Affinity Sequence Research Articles

Distribution and Removal of Silver and Lead in the Nearshore Waters of Western Taiwan

Concentrations of Al, Mn, Fe, Ag, and Pb in dissolved and particulate phases of the surface water were determined at 15 stations along the coastline off western Taiwan in April of 2007. This study presents the first set of data for Al, Ag, and Pb in the nearshore waters. Latitudinal distribution of these metals showed that high values were present in the regions affected by high fluvial discharge from the Dan-Sui River and the Cho-Sui River. Using the particle fluxes from 210Po/210Pb disequilibria, the removal fluxes and the residence times of the trace metals were calculated. Based on the K d values, the sequence of particle affinity of trace metals, Fe ~ Al >> Pb > Mn > Ag, was found. The correlation of the residence times and of the partitioning coefficients of multiple metals in the nearshore waters implies that the affinities to the particles determine the geochemical cycling of metals in the coastal water.

Chiral Peptide Nucleic Acids with a Substituent in the N-(2-Aminoethy)glycine Backbone

A peptide nucleic acid (PNA) is a synthetic nucleic acid mimic in which the sugar-phosphate backbone is replaced by a peptide backbone. PNAs hybridize to complementary DNA and RNA with higher affinity and superior sequence selectivity compared to DNA. PNAs are resistant to nucleases and proteases and have a low affinity for proteins. These properties make PNAs an attractive agent for biological and medical applications. To improve the antisense and antigene properties of PNAs, many backbone modifications of PNAs have been explored under the concept of preorganization. This review focuses on chiral PNAs bearing a substituent in the N-(2-aminoethyl)glycine backbone. Syntheses, properties, and applications of chiral PNAs are described.

Aptamer-Based Impedimetric Sensor for Bacterial Typing

The development of an aptamer-based impedimetric sensor for typing of bacteria (AIST-B) is presented. Highly specific DNA aptamers to Salmonella enteritidis were selected via Cell-SELEX technique. Twelve rounds of selection were performed; each comprises a positive selection step against S. enteritidis and a negative selection step against a mixture of related pathogens, including Salmonella typhimurium, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Citrobacter freundii, to ensure the species-specificity of the selected aptamers. After sequencing of the pool showing the highest binding affinity to S. enteritidis, a DNA sequence of high affinity to the bacteria was integrated into an impedimetric sensor via self-assembly onto a gold nanoparticles-modified screen-printed carbon electrode (GNPs-SPCE). Remarkably, this aptasensor is highly selective and can successfully detect S. enteritidis down to 600 CFU mL(-1) (equivalent to 18 CFU in 30 μL assay volume) in 10 min and distinguish it from other Salmonella species, including S. typhimurium and S. choleraesuis. This report is envisaged to open a new venue for the aptamer-based typing of a variety of microorganisms using a rapid, economic, and label-free electrochemical platform.

Distributions and removal fluxes of trace metals in the water column of the Hung-Tsai Trough off southwestern Taiwan

Vertical profiles of dissolved and particulate Mn, Fe, Ni, Cu, Zn, Cd, Pb, and 234Th were determined in the Hung-Tsai Trough off southwestern Taiwan during 19–23 November, 2004. Except in the case of Cd, the distribution coefficient (Kd) of the trace elements showed a negative correlation with the suspended particle concentration. Based on the average Kd values, the general sequence of particle affinities for the eight trace elements is, from highest to lowest, Fe>Mn≈Pb>Zn≈Th>Cd≈Cu≈Ni. The trace metal data was coupled with the particle removal flux estimated from 234Th/238U disequilibrium to investigate metal removal by particle sinking from the euphotic layer. The residence time of trace elements with respect to particle removal from the euphotic layer was estimated. A negative correlation between the residence time and the distribution coefficient for the trace metals was found.

