Adenine Thymine Research Articles

Ab Initio Molecular Dynamics Studies of Stacked Adenine–Thymine and Guanine–Cytosine Nucleic Acid Base Pairs in Aqueous Solution

Ab initio MD studies have been performed on stacked adenine–thymine (A–T) and guanine–cytosine (G–C) nucleobase pairs solvated in water using Born–Oppenheimer molecular dynamics. These two systems have been analyzed using RDF, SDF, angle–distance CDF (combined distribution functions), plane projection analysis, hydrogen bond analysis, and non–covalent interaction (NCI) plots. The stacking property studies have shown that the molecular orientation of the A–T pair is completely opposite to that of the G–C pair though the center of mass distance between the two molecules is similar. The G–C pair shows significantly more stability in water than the A–T system does. RDF analyses show that the –NH– group and carbonyl groups show predominant interaction with water molecules. Water molecules are found to be most in numbers around the cytosine molecule and least around the adenine molecule. Hydrogen bonding studies show that the guanine molecule forms the highest number of hydrogen bonds with water molecules. On the other hand, the hydrogen atom attached to the –NH– group of adenine molecule shows the longest mean H–bond lifetime with water oxygen atoms. NCI interactions calculated through the ab initio method help us to visualize the [Formula: see text]-electron stacking and H–bonding between aromatic nucleobases and water molecules. A great shift in bond polarity and interaction intensity in different functional groups is observed for the nucleobases going from individually solvated molecules to paired states.

Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation

BackgroundThe Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families.MethodsHere, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated.ResultsThe mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period.ConclusionsThis study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder.

Endemic Radiation of African Moonfish, Selene dorsalis (Gill 1863), in the Eastern Atlantic: Mitogenomic Characterization and Phylogenetic Implications of Carangids (Teleostei: Carangiformes).

This study offers an in-depth analysis of the mitochondrial genome of Selene dorsalis (Gill 1863), a species native to the Eastern Atlantic Ocean. The circular mitochondrial DNA molecule measures 16,541 base pairs and comprises 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a control region (CR). The nucleotide composition exhibits a notable adenine-thymine (AT) bias, accounting for 53.13%, which aligns with other species in the Carangidae family. Most PCGs initiate with the ATG codon, with the exception of Cytochrome C oxidase subunit I, which starts with GTG. Analysis of relative synonymous codon usage reveals that leucine and serine are the most prevalent amino acids in the mitochondrial genome of S. dorsalis and its congeners (S. vomer and S. setapinnis). All tRNAs display the typical cloverleaf structure, though tRNA Serine (S1) lacks a dihydrouracil arm. Pairwise comparisons of synonymous and nonsynonymous substitutions for all PCGs yielded values below '1', indicating strong purifying selection. The CR spans 847 bp, representing 5.12% of the mitochondrial genome, and is characterized by high AT content (62.81%). It is situated between tRNA-Pro (TGG) and tRNA-Phe (GAA). The CR contains conserved sequence blocks, with CSB-1 being the longest at 22 bp and CSB-D the shortest at 18 bp. Phylogenetic analysis, using Bayesian and Maximum-likelihood trees constructed from concatenated PCGs across 72 species, successfully differentiates S. dorsalis from other carangids. This study also explores how ocean currents and gyres might influence lineage diversification and parapatric speciation of Selene species between the Atlantic and Pacific Oceans. These results highlight the importance of the mitochondrial genome in elucidating the structural organization and evolutionary dynamics of S. dorsalis and its relatives within marine ecosystems.

Theoretical Investigation of the structure and Raman scattering properties of Hoogsteen- and Watson-Crick-type Adenine-Thymine base pair

Hoogsteen (HG) and Watson-Crick (WC) adenine–thymine (A-T) base pairs are fundamental to gene expression and genomic stability. Our research applied density functional theory (DFT) calculations to analyze these base pairs, demonstrating that linking them with ribose or deoxyribose and their immersion in solvents markedly enhances the distinctions in their optical properties. DFT results reveal that N···HN hydrogen bonds in both HG and WC pairs exhibit characteristics of both ionic and covalent bonds, playing a crucial role in their stability. While WC base pairs demonstrate stronger orbital interactions, they also experience greater repulsion than HG pairs. This repulsion offsets the positive interactions to a degree, making the interaction energy of WC pairs slightly lower than that of HG pairs. Furthermore, the distinct conformations of these base pairs result in different vibrational modes, suggesting Raman spectroscopy as an effective method for distinguishing between WC and HG base pairs.

