the ability for DNA structure and topology to alter nucleic acid condensation and suggest the potential for the use of this form of DNA in the design of vectors for oligonucleotide and gene delivery. The results presented here also provide new insights into the role of DNA flexibility in condensate formation.     

Improved selectivity for the binding of naphthyridine dimer to guanine-guanine mismatch.

Naphthyridine dimer composed of two 2-amino-1,8-naphthyridines and a connecting linker strongly binds to guanine-guanine (G-G) mismatch in duplex DNA. In order to improve G-G selectivity for the binding, we have examined structure modification of the linker. A new naphthyridine dimer possessing 3,6-diazaoctanedioic acid linker binds to G-G mismatch with an association constant of 1.18 x 10(7) M(-1), which is somewhat weaker than that of the original naphthyridine dimer having a shorter connecting linker. However, the binding of the modified naphthyridine dimer to G-A mismatch was almost negligible as compared to that of the original. This results in a net increase of the selectivity for the binding to G-G mismatch by 4-folds.     

Probing structural factors stabilizing antisense oligonucleotide duplexes: NMR studies of a DNA.DNA duplex containing a formacetal linkage.

The duplex formed by annealing the formacetal backbone modified dodecamer d-(CGCGTTOCH2OTTGCGC) to its complementary strand, d(GCGCAAAACGCG) (duplex I), has been studied by NMR techniques and analyzed with reference to its unmodified counterpart (duplex II). Comparison of parameters such as 2D cross-peak intensities, coupling constants, and spectral patterns indicates that structural perturbations caused by the incorporation of the formacetal linkage are minimal and localized to the central T4.A4 block. Duplex I adopts a B-type helical conformation with regular Watson-Crick base pairing and normal minor groove width. The methylene group is accommodated along the phosphate backbone in a conformation similar to that of the PO2 group found in the B-form DNA family. The central T6-T7 base pairs of duplex I melt simultaneously with the duplex, indicating a cooperative transition to single strands. Although the formacetal linkage affects global melting, as evidenced by a 3 degree C reduction in Tm for duplex I with respect to duplex II, the present study indicates that this is not the result of localized premelting at the formacetal site of duplex I but rather reflects the subtle interplay of several structural and energy factors which need to be further explored.     

Spongelike alginate nanoparticles as a new potential system for the delivery of antisense oligonucleotides.

The aim of this study was to design a new antisense oligonucleotide (ON) carrier system based on alginate nanoparticles and to investigate its ability to protect ON from degradation in the presence of serum. Pharmacokinetics and tissue distribution of ON-loaded nanoparticles have been determined after intravenous administration. An original and dynamic process for ON loading into polymeric nanoparticles has been applied. It is based on the diffusion of ON or ON/polylysine complex into the nanoparticle or the alginate gel, respectively. Indeed, the single coincubation of ON with nanoparticles led, within a few days, to an extremely efficient association. The diffusion kinetic of ON was shown to be dependent on several parameters, incubation temperature, ON concentration, presence or absence of polylysine, polylysine molecular weight, and nanoparticle preparation procedure. This new alginate-based system was found to be able to protect [33P]-radiolabeled ON from degradation in bovine serum medium and to modify their biodistribution, as an important accumulation of radioactivity was observed in the lungs, in the liver, and in the spleen after intravenous administration into mice. ON may be associated efficiently with calcium alginate in a colloidal state. Such nanosponges are promising carriers for specific delivery of ON to lungs, liver, and spleen.     

Drosophila: a "model" model system to study neurodegeneration

The fruit fly, Drosophila melanogaster, is a powerful model genetic organism that has been used since the turn of the previous century in the study of complex biological problems. In the last decade, numerous researchers have focused their attention on understanding neurodegenerative diseases by utilizing this model system. Numerous Drosophila mutants have been isolated that profoundly affect neural viability and integrity of the nervous system with age. Additionally, many transgenic strains have been developed as models of human disease conditions. We review the existing Drosophila neurodegenerative mutants and transgenic disease models, and discuss the role of the fruit fly in therapeutic development for neurodegenerative diseases.     

前庭代偿：研究中枢神经系统可塑性的一个理想模型

前庭代偿是一个研究神经系统损伤后机制修复和替代的理想模型,这个模型在中枢神经系统可塑性和机能恢复的研究机具有普遍意义,本文综述了有关前庭代偿的电生理学,生物化学和分子神经生物学的研究现状,还特别讨论了在前庭代偿中神经生长相关蛋白（ＧＡＰ－４３）ｍＲＮＡ的表达以及银杏叶提取物在前庭代偿过程中的促进作用。     

Raman study of the interaction between polyamines and a GC oligonucleotide.