Probing High Affinity Sequences of DNA Aptamer against VEGF165

Vascular endothelial growth factor (VEGF165) is a potent angiogenic mitogen commonly overexpressed in cancerous cells. It contains two main binding domains, the receptor-binding domain (RBD) and the heparin-binding domain (HBD). This study attempted to identify the specific sequences of the VEa5 DNA aptamer that exhibit high binding affinity towards the VEGF165 protein by truncating the original VEa5 aptamer into different segments. Using surface plasmon resonance (SPR) spectroscopy for binding affinity analysis, one of the truncated aptamers showed a >200-fold increase in the binding affinity for HBD. This truncated aptamer also exhibited high specificity to HBD with negligible binding affinity for VEGF121, an isoform of VEGF lacking HBD. Exposing colorectal cancer cells to the truncated aptamer sequence further confirmed the binding affinity and specificity of the aptamer to the target VEGF165 protein. Hence, our approach of aptamer truncation can potentially be useful in identifying high affinity aptamer sequences for the biological molecules and targeting them as antagonist for cancer cell detection.

Oriented immobilization of the tobacco etch virus protease for the cleavage of fusion proteins

The tobacco etch virus (TEV) protease is a useful tool for the removal of fusion tags from recombinant proteins. The difficulty in obtaining this enzyme led us to look for an optimal method for its use. In this work, we produced both the wild-type and the S219V mutant TEV proteases fused to the Streptag II affinity sequence (Streptag II-TEV(WT), and Streptag II-TEV(S219V), respectively). The two enzymes were affinity immobilized on a streptavidin-agarose matrix and compared to their respective free forms. Both immobilized Streptag II-TEV(WT) and Streptag II-TEV(S219V) were active on the 74-kDa Streptag II substrate with a retained activity of 83.5% and 81%, respectively compared to their free corresponding forms. The slight enzyme activity decrease caused by the immobilization was balanced by the enhanced stability and the successful repetitive use of the proteolytic columns. Thus, the wild-type and the mutant immobilized proteases were used, during a period of 18 months, for nine batch reactions with retention of 38% and 51% of their initial activities, respectively. The present results demonstrate that immobilized TEV protease on streptavidin-agarose is an attractive and efficient tool for fusion protein cleavage, especially when the target protein is fused to a streptagged fusion partner. Using this strategy, the total process can be shortened by performing the cleavage and the recovery of the purified target protein in one step.

Evaluation of the potential capacity as biosorbents of two MSW composts with different Cu, Pb and Zn concentrations

The Cu, Pb and Zn adsorption capacity of two municipal solid waste composts was studied in batch experiments where the equilibrium isotherms were determined. Both composts, despite having very different metal concentrations, showed high sorption capacities for the three elements, with the following affinity sequence: Pb>Cu>Zn. The maximum sorption capacities of the composts, on the basis of the Langmuir isotherm, were roughly equivalent to 1mmolg−1 for Pb, 1/2mmolg−1 for Cu, and 1/3mmolg−1 for Zn, which makes of both composts good biosorbents. Although a slightly higher adsorption capacity was seen for the compost with the lowest previous metal content, this fact alone could not explain the difference in the performance of the composts, and other factors such as its higher organic matter concentration and higher cation exchange capacity could have been more determinant.

Improvement of drinking water quality by using plant biomass through household biosand filter – A decentralized approach

The removal of microbial and physico-chemical contaminants was investigated using an innovative biosand filter (BSF) containing three combinations of coniferous pinus bark biomass (CPBB), i.e. 1 cm (treatment 2), 2.5 cm (treatment 3) and 5 cm (treatment 4). The efficiency of BSF was assessed in batch mode experiments and the comparative reductions of contaminants were monitored over the control treatment (1) at temperature range of 1–15 °C for 90 days. Standard methods were used to analyze 9 operating, physico-chemicals and biological water quality parameters of pre-and post-water filtration samples after 15 days interval. The results showed mean 93 ± 2% and 95 ± 3% reductions of Eischerichia coli and total coliforms, respectively, for BSF containing the highest depth of CPBB (5 cm), whereby 100% removal was observed during the treatment time T30 to T45 days. The general affinity sequence for E. coli, total coliforms and turbidity removal in the four treatments was: BSF with 5 cm CPBB > BSF with 2.5 cm CPBB > BSF with 1 cm CPBB > Control. It was concluded that modified BSF with additional adsorbent of locally available CPBB is a very good decentralized treatment option for drinking water.

