A rational method for probing macromolecules dissociation: the antibody-hapten system

The unbinding process of a protein-ligand complex of major biological interest was investigated by means of a computational approach at atomistic classical mechanical level. An energy minimisation-based technique was used to determine the dissociation paths of the system by probing only a relevant set of generalized coordinates. The complex problem was reduced to a low-dimensional scanning along a selected distance between the protein and the ligand. Orientational coordinates of the escaping fragment (the ligand) were also assessed in order to further characterise the unbinding. Solvent effects were accounted for by means of the Poisson–Boltzmann continuum model. The corresponding dissociation time was derived from the calculated barrier height, in compliance with the experimentally reported Arrhenius-like behaviour. The computed results are in good agreement with the available experimental data.     

Parametrization of the hybrid potential for pairs of neutral atoms

The hybrid form is a combination of the Rydberg potential and the London inverse-sixth-power energy. It is accurate at all relevant distance scales and simple enough for use in all-atom simulations of biomolecules. One may compute the parameters of the hybrid potential for the ground state of a pair of neutral atoms from their internuclear separation, the depth and curvature of their potential at its minimum, and from their van der Waals coefficient of dispersion C₆.     

Modelling disorder: the cases of wetting and DNA denaturation

We study the effect of the composition of the genetic sequence on the melting temperature of double stranded DNA, using some simple analytically solvable models proposed in the framework of the wetting problem. We review previous work on disordered versions of these models and solve them when there were not preexistent solutions. We check the solutions with Monte Carlo simulations and transfer matrix numerical calculations. We present numerical evidence that suggests that the logarithmic corrections to the critical temperature due to disorder, previously found in RSOS models, apply more generally to ASOS and continuous models. The agreement between the theoretical models and experimental data shows that, in this context, disorder should be the crucial ingredient of any model while other aspects may be kept very simple, an approach that can be useful for a wider class of problems. Our work has also implications for the existence of correlations in DNA sequences.     

Counterion vibrations in the DNA low-frequency spectra

The vibrations of univalent metal cations with respect to phosphate groups of the DNA backbone are described using the four-mass model approach (S.N. Volkov, S.N. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991)) extended in this paper. The force constant of the counterion-phosphate interaction is determined by considering the DNA with counterions as a lattice of ion crystal. For such ion-phosphate lattice the Madelung constant and the dielectric constant are estimated. The obtained value of the Madelung constant is lower than for the NaCl crystal, and its value is about 1.3. The dielectric constant is within 2.3-2.7 depending on the counterion type and form of the double helix. The calculations of the low-frequency spectra show that for the DNA with metal cations Na⁺ , K⁺ , Rb⁺ and Cs⁺ the frequency of ion-phosphate vibrations decreases from 174 to 96cm^-1 as the counterion mass increases. The obtained frequencies agree well with the vibrational spectra of polynucleotides in a dry state which prove our suggestion about the existence of the ion-phosphate lattice around the DNA double helix. The amplitudes of conformational vibrations for DNA in B -form are calculated as well. The results demonstrate that light counterions ( Na⁺ do not disturb the internal dynamics of the DNA. However, heavy counterions ( Cs⁺ have effect on the internal vibrations of the DNA structural elements.     

3-(4-Carboxybenzoyl)quinoline-2-carboxaldehyde labeling for direct analysis of amino acids in plasma is not suitable for simultaneous quantification of tryptophan,tyrosine, valine,and isoleucine by CE/fluorescence

Capillary electrophoresis coupled to LED-induced fluorescence detection is a robust and sensitive technique used for amino acids (AA) analysis in biological media, after labeling with 3-(4-carboxybenzoyl)quinoline-2-carboxaldehyde (CBQCA). We wanted to quantitate in plasma tryptophan (Trp), tyrosine (Tyr), valine (Val), and isoleucine (Ile). Among the different labeled AA-CBQCA, Trp has the lowest fluorescence yield, which makes its detection and quantification very difficult in biological samples such as plasma. We tried to improve Trp analysis by CE/LED-induced fluorescence detection to its maximal sensitivity by using large volume sample stacking as a preconcentration step in our analytical protocol. At pH 9.5, this step caused a drop in resolution during the separation of the four AAs and it was therefore necessary to work at pH 10. We have found that Tyr, Val, Ile, and Trp are detected and well separated from the other AAs, but Trp cannot be quantified in plasma samples, mainly because of the low fluorescence yield of the Trp-CBQCA derivative. The recorded LOD is 0.18 μM for Trp-CBQCA in standard solution with a resolution between Trp and Tyr of 1.2, while the LOD is 6 μM in plasma with the same resolution. Trp, Tyr, Val, and Ile are, however, efficiently quantified when using a 3 M acetic acid electrolyte and CE associated with capacitively coupled contactless conductivity detection, which also has the advantage of not requiring derivatization or large volume sample stacking. This article demonstrates, for the CE user, that quantitative analysis of these four AA in mouse plasma can be performed by CE-fluorescence after CBQCA labeling, with the exception of Trp. It can be advantageously replaced by CE/capacitively coupled contactless conductivity detection, the only efficient one for Trp, Tyr, Val, and Ile quantification. In this case, the LOD for Trp is 2 μM. The four AAs are separated with resolution with neighbors above 1.5.     