Ligation initiated self-priming isothermal polymerization enabled nano-signal amplification for APE1 sensing and logical unlocking

In this work, we developed a label-free and one-tube method for apurinic/apyrimidinic endonuclease 1 (APE1) sensing based on ligation initiated self-priming isothermal polymerization (SPIP) and signal amplification of fluorescent copper nanoparticles (CuNPs). This method was rationally proposed with modular design. In target recognition module, APE1 could specifically cleave substrate to release a linker DNA that served the ligation of an adenine/thymine (AT)-rich hairpin and a phosphorothioate-modified hairpin with the assistance of ligase. Then in SPIP amplification and signal transduction modules, once driven by polymerase, enzymatic extension and self-folding alternately occurred on the primary DNA originated from the ligation reaction, which resulted in accumulation of numerous AT-rich templates repeatedly included in the elongated dsDNA products, and ultimately enabled rapid formation of fluorescent CuNPs to output amplified signal. The accurate target identification and efficient signal amplification facilitated the highly selective and sensitive detection of APE1 with limit of detection of 8.6 × 10−4 U/mL. Benefiting from the robustness of this method, the normal cells and tumor cells could be distinguished unambiguously with this method according to the test results of cellular APE1. Moreover, the sensing strategy was employed in the concatenated AND logical operation and molecular keypad unlocking, which further displayed its extensibility and versatility.

Next-generation sequencing based Cyperus niveus (Cyperaceae) complete chloroplast genome: A comparative analysis and phylogeny

Cyperus niveus, a perennial herb, holds significant traditional and scientific medicinal value. In this study, the complete chloroplast genome sequence of C. niveus was assembled and comparisons were conducted among species in the genus Cyperus. Molecular phylogenetic analysis was also conducted in Cyperaceae. The chloroplast genome of C. niveus exhibits a quadripartite structure, spanning a length of 185,454 base pairs (bp). The genome contains a large single-copy region (99,339 bp), flanked by two inverted repeats (IRs) (IRA and IRB: each 38,021 bp) separated by a small single-copy (SSC) region (10,073 bp). The chloroplast genome of C. niveus was rich in adenine-thymine (AT) at 66.7% and guanine-cytosine (GC) at 33.3%. A total of 140 unique genes were identified in the chloroplast genome of C. niveus, including 83 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. An amino acid frequency analysis uncovered the prevalence of leucine (10.90%) and isoleucine (9.20%). One hundred and forty-six simple sequence repeats and 49 oligonucleotide repeats were found in the chloroplast genome of C. niveus. A comparative analysis highlighted greater divergence within the IR and SSC regions. A phylogenetic assessment revealed that species within the genus Cyperus display phylogenetic conservation compared to other genera. Notably, the genus Carex exhibited substantial divergence, indicative of rapid evolutionary changes. C. niveus showed close resemblance with C. iria and C. exaltatus. In essence, this study and of chloroplast genome of C. niveus represents a valuable genomic asset that holds significance in species identification and comparative genomic research, presenting the first evolutionary relationship in Cyperaceae on the basis of chloroplast genome.

Flow Cytometry for Estimating Plant Genome Size: Revisiting Assumptions, Sources of Variation, Reference Standards, and Best Practices

Flow cytometry has been widely used to estimate relative and absolute genome sizes (DNA contents) of plants for more than 50 years. However, the accuracy of these estimates can vary widely because of many factors, including errors in the genome size estimates of reference standards and various experimental methods. The objectives of this study were to reassess genome sizes of commonly used reference standards and quantify sources of variation and error in estimating plant genome sizes that arise from buffers, confounding plant tissues, tissue types, and plant reference standards using both 4′,6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI) fluorochromes. Five separate studies were performed to elucidate these objectives. Revised estimates of genome sizes of commonly used plant reference standards were determined using human male leukocytes as a primary standard with an updated genome size (6.15 pg; 12.14% lower than that of earlier studies) using both DAPI and PI fluorochromes. Comparison of six different buffers (Galbraith’s, LB01, MB01, MgSO4, Otto’s, and Sysmex) resulted in variations in genome size estimates by as much as 18.1% for a given taxon, depending on the buffer–fluorochrome combination. The addition of different confounding plant tissues (representing 10 diverse taxa and associated secondary metabolites) resulted in variations in genome size estimates by as much as 10.3%, depending on the tissue–fluorochrome combination. Different plant tissue types (leaf color/exposure and roots) resulted in a variation in genome size estimates of 10.7%, independent of the fluorochrome. The selection of different internal reference standards introduced an additional variation in genome size estimates of 5.9%, depending on the standard–fluorochrome combination. The choice of fluorochrome (DAPI vs. PI) had one of the largest impacts on genome size estimates and differed by as much as 32.9% for Glycine max ‘Polanka’ when using human male leukocytes as an internal standard. A portion of this variation (∼10.0%) can be attributed to the base pair (bp) bias of DAPI and variations in Guanine-Cytosine (GC):Adenine-Thymine (AT) ratios between the sample and standard. However, as much as 22.9% of the variation in genome size estimates may result from how effectively these fluorochromes stain and report the genome. The combined variation/error from all these factors (excluding variation from bp bias for different fluorochromes, and assuming variations from confounding tissues and tissue types to both result from secondary metabolites) totaled 57.6%. Additional details of how selected factors impact accuracy, precision, and the interaction of these factors are presented. Overall, flow cytometry can be precise, repeatable, and extremely valuable for determining the relative genome size and ploidy of closely related plants when using consistent methods, regardless of fluorochrome. However, accurate determination of the absolute genome size by flow cytometry remains elusive, and estimates of genome size using flow cytometry should be considered gross approximations that may vary by ±29% or more as a function of experimental methods and plant environments. Additional recommendations of best practices are provided.