The interaction between the oligonucleotide d[G(CG)(7)]. d[C(GC)(7)] and the three biogenic polyamines putrescine, spermidine, and spermine under physiological conditions has been studied by Raman spectroscopy. The results indicate the formation of highly ordered aggregated structures in solution, largely stabilized by electrostatic attractions, which have been described as cholesteric phases. Aggregation seems to be preceded by a partial B --> Z conformational transition for spermidine and spermine, which would allow for a deeper oligonucleotide-polyamine interaction. Interaction with the nucleic bases has also been evidenced for aggregates. At low polyamine concentrations the preferential binding sites are similar to those proposed for their interactions with ct-DNA. With increasing the polyamine concentration, the oligonucleotide-polyamine interactions involve both minor and major grooves, which is consistent with the formation of cholesteric phases.     

Drosophila melanogaster as a model system for the evaluation of anti-aging compounds

Understanding the causes of aging is a complex problem due to the multiple factors that influence aging, which include genetics, environment, metabolism and reproduction, among others. These multiple factors create logistical difficulties in the evaluation of anti-aging agents. There is a need for good model systems to evaluate potential anti-aging compounds. The model systems used should represent the complexities of aging in humans, so that the findings may be extrapolated to human studies, but they should also present an opportunity to minimize the variables so that the experimental results can be accurately interpreted. In addition to positively affecting lifespan, the impact of the compound on the physiologic confounders of aging, including fecundity and the health span-the period of life where an organism is generally healthy and free from serious or chronic illness-of the model organism needs to be evaluated. Fecundity is considered a major confounder of aging in fruit flies. It is well established that female flies that are exposed to toxic substances typically reduce their dietary intake and their reproductive output and display an artifactual lifespan extension. As a result, drugs that achieve longevity benefits by reducing fecundity as a result of diminished food intake are probably not useful candidates for eventual treatment of aging in humans and should be eliminated during the screening process.     

N-Acetyl-D-glucosamine binding lectins. A model system for the study of binding specificity

Synthetic glycoconjugates prepared by the direct reductive amination of di-N-acetylchitobiose and tetra-N-acetyl-chitotetraose to poly-l-lysine with sodium cyanoborohydride have been used to explore the binding specificities of the lectins wheat germ agglutinin and Bandeiraea simplicifolia II. These conjugates are effective precipitating antigens for these lectins, and hapten inhibition experiments, employing the per-N-acetylated oligomers of chitin as inhibitors, demonstrate that wheat germ agglutinin and Bandeiraea simplicifolia II lectin have binding sites complementary to three and two contiguous β 1,4-linked N-acetyl-d-glucosamine residues, respectively, in agreement with conclusions reached using other methods. Conjugates prepared by this technique should be useful for examining the binding specificities of other lectins, and the results of a study of the effect of chain length of the hapten on the affinity of the lectin for these conjugates should provide guidance in selection of the hapten most appropriate for these studies.     

Ladybirds as a model system for the study of male-killing symbionts

Maternally inherited bacteria that kill male but not female hosts during embryogenesis occur in a number of aphidophagous coccinellids. Work on EnglishAdalia bipunctata (L.), has shown the causative agent of male-killing to be a member of the bacterial genusRickettsia. In coccinellids, the primary advantage of male-killing behaviour to the bacterium has been identified. Following male death, resource reallocation occurs through sibling egg cannibalism: female neonate larvae of infected mothers gain a significant survival advantage by eating the soma of their dead male siblings. In addition, daughters of infected females suffer a reduced risk of cannibalism as a result of the lower egg hatch rate in infected clutches. Predictions as to which species of coccinellid are liable to harbour male-killers may be made on the basis of the selective advantages of male-killing identified inA. bipunctata. Species which may harbour male-killers are likely to lay eggs in clutches, show sibling egg cannibalism, and exhibit high neonate mortality. Recent work has shown male-killing to occur in a number of other aphidophagous coccinellids with the predicted characteristics. Molecular genetic analysis has putatively identified three bacterial symbionts associated with male-killing, coming from three phylogenetically distant bacterial taxa. We therefore suggest that within coccinellids that possess these features, male-killing may evolve in a taxonomically diverse range of inherited bacteria. The implications of the presence of male-killing bacteria on the population demography of host coccinellids, and on host mitochondrial DNA variability are discussed. The aphidophagous coccinellids are proposed as a model system for studying the evolution and consequences of infection with male-killers.     