Probing the interaction between 3 flavonoids and pancreatic lipase by methods of fluorescence spectroscopy and enzymatic kinetics

The interactions between pancreatic lipase and 3 flavonoids from tartary buckwheat bran, namely, quercetin (Que), its monoglycoside isoquercetin (Iso) and diglycoside rutin (Rut), had been studied by fluorescence spectroscopy and enzymatic kinetics and have also been compared with the best-selling antiobesity drug, Orlistat. The results showed that Que, Iso, and Rut all had a strong ability to quench the intrinsic fluorescence of pancreatic lipase by the formation of a new complex and nonradiation energy transfer mechanism. The sequence of binding constant (KA) was Rut > Que > Iso, and the number of binding site was one in all of the cases. The data of thermodynamic parameters at different temperatures indicated that hydrogen bonds and van der Waals forces played a major role in the previously mentioned interaction. Enzymatic kinetics measurements showed that Rut, Iso, and Que had a satisfied inhibitory ability toward pancreatic lipase in a dose-dependent manner, with the IC50 values as 0.97, 1.1, and 1.49 mg/mL and the maximum of inhibitory rate as 85, 81.2 and 67.9%. All the inhibitory modes of the 3 flavonoids belonged to noncompetitive type. The sequence of affinity (1/Ki) was Rut > Iso > Que, consistent with the inhibitory sequence.

Acyclic Identification of Aptamers for Human alpha-Thrombin Using Over-Represented Libraries and Deep Sequencing

BackgroundAptamers are oligonucleotides that bind proteins and other targets with high affinity and selectivity. Twenty years ago elements of natural selection were adapted to in vitro selection in order to distinguish aptamers among randomized sequence libraries. The primary bottleneck in traditional aptamer discovery is multiple cycles of in vitro evolution.Methodology/Principal FindingsWe show that over-representation of sequences in aptamer libraries and deep sequencing enables acyclic identification of aptamers. We demonstrated this by isolating a known family of aptamers for human α-thrombin. Aptamers were found within a library containing an average of 56,000 copies of each possible randomized 15mer segment. The high affinity sequences were counted many times above the background in 2–6 million reads. Clustering analysis of sequences with more than 10 counts distinguished two sequence motifs with candidates at high abundance. Motif I contained the previously observed consensus 15mer, Thb1 (46,000 counts), and related variants with mostly G/T substitutions; secondary analysis showed that affinity for thrombin correlated with abundance (Kd = 12 nM for Thb1). The signal-to-noise ratio for this experiment was roughly 10,000∶1 for Thb1. Motif II was unrelated to Thb1 with the leading candidate (29,000 counts) being a novel aptamer against hexose sugars in the storage and elution buffers for Concanavilin A (Kd = 0.5 µM for α-methyl-mannoside); ConA was used to immobilize α-thrombin.Conclusions/SignificanceOver-representation together with deep sequencing can dramatically shorten the discovery process, distinguish aptamers having a wide range of affinity for the target, allow an exhaustive search of the sequence space within a simplified library, reduce the quantity of the target required, eliminate cycling artifacts, and should allow multiplexing of sequencing experiments and targets.