Enhanced sampling strategies for molecular simulation of DNA

AbstractMolecular dynamics (MD) simulations can provide detailed insights into complex molecular systems, such as DNA, at high resolution in space and time. Using current computer architectures, time scales of tens of microseconds are feasible with contemporary all‐atom force fields. However, these timescales are insufficient to accurately characterize large conformational transitions in DNA and compare calculations to experimental data. This review discusses the advantages and drawbacks of two simulation approaches to overcome the timescale challenge. The first approach is based on adding biasing potentials to the system to drive transitions. Umbrella sampling, steered MD, and metadynamics are examples of these methods. A key challenge of such methods is the necessity of selecting one or a few efficient coordinates, commonly referred to as collective variables (CVs), along which to apply the biasing potential. The path‐metadynamics methodology addresses this issue by finding the optimal route(s) between states in a multi‐dimensional CV space. The second strategy is path sampling, which focuses MD simulations on the transitions. The assumption is that even though transitions between states are rare, they are generally fast. Stopping the simulations as soon as they reach a stable state can significantly increase simulation efficiency. We introduce these methods on the two‐dimensional Müller–Brown potential. DNA applications are featured for two different processes: the Watson–Crick–Franklin to Hoogsteen transition in adenine–thymine base pairs and the binding of a DNA‐binding protein domain to DNA.This article is categorized under: Molecular and Statistical Mechanics Molecular Dynamics and Monte‐Carlo Methods Molecular and Statistical Mechanics Free Energy Methods Software Simulation Methods

Intermolecular hydrogen bonding in DNA base pairs interacting with different numbers of bare and hydrated Li+: NBO, QTAIM, and computational spectroscopic studies

In this study, the effect of different numbers of Li+ interacting with various sites of DNA base pairs (adenine–thymine (AT) and cytosine-guanine (GC)) on the base pair structures, the strength of hydrogen bonding between the bases, and spectroscopic properties (IR and absorption spectra) of the base pairs was investigated. Two quantum computational analyses, the natural bonding orbitals (NBO) and the quantum theory of atoms in molecules (QTAIM), were used to follow the change in the strength of hydrogen bonds between the bases in each pair. The type of base pair’s site interacting with Li+ showed different effects on the change in the strength of the hydrogen bonds between the bases. The IR and absorption spectra of the lithiated base pairs were calculated and compared with those of bare base pairs. This comparison provided the changes in the spectra as a fingerprint for the structural identification of different lithiated base pairs. Also, the determination of the change in the strength of hydrogen bonds in the lithiated base pairs compared to their bare base pairs. In the other part of this study, the effect of the hydration of the attached Li+ in the structure of lithiated base pairs on the strength of their hydrogen bonds and spectra was investigated.

Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements.

Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011Å and 1.060 ± 0.011Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083Å and 1.087Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments.

Interactions of adenine–thymine base pair with potassium cation and water clusters

The structures of Ade-Thy-K+(H2O)n (n = 0–6) clusters were determined, and the interaction mechanism of K+-base pair (A-T) in water clusters was elucidated. The non-hydrated Ade-Thy-K+ shows a planar structure, while the complex transforms into a stacked form when the water molecules are involved. It is noted that K+ no longer connects to adenine but is tricoordinated with thymine and the adjacent water from n = 3, and then forms a tetracoordinate ion from n = 4. The RDG, AIM, and EDA combined with interaction energy analyses show that the interaction between K+ and base pair weakens gradually when the first four water molecules are involved successively, and then strengthens for n = 5, 6. The interaction between K+ and the A-T base pair is dominated by an electrostatic power, followed by dispersion, whereas the interactions between adenine and thymine are always dominated by dispersion from n = 1 to 6.