The zebrafish as a model system for assessing the reinforcing properties of drugs of abuse

Recent reports make use of the zebrafish to study complex behavior such as addiction, anxiety, or learning and memory. We have established reliable tests and appropriate controls to measure these behavioral parameters in the zebrafish adult. Our assays are robust enough to permit the detection of dominant mutations affecting drug-induced reward, and therefore can be used in forward genetic screens. We provide the reader with the technical details of these tests, as well as their appropriate and crucial, although often overlooked, control assays. In particular, our results make it possible to use the zebrafish as a promising model to identify new genetic components of the reward pathway, or other measurable behaviors.     

Extracellular loops of the serotonin transporter act as a selectivity filter for drug binding

The serotonin transporter (SERT) shapes serotonergic neurotransmission by retrieving its eponymous substrate from the synaptic cleft. Ligands that discriminate between SERT and its close relative, the dopamine transporter DAT, differ in their association rate constant rather than their dissociation rate. The structural basis for this phenomenon is not known. Here we examined the hypothesis that the extracellular loops 2 (EL2) and 4 (EL4) limit access to the ligand-binding site of SERT. We employed an antibody directed against EL4 (residues 388–400) and the antibody fragments 8B6 scFv (directed against EL2 and EL4) and 15B8 Fab (directed against EL2) and analyzed their effects on the transport cycle of and inhibitor binding to SERT. Electrophysiological recordings showed that the EL4 antibody and 8B6 scFv impeded the initial substrate-induced transition from the outward to the inward-facing conformation but not the forward cycling mode of SERT. In contrast, binding of radiolabeled inhibitors to SERT was enhanced by either EL4- or EL2-directed antibodies. We confirmed this observation by determining the association and dissociation rate of the DAT-selective inhibitor methylphenidate via electrophysiological recordings; occupancy of EL2 with 15B8 Fab enhanced the affinity of SERT for methylphenidate by accelerating its binding. Based on these observations, we conclude that (i) EL4 undergoes a major movement during the transition from the outward to the inward-facing state, and (ii) EL2 and EL4 limit access of inhibitors to the binding of SERT, thus acting as a selectivity filter. This insight has repercussions for drug development.     

Electrophorus electricus as a model system for the study of membrane excitability

The stunning sensations produced by electric fish, particularly the electric eel, Electrophorus electricus, have fascinated scientists for centuries. Within the last 50 years, however, electric cells of Electrophorus have provided a unique model system that is both specialized and appropriate for the study of excitable cell membrane electrophysiology and biochemistry. Electric tissue generates whole animal electrical discharges by means of membrane potentials that are remarkably similar to those of mammalian neurons, myocytes and secretory cells. Electrocytes express ion channels, ATPases and signal transduction proteins common to these other excitable cells. Action potentials of electrocytes represent the specialized end function of electric tissue whereas other excitable cells use membrane potential changes to trigger sophisticated cellular processes, such as myofilament cross-bridging for contraction, or exocytosis for secretion. Because electric tissue lacks these functions and the proteins associated with them, it provides a highly specialized membrane model system. This review examines the basic mechanisms involved in the generation of the electrical discharge of the electric eel and the membrane proteins involved. The valuable contributions that electric tissue continues to make toward the understanding of excitable cell physiology and biochemistry are summarized, particularly those studies using electrocytes as a model system for the study of the regulation of membrane excitability by second messengers and signal transduction pathways.     

The fish heart as a model system for the study of myoglobin

A model is presented for myoglobin study based upon naturally occurring differences in myocardial myoglobin content in fish. The sea raven (Hemitripterus americanus) and the ocean pout (Macrozoarces americanus) have heart myoglobin contents of approx. 65 and 5 nmol/g wet wt, respectively. The maximal activities of enzymes associated with energy metabolism are similar in the two hearts. Isolated perfused hearts performed with similar efficiencies based upon similar rates of work, oxygen consumption and lactate production. Under normoxic perfusion conditions both hearts met 98% of the ATP demand by oxidative mechanisms. Myoglobin-rich sea raven hearts performed significantly better than myoglobin-poor ocean pout hearts under conditions of hypoxia and glycolytic blockage. The performance of sea raven hearts was impaired during hypoxia by decreasing the content of functional myoglobin with hydroxylamine. No effect upon performance was observed with the ocean pout heart. The data provide the first evidence that myoglobin plays a role in the maintenance of contractility in heart under hypoxic conditions.     