Genome sequence analysis of H5N1 influenza a virus isolated from a vietnamese in 2007

Highly pathogenic H5N1 avian influenza A virus (AIV) crossed the species barrier and caused a number of deaths in humans in Vietnam and 14 other countries. Since the last report of human H5N1 infection in November 2005, the first documented H5N1 human infection was reported in June 2007 in Vietnam and was followed by 7 more cases, including 5 fatalities. In this study, we isolated and analyzed the full length of the H5N1 genome from a sample from the first patient in 2007. Phylogenetic analysis of eight genomic segments of the H5N1 virus strain (A/Vietnam/HN/2007, VNH07) revealed that this strain appears to be of genotype V and contains the HA gene, which is classified into clade 2.3.4. The deduced amino acid sequence of the HA protein has a typical affinity sequence for α2,3 linkage (SAα2,3-Gal) receptors and typical multibasic cleavage sequences. Compared with other H5N1 isolates, VNH07 showed that the possible reassortments for the NA and NP segments occurred between A/goose/Guangxi/3017/2005-like isolates (2.3.2) and A/human/Zhejiang/16/2006-like isolates (2.3.4).

Long-term performance of bicarbonate-form anion exchange: Removal of dissolved organic matter and bromide from the St. Johns River, FL, USA

The goal of this research was to evaluate the long-term performance of magnetic ion exchange (MIEX) treatment using bicarbonate as the mobile counter ion (i.e., MIEX-HCO 3) and sodium bicarbonate for regeneration. This work is important because there are many unknowns concerning the affinity and regeneration efficiency of bicarbonate-form anion exchange, whereas chloride-form anion exchange (i.e., MIEX-Cl resin) is well-studied. Raw water samples were collected approximately two times per month for one year from a single location on the St. Johns River (SJR), FL, USA. The SJR is characterized by high concentrations of dissolved organic carbon (DOC; 12–26 mg C/L) and bromide (550–1100 μg/L), and is being considered as an alternative drinking water supply. Jar tests were conducted using MIEX-HCO 3 resin, and MIEX-Cl resin was used as a baseline for comparison. The same batch of MIEX-HCO 3 and MIEX-Cl resin was used for the entire study, which was accomplished by regenerating the resins after each jar test in concentrated solutions of sodium bicarbonate and sodium chloride, respectively, and resulted in 21 regeneration cycles. Maximum removal efficiency was achieved with fresh MIEX-HCO 3 resin and virgin MIEX-Cl resin. Both forms of fresh/virgin MIEX resin also had the same affinity sequence with sulfate ≈ UV-absorbing substance > DOC > bromide. The removal efficiency of both forms of MIEX resin decreased as the number of regeneration cycles increased, with MIEX-HCO 3 resin showing 7–18% lower removals than MIEX-Cl resin after 21 regeneration cycles. The affinity sequence of regenerated MIEX-HCO 3 and MIEX-Cl resins differed from fresh resin with UV-absorbing substances > DOC > sulfate > bromide. Scanning electron microscopy and simulated MIEX-HCO 3 treatment under rapidly changing water quality were also used to improve the understanding of bicarbonate-form anion exchange. The major contribution of this research is a systematic study of the extended use of bicarbonate-form anion exchange resin in the context of affinity, regeneration efficiency, and changing water quality.

Using the recognition code to swap homeodomain target specificity in cell culture

The homeodomain (HD) is a 60 amino acid-long DNA-binding domain. A large fraction of HDs binds with high affinity sequences containing the 5'-TAAT-3' core motif. However, NK-2 class HDs recognizes sequences containing the 5'-CAAG-3' core motif. By using a cell transfection approach, here we show that modification of residues located in the N-terminal arm (at positions 6, 7 and 8) and in the recognition helix (at position 54) is enough to swap the "in vivo" binding specificity of TTF-1 HD (which is a member of the NK-2 class HD) from 5'-CAAG-3' to 5'-TAAT-3'-containing targets. The role of residue at position 54 is also supported by data obtained with the HD of the Drosophila engrailed protein. These data support the notion that DNA-binding specificity "in vivo" is dictated by few critical residues.