The complete chloroplast genome sequence of Nepeta bracteata and comparison with congeneric species

Nepeta bracteata (N. bracteata) is an important medicinal plant used by Chinese ethnic minorities. However, the lack of knowledge regarding the chloroplast genome of N. bracteata has imposed current limitations on our study. Here, we used Next-generation sequencing to obtain the chloroplast genome of N. bracteata. The findings suggested that the 151,588 bp cp genome of N. bracteata comprises 130 genes, including 35 tRNA genes and 87 protein-coding genes. And its chloroplast genome exhibits a typical quadripartite structure, the largest single copy (LSC; 82,819 bp) and the smallest single copy (SSC; 17,557 bp) separate a pair of inverted repeats IR regions (IRa and IRb; 25,606 bp) from one another. Interestingly, palindromic repeats are more common, as shown by the examination of repetition. In the interim, 18 SSRs were discovered in the interim, the bulk of which were Adenine-Thymine (A-T) mononucleotides. Meanwhile, we compared it with five other species from the Nepeta genus. Five hypervariable areas were found by the study, including ndhH-rps15, accD-psal, ndhG-ndhl, trnH-GUG-psbA, and rpoC1-rpoB. Furthermore, the phylogenetic study revealed that N. bracteata and Nepeta stewartiana (N. stewartiana) were linked to each other most closely. In summary, our findings enrich the resources available for chloroplast genomes in the Nepeta genus. Moreover, these hypervariable regions have the potential to be developed into molecular markers, enabling the rapid identification of species within the Nepeta genus. Comparative analysis of species within the Nepeta genus can help enhance our study of their phylogenetic relationships, potential medicinal properties and bioprospecting.

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene.

To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.

A Sensitive Fluorescence Sensor for Tetracycline Determination Based on Adenine Thymine-Rich Single-Stranded DNA-Templated Copper Nanoclusters.

A sensitive fluorescent sensor has been developed for the determination of tetracycline (TC) using adenine thymine (AT)-rich single-stranded DNA (ssDNA) templated copper nanoclusters (CuNCs) as a fluorescent probe. Fluorescent ssDNA-CuNCs were synthesized by employing AT-rich ssDNA as templates and ascorbic acid as reducing agents through a facile one-step method. The as-prepared ssDNA-CuNCs exhibited strong fluorescence with a large Stokes shift (240 nm) and stable fluorescence emission. In the presence of TC, the fluorescent intensity of ssDNA-CuNCs was obviously decreased through the inner filter effect, due to the spectral overlapping between ssDNA-CuNCs and TC. Under the optimal conditions, the strategy exhibited sensitive detection of TC with a linear range from 2 nM to 30 μM and with a limit of detection of 0.5 nM. Furthermore, the sensor was successfully applied for the detection of TC in milk samples. Therefore, it provided a simple, rapid, and label-free fluorescent method for TC detection.

Investigation of hydrogen bonding in small nucleobases using DFT, AIM, NCI and NBO technique

In this work hydrogen bonded base pairing properties of two adenine analogue nucleobases and thymine were investigated. wB97XD/6-311++G(2d,2p) level of theory was employed to optimize the monomers and the base pairs in different orientations. Atoms In Molecule, AIM analysis was carried out to analyse the individual hydrogen bonds in the studied complexes. NH…N and OH…N were found to be major contributors to the overall interaction energy than O…HC and N…HC bonds. Non Covalent Interaction, NCI and Reduced Density Gradient, RDG plots revealed that interactions are mainly weak and intermediate in nature. Finally Natural Bond Orbital, NBO calculations were performed to calculate the second order perturbation energy E(2) which helped to understand the interaction between electron donor and acceptors in the individual complexes.