Stability of DNA duplexes with Watson-Crick base pairs: a predicted model

The conformational stability (difference between the free energies of the folded and unfolded states, DeltaG degrees ) of a DNA duplex is considered as a function of component energy terms, hydrophobic, base stacking, hydrogen bonding, van der Waals, and electrostatic, and a trinucleotide-level helix stiffness parameter measured in terms of its Young's modulus. Hydrophobic and base stacking energy components were determined with the use of the crystal structure data of 30 DNA duplexes judicially selected within a resolution of 1.5 A, and hydrogen bonding, van der Waals and electrostatic terms were determined through an extensive review of experimental and theoretical studies. The stiffness indices for the trinucleotides were the ones realized by M. M. Gromiha [(2000) J. Biol. Phys. 26, 43-50] using the crystal structure data of 70 DNA duplexes. The unfolded state was treated in the classical way to determine its stability. Thermodynamically determined DeltaG degrees values for 111 DNA duplexes, with the number of base pairs ranging from 4 to 16, were selected in two sets, and the regression equation formed with one set was used to predict the stabilities of the other set, taking the energy components and the stiffness parameter to be independent variables. The computed energy terms indicate that the base stacking and hydrogen bonding forces are the dominant and the hydrophobic and electrostatic forces the weak partners in imparting stability to the duplexes. This model predicts DeltaG degrees values for DNA duplexes examined with a level of accuracy similar to that used for predictions made by the widely used nearest-neighbor models. The uniqueness of this model is that it combines the crystal and thermodynamic data for interpretation of conformational stability.     

Making cool drugs hot: isothermal titration calorimetry as a tool to study binding energetics

Characterization of the thermodynamics of binding interactions is important in improving our understanding of bimolecular recognition and forms an essential part of the rational drug design process. Isothermal titration calorimetry (ITC) is rapidly becoming established as the method of choice for undertaking such studies. The power of ITC lies in its unique ability to measure binding reactions by the detection of the heat change during the binding interaction. Since heat changes occur during many physicochemical processes, ITC has a broad application, ranging from chemical and biochemical binding studies to more complex processes involving enthalpy changes, such as enzyme kinetics. Several features of ITC have facilitated its preferential use compared to other techniques that estimate affinity. It is a sensitive, rapid, and direct method with no requirement for chemical modification or immobilization. It is the only technique that directly measures enthalpy of binding and so eliminates the need for van't Hoff analysis, which can be time consuming and prone to uncertainty in parameter values. Although ITC has facilitated the measurement of the thermodynamics governing binding reactions, interpretation of these parameters in structural terms is still a major challenge.     

Oligonucleotide conjugates as potential antisense drugs with improved uptake,biodistribution, targeted delivery,and mechanism of action

This review summarizes the effect of conjugating small molecules and large biomacromolecules to antisense oligonucleotides to improve their therapeutic potential. In many cases, favorable changes in pharmacokinetic and pharmacodynamic properties were observed. Opportunities exist to change the terminating mechanism of antisense action or to enhance the RNase H mode of action via conjugate formation.     

Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: implications for antisense design and targeting a group I intron

Antisense compounds are designed to optimize selective hybridization of an exogenous oligonucleotide to a cellular target. Typically, Watson-Crick base pairing between the antisense compound and target provides the key recognition element. Uridine (U), however, not only stably base pairs with adenosine (A) but also with guanosine (G), thus reducing specificity. Studies of duplex formation by oligonucleotides with either an internal or a terminal 2- or 4-thiouridine (s(2)U or s(4)U) show that s(2)U can increase the stability of base pairing with A more than with G, while s(4)U can increase the stability of base pairing with G more than with A. The latter may be useful when binding can be enhanced by tertiary interactions with a s(4)U-G pair. To test the effects of s(2)U and s(4)U substitutions on tertiary interactions, binding to a group I intron ribozyme from mouse-derived Pneumocystis carinii was measured for the hexamers, r(AUGACU), r(AUGACs(2)U), and r(AUGACs(4)U), which mimic the 3' end of the 5' exon. The results suggest that at least one of the carbonyl groups of the 3' terminal U of r(AUGACU) is involved in tertiary interactions with the catalytic core of the ribozyme and/or thio groups change the orientation of a terminal U-G base pair. Thus thio substitutions may affect tertiary interactions. Studies of trans-splicing of 5' exon mimics to a truncated rRNA precursor, however, indicate that thio substitutions have negligible effects on overall reactivity. Therefore, modified bases can enhance the specificity of base pairing while retaining other activities and, thus, increase the specificity of antisense compounds targeting cellular RNA.