Binding of CDR‐derived peptides is mechanistically different from that of high‐affinity parental antibodies

We present data that reveal crucial differences between the binding mode of anti-gastrin17 (G17, pyroEGPWLEEEEEAYGWMDF-NH(2)) monoclonal antibodies (mAbs) and their CDR-derived synthetic binders (SBs) with G17. The mAbs recognize the N-terminal sequence of G17 (pyroEGPWL) with nanomolar affinity and high sequence selectivity. Molecular simulations suggest that G17 recognition is based primarily on a multitude of weak antibody-ligand interactions (H-bonding, van der Waals, etc.) inside a structurally well-defined cleft-like binding pocket. Relatively small structural changes (e.g. G-2 to A for G17) have a drastic impact on affinity, which is characteristic for antibody-like binding. In contrast, SBs recognize various sequences, including G17-unrelated targets with affinities of 1:1 complexes estimated in the 0.1-1.0 mM range. In most cases however, the G17/SB complex stoichiometries are not well-defined, giving rise to multimer aggregate formation with high apparent complex stabilities. Mutational studies on both G17 and SBs reveal the importance of positively charged (K/R) and aromatic residues (W/Y/F) for G17/SB complex formation. We propose that the synthetic binders use combinations of electrostatic, hydrophobic, and/or cation-π interactions in a variety of ways due to their intrinsic flexibility. This may also be the reason for their relatively low target specificity. We speculate that our findings are of general relevance, in showing that high-affinity mAbs do not necessarily provide the optimal basis for functional mimics design.

Short GC-rich RNA similar to miR 1909 and 1915 folds in silico with the 5'-UTR and ORF of Notch and responders: Potential for the elimination of cancer stem cells

Novel therapeutic approaches to eliminate cancer stem cells (CSCs) are being developed. This development is imperative as CSCs are resistant to drugs; they divide activated by ligands on the epithelium or on neighboring cancer cells. Specific commands for division originate from Notch-1 ligands. Notch-1 cleavage inhibitors can have opposite effects from the ones expected when the levels of Notch ligands are high on neighboring cancer cells. High levels of Jagged-1 are a common feature of ovarian tumors. Some gene pathways enhance, others repress transcription of Notch-1, while Notch-1 itself activates Myc and HIF-1α. RNA-based therapies need effector RNAs (eRNAs) with broad and focused specificity. eRNAs are short RNAs (20-30 nt long) which mediate biological effects. Two to three inhibitory RNAs with high net folding/hybridization/binding (and thereafter folding), and free energy (Net-ΔG) with multiple mRNAs can replace many miRs as eRNAs and overcome the complexity of identification of specific targets for each miR and competitive inhibition on delivery of small amounts of many miRs at the same time. To discover candidate eRNAs with multiple high affinity target sites or sequences (and thereafter targets), we searched for sequences containing more than randomly probable G and C. G and C bind with more hydrogen bonds than the pair A:T. We identified the sequence, Notch-1,33-56 in the ORF of Notch-1 mRNA. Notch-1,33-56 has a GC frame of 2 asymmetrical halves in 24 nucleotides. Each GC group has a different third nucleotide. Since GC is repeated, the third nucleotide defines the specificity as a 'bar code'. The complementary strand to Notch-1,33-56, binds in silico nt at 5'-UTR, ORF and 3'-UTR of mRNA. For simplification, the sequence of Notch-1,33-56 was designated HHN1 and its complementary strand, anti-HHB. We introduced novel quantitative parameters: Net-ΔG and mean Net-ΔG/bond. We quantified the Net-ΔG of folding, in silico, of anti-HHB with additional targets in Notch-1,1-404. The targets of anti-HHB contained 11-12 complementary nucleotides and formed small loops with anti-HHB upon folding. Anti-HHB folded with 3-4 distinct targets in each mRNA from 50 mRNAs. Targets were in 5'-UTR (40%), ORF (50%) and 3'-UTR (10%). Anti-HHB also folded with high Net-ΔG with Notch-1 targets, c-Myc and HIF-1α, suggesting it can inhibit EMT. Human embryonal stem cell (hESC) miRs, 1909 and 1915, folded with Notch-1,8-29 and Notch-1,33-56, respectively with a similar Net-ΔG as anti-HHB. This finding suggested a natural feedback mechanism aiming to inhibit Notch-1 translation which is activated in stem cells by miRs with a similar sequence as anti-HHB, and anti-HHB can be used when the miRs 1915 and 1909 are absent. The consensus sequence of 18 targets folded with HHB with the highest Net-ΔG (range -10.20 to 24.00 Kcal/mol) similar to that of two Drosophila transposons. Targeting 'domesticated transposons' carried by humans with eRNAs may become a universal approach to treat cancer. Anti-HHB is the first candidate eRNA to fold, in silico, with multiple targets in 5'-UTR and ORF of Notch-1 partners with at least 2-times higher ΔG than natural miRs with 3'-UTR Notch-1.