Photoionization Dynamics and Proton Transfer within the Adenine-Thymine Nucleobase Pair

Studying the stability of hydrogen-bonded nucleobase pairs, at the heart of the genetic code, is of utmost importance for an in-depth understanding of basic mechanisms of life and biomolecular evolution. We present here a VUV single photon ionization dynamic study of the nucleobase pair adenine-thymine (AT), revealing its ionization and dissociative ionization thresholds via double imaging electron/ion coincidence spectroscopy. The experimental data, consisting of cluster mass-resolved threshold photoelectron spectra and photon energy-dependent ion kinetic energy release distributions, allow the unambiguous distinction of the dissociation of AT into protonated adenine AH+ and a dehydrogenated thymine radical T(-H) from dissociative ionization processes of other nucleobase clusters. Comparison to high-level ab initio calculations indicates that our experimental observations can be explained by a single hydrogen-bonded conformer present in our molecular beam and allows the estimation of an upper limit of the barrier of the proton transfer in the ionized AT pair.

Oligonucleotides as Inhibitors of Ice Recrystallization.

Oligonucleotides of adenine (A20), guanine (G20), cytosine (C20), thymine (T20), cytosine-guanine ((CG)20), and adenine-thymine ((AT)20) were investigated as model compounds for ice recrystallization inhibition (IRI). Dehydroxy uracil (dU20), U20, and T20 were also compared to investigate the effect of minute changes in the hydrophobicity of the oligonucleotides on the IRI activity. Among the oligonucleotides considered in this study, T20 exhibited the best performance for IRI. In addition, the degree of polymerization of oligothymines varied over 5, 10, 20, 30, 50, and 100, and T20 was found to be the most effective for IRI. The IRI mechanism was investigated by comparing U20 and T20, which exhibited the lowest and highest IRI activity, respectively, among the oligonucleotides for their dynamic ice-shaping, thermal hysteresis, and ice nucleation inhibition. Little or no dynamic ice-shaping activity and small thermal hysteresis were observed for both nucleotides. All of the findings suggest that not the ice-polymer adhesion but the hydrophobic interactions of T20 in the interface layer might interfere with the water deposition on the ice crystal surfaces and contribute to the IRI activity of the T20 oligonucleotide.

COI Gene Analysis of Asian Horseshoe Crab in Banyuasin Estuarine Waters, Sumatra, Indonesia

There is limited study on DNA barcoding of horseshoe crabs in South Sumatra, Indonesia. The present study was the first to record horseshoe crabs' COI DNA barcoding in three localities of Banyasin estuarine waters. The nucleotide composition was in a strong adenine thymine bias (AT = 63.90%) with high haplotypic diversity (Hd = 0.858) relative to low nucleotide diversity (π = 0.0534). A total of 16 haplotypes were recorded, of which two were in Carat Cape, 4 in Makati Jaya, and 12 in the Banyuasin river estuary (BRE), and Hap 1 was a dominant type (62.5%). The population differentiation (FST) value was varied, and only in the comparison of BRE-Carat Cape was significant (FST = 0.637), while the gene flow (Nm) value in Makati Jaya-BRE was high (6.563). The neutrality test, Tajima's D (0.4142), and Fu's Fs values were negative (-0.492), suggesting these populations have experienced a current bottleneck or multiplication. Analysis of molecular variation (AMOVA) suggested that 68% was distributed within populations. The haplotype network, PCoA, and phylogenetic of COI DNA sequences clustered in three groups correspond to Carcinoscorpius rotundicauda, Tachypleus gigas, and Tachypleus tridentatus. This finding is a matter of concern for managing and conserving horseshoe crab species in Banyuasin estuarine waters.

Bubble Relaxation Dynamics in Homopolymer DNA Sequences.

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.5-500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.

Influence of a Methyl Group on the Unidirectional Flow of Vibrational Energy in an Adenine-Thymine Base Pair.

The role of a methyl group in intramolecular vibrational energy redistribution (IVR) of the hydrogen-bonded adenine-thymine base pair has been studied using classical dynamics procedures. Energy transferred to the doorway bond thymine-NH from the vibrationally excited H2O(v) efficiently redistributes among various bonds of the base pair through vibration-to-vibration coupling, depositing a large fraction of the available energy in the terminal bond adenine-NH. On the other hand, the extent of energy flow in the reverse direction from the excited adenine-NH to thymine-NH is insignificant, indicating IVR in adenine-thymine resulting from the intermolecular interaction with a vibrationally excited H2O molecule, is direction-specific. The unidirectional flow is due to the coupling of stretch-torsion vibrations of a methyl group with conjugated bonds on the thymine ring, when the methyl rotor is present and is adjacent to the vibrationally excited thymine-NH. The insignificance of energy flow from the terminal-to-terminal bond in the reverse direction is attributed to the absence of a methyl group on the adenine moiety, even though the molecule has many CC and CN bonds coupled to their neighbors.