Phenylimido Complexes of Technetium and Rhenium with Maleonitriledithiolate

[Tc(NPh)Cl₃(PPh₃)₂] or [Re(NPh)Cl₃(PPh₃)₂] react with two equivalents of Na₂mnt (mnt^2– = 1,2‐dicyanoethene‐1,2‐dithiolate) with formation of anionic complexes of the composition [M(NPh)(mnt)₂]^–. The products can be isolated as large red blocks of their AsPh₄⁺ salts. The complex anions contain square‐pyramidal coordinated metal atoms with the phenylimido ligands in apical positions. The M–N–C bonds are almost linear. A similar phenylimido complex with an additional amino group was synthesized from [Re(NC₆H₄‐4‐NH₂)Cl₃(PPh₃)₂]. The presence of such substituents may allow coupling of the metal complexes to biomolecules such as peptides, proteins, or sugars, provided the M=N bonds are sufficiently stable against hydrolysis.     

Cascaded strand displacement for non-enzymatic target recycling amplification electrochemical detection of SARS-CoV-2EI北大核心CSCD

An electrochemical biosensor for low cost and highly sensitive and selective detection of SARS-CoV-2 target nucleic acid was developed based on two cascaded toehold-mediated strand displacement reactions (TSDRs). Driven by thermodynamic entropy, the target nucleic acid bound to the first toehold region of the probes, leading to the first TSDR and the second toehold region exposed. Subsequently, the methylene blue (MB)-modified signal probe triggered the second TSDR and led to cyclic reuse of the target nucleic acid. Based on cascaded TSDRs, a large number of signal probes were combined on the sensor surface to produce significantly enhanced square wave voltammetry (SWV)electrochemical signals. The results showed that the SWV signal intensity was proportional to the logarithm of the target nucleic acid concentration, and had a good linear relationship in the range of 5×10-14-5×10-10 mol/L with a detection limit of 1.8×10-14 mol/L. Moreover, the sensor could be employed to monitor SARS-CoV-2 nucleic acid in 10% serum samples. © 2023, Youke Publishing Co.,Ltd. All rights reserved.     

Determination of digoxin and its metabolites in biological samples by solidphase supported liquid-liquid extraction-liquid chromatography-tandem mass spectrometryEI北大核心CSCD

采用固相支撑液液萃取-超高效液相色谱-串联质谱（SLE-UPLC-MS/MS）技术建立了生物样本血液、尿液和肝组织中地高辛（DG）及其3种代谢物的分析方法。生物样本经匀浆、蛋白沉淀后,通过含有硅藻土的固相支撑液液萃取（SLE）柱净化富集,经洗脱、定容后进行LC-MS/MS分析。结果表明,血液基质中,地高辛在0.1～100 ng/mL浓度范围内线性关系良好;肝脏和尿液基质中,地高辛在0.2～100 ng/mL浓度范围内线性关系良好,地高辛的3种代谢物在0.5～100 ng/mL浓度范围内线性关系良好,3个浓度水平（10, 50和100 ng/mL）的加标回收率为60.5%～95.6%,基质效应80.7%～113.6%,日内、日间相对标准偏差（RSD）均小于13%,检出限为0.1～0.5 ng/mL。所建立的方法可用于生物样本中地高辛及其代谢物的定性定量分析。     

Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences

In this work, we consider the critical force required to unzip two different naturally occurring sequences of double-stranded DNA (dsDNA) at temperatures ranging from 20 ^°C to 50 ^°C, where one of the sequences has a 53% average guanine-cytosine (GC) content and the other has a 40% GC content. We demonstrate that the force required to separate the dsDNA of the 53% GC sequence into single-stranded DNA (ssDNA) is approximately 0.5 pN, or approximately 5% greater than the critical force required to unzip the 40% GC sequence at the same temperature. In the temperature range between 20 and 40 ^°C the measured critical forces correspond reasonably well to predictions based on a simple theoretical homopolymeric model, but at temperatures above 40 ^°C the measured critical forces are much smaller than the predicted forces. The correspondence between theory and experiment is not improved by using Monte Carlo simulations that consider the heteropolymeric nature of the sequences.     

Recent advances in analytical chemistry--a material approach

Advancements of materials research have profound direct impacts on developments in analytical chemistry and may hold the key to improvement of existing or new techniques at present times and near future. Applications of materials in analytical chemistry are reviewed, with focus on sensors, separations and extraction techniques. This review aims to survey examples of interesting works carried out in the last five years over a broad spectrum of materials classified as hybrids, nanomaterials and biomolecular materials.