Synthesis, characterization and evaluation of nano-zirconium vanadate ion exchanger by using three different preparation techniques

Sol–gel, homogeneous precipitation and hydrothermal synthesis are three different preparation techniques have been used as an attempt to synthesize nano-zirconium vanadate with properties suitable to be used as ion exchangers. The impact of the synthetic preparation variables such as the reactant concentrations, reaction temperature and reaction time on the ion exchange capacity of the produced ion exchanger has been considered for each preparation technique. One sample from each preparation technique having the largest ion exchange capacity has been selected to be physically and chemically characterized using various analytical techniques such as XRD, TGA, DSC, pH titration, FTIR and SEM in order to determine the properties of the ion exchanger produced from each technique. For all the studied ZrV samples it can be presumed that they have the ion exchange affinity sequences for alkali metal ions K > Na > Li, the order for the alkaline earth metals is Ba > Ca > Mg and their affinity for radioactive metals follow Cs > Sr. Moreover, the prepared materials are of high thermal and radiation stabilities. Also they have high chemical stabilities toward wide concentration ranges of acid, basic as well as polar solvents. It has been deduced from the X-ray analysis that ZrV produced from the sol–gel technique has an amorphous structural. While those produced from the homogeneous precipitation and hydrothermal synthesis techniques, in the nano-scale have semi-crystalline structural. Furthermore, SEM confirms that particle size of the all studied prepared ZrV samples have nano-diameters of range 50–60 nm. Specific surface area of the three different prepared ion exchangers are found to be equal to 187, 192 and 320 m 2/g for sol–gel, homogeneous precipitation and hydrothermal, respectively. A tentative structural formula of Zr(OH) 2(HVO 4) 2·2H 2O has been proposed for all studied samples on the basis of on FTIR, DSC and TGA results.

Reactive green HE‐4BD functionalized supermacroporous poly(hydroxyethyl methacrylate) cryogel for heavy metal removal

AbstractThe aim of this study was to investigate the heavy metal adsorption performance of supermacroporous poly(hydroxyethyl methacrylate) [PHEMA] cryogel. The PHEMA cryogel was produced by cryo‐polymerization. The PHEMA cryogel was characterized by scanning electron microscopy (SEM). The PHEMA cryogel containing 385 μmol Reactive Green HE‐4BD/g were used in the adsorption studies. Adsorption capacity of the PHEMA cryogel for the metal ions, i.e., Cu2+, Cd2+, and Pb2+ were investigated in aqueous media containing different amounts of the ions (5–600 mg/L) and at different pH values (3.2–6.9). The maximum adsorption capacities of the PHEMA cryogel were 11.6 mg/g (56 μmol/g) for Pb2+, 24.5 mg/g (385 μmol/g) for Cu2+ and 29.1 mg/g (256 μmol/g) for Cd2+. The competitive adsorption capacities were 10.9 mg/g (52 μmol/g) for Pb2+, 22.1 mg/g for Cd2+ (196 μmol/g) and 23.2 mg/g (365 μmol/g) for Cu2+. The PHEMA/Reactive Green HE‐4BD cryogel exhibited the following metal ion affinity sequence on molar basis: Cu2+ > Cd2+ > Pb2+. The PHEMA/Reactive Green HE‐4BD cryogel can be easily regenerated by 50 mM EDTA with higher effectiveness. These features make the PHEMA/Reactive Green HE‐4BD cryogel a potential adsorbent for heavy metal removal. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010

The Investigation of Interaction Competition Between ATP and DIPP-Ala, Boc-Ala, or Ala by ESI-MS/MS and Theoretical Calculation

The interactions between ATP and N-(O,O-diisopropyl) phosphoryl-L-alanine (DIPP-Ala), N-(tert-butoxycarbonyl)-L-alanine (Boc-Ala), or L-alanine (Ala) were investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). The non-covalent complexes between ATP and Boc-Ala or DIPP-Ala were observed, while the complex between ATP and Ala was not found in the mass spectra. The affinity of DIPP-Ala for ATP was confirmed to be stronger than that of Boc-Ala by competition experiment. Through molecular modeling calculations, it was found that the non-covalent complexes were stabilized by intermolecular hydrogen bonds, and the affinity sequence for ATP was DIPP-Ala > Boc-Ala > Ala by comparing their binding energy, −35.407 kcal/mol, −15.634 kcal/mol, −6.555 kcal/mol, respectively. The results implied that a phosphoryl group was a very important functional group to provide an interaction site between amino acids and ATP, and that N-phosphoryl amino acids can be used as a good model of protein in the studies of molecular recognition of ATP.

Experimental evidence for the functional relevance of anion–π interactions

Attractive in theory and confirmed to exist, anion-pi interactions have never really been seen at work. To catch them in action, we prepared a collection of monomeric, cyclic and rod-shaped naphthalenediimide transporters. Their ability to exert anion-pi interactions was demonstrated by electrospray tandem mass spectrometry in combination with theoretical calculations. To relate this structural evidence to transport activity in bilayer membranes, affinity and selectivity sequences were recorded. pi-acidification and active-site decrowding increased binding, transport and chloride > bromide > iodide selectivity, and supramolecular organization inverted acetate > nitrate to nitrate > acetate selectivity. We conclude that anion-pi interactions on monomeric surfaces are ideal for chloride recognition, whereas their supramolecular enhancement by pi,pi-interactions appears perfect to target nitrate. Chloride transporters are relevant to treat channelopathies, and nitrate sensors to monitor cellular signaling and cardiovascular diseases. A big impact on organocatalysis can be expected from the stabilization of anionic transition states on chiral pi-acidic surfaces.

Dinucleotide Weight Matrices for Predicting Transcription Factor Binding Sites: Generalizing the Position Weight Matrix

BackgroundIdentifying transcription factor binding sites (TFBS) in silico is key in understanding gene regulation. TFBS are string patterns that exhibit some variability, commonly modelled as “position weight matrices” (PWMs). Though convenient, the PWM has significant limitations, in particular the assumed independence of positions within the binding motif; and predictions based on PWMs are usually not very specific to known functional sites. Analysis here on binding sites in yeast suggests that correlation of dinucleotides is not limited to near-neighbours, but can extend over considerable gaps.Methodology/Principal FindingsI describe a straightforward generalization of the PWM model, that considers frequencies of dinucleotides instead of individual nucleotides. Unlike previous efforts, this method considers all dinucleotides within an extended binding region, and does not make an attempt to determine a priori the significance of particular dinucleotide correlations. I describe how to use a “dinucleotide weight matrix” (DWM) to predict binding sites, dealing in particular with the complication that its entries are not independent probabilities. Benchmarks show, for many factors, a dramatic improvement over PWMs in precision of predicting known targets. In most cases, significant further improvement arises by extending the commonly defined “core motifs” by about 10bp on either side. Though this flanking sequence shows no strong motif at the nucleotide level, the predictive power of the dinucleotide model suggests that the “signature” in DNA sequence of protein-binding affinity extends beyond the core protein-DNA contact region.Conclusion/SignificanceWhile computationally more demanding and slower than PWM-based approaches, this dinucleotide method is straightforward, both conceptually and in implementation, and can serve as a basis for future improvements.