Deoxyribonucleic Acid Nucleotide Research Articles

Classifying promoters by interpreting the hidden information of DNA sequences for disease prediction in clinical laboratories using Gaussian decision boundary estimation

A promoter is a brief stretch of DNA (100–1,000 bp) where RNA polymerase starts to transcribe a gene. A DNA (Deoxyribonucleic Acid) base pair is a fundamental unit of DNA structure and represents the pairing of two complementary nucleotide bases within the DNA double helix. The four DNA nucleotide bases are adenine (A), thymine (T), cytosine (C), and guanine (G). DNA base pairs are the building blocks of the DNA molecule, and their complementary pairing is central to the storage and transmission of genetic information in all living organisms. Normally, a promoter is found at the 5′ end of the transcription initiation site or immediately upstream. Numerous human disorders, particularly diabetes, cancer, and Huntington’s disease, have been shown to have DNA promoter as their root cause. The scientific community has long been interested in learning crucial information about protein-coding genes. Finding the promoters is therefore the first step in finding genes in DNA sequences. The scientific world has always been attracted by the effort to glean crucial knowledge about protein-coding genes. Consequently, identifying promoters has emerged as an intriguing challenge that has caught the interest of numerous researchers in the field of bioinformatics. We proposed Gaussian Decision Boundary Estimation in machine learning models to detect transcription start sites (promoters) in the DNA sequences of a common bacteria, Escherichia coli. The best features are identified through a score-based function to select relevant nucleotides that are directly responsible for promoter recognition, in order maximise the models’ performance. The Gaussian Decision Boundary Estimation based support-vector-machine model is trained with these features and finds the best hyperplane that separates the data into different classes. Throughout this study, promoter regions could be identified with high accuracy 99.9% which is better compared to other state of art algorithms. The comparison of machine learning classification models is another major emphasis of this paper in order to identify the model that most accurately predicts DNA sequence promoters. It provides analysis for further biological research as well as precision medicine.

An Artificial Intelligence Approach for Verifying Persons by Employing the Deoxyribonucleic Acid (DNA) Nucleotides

Deoxyribonucleic acid (DNA) can be considered as one of the most useful biometrics. It has effectively been used for recognizing persons. However, it seems that there is still a need to propose a new approach for verifying humans, especially after the recent big wars, where too many people lost and die. This approach should have the capability to provide high personal verification performance. In this paper, a personal recognition approach based on artificial intelligence is proposed. This approach is called the artificial DNA algorithm for recognition (ADAR). It utilizes a unique identity for each person acquired from DNA nucleotides, and it can verify individuals efficiently with high performance. The ADAR has been designed and applied to multiple datasets, namely, the DNA classification (DC), sample DNA sequence (SDS), human DNA sequences (HDS), and DNA sequences (DS). For all datasets, a low value of 0% is achieved for each of the false acceptance rate (FAR) and false rejection rate (FRR).

Xeroderma Pigmentosum-Associated Childhood Interstitial Lung Disease.

Chromosomal breakage syndromes are a group of genetic disorders that are ascribable to the autosomal recessive mode of inheritance. Xeroderma pigmentosum is one of the chromosomal breakage syndromes which is due to the involvement of deformity in the deoxyribonucleic acid’s nucleotide excision repair. Xeroderma pigmentosum is a genetic disorder, which is autosomal recessive, heterogeneous, and more common in cases of consanguinity, caused by mutations in at least 10 genes and 9 complementation groups. The disorder is very rare. Patients experience photophobia and extreme photosensitivity and have pigmentary changes in ultraviolet light-exposed areas of the body with freckling, premalignant, and malignant skin lesions arising in keratinocytes soon after the fleeting exposure to sunlight. Patients are also oversensitive to environmental mutagens such as cigarette smoke and possibly to the widely used agricultural insecticide, diazinon. Progressive neurological abnormalities along with some rare complications are also noticed among these patients. Symptoms and thoracic high-resolution computed tomography are considered for diagnosis. Only corticosteroids can be given to limit the progression of the disease. Xeroderma pigmentosum-related interstitial lung disease is one of the rarest forms and we thereby report an interesting case.

Identifying Single-Stranded DNA by Tuning the Graphene Nanogap Size: An Ionic Current Approach.

Solid nanopore-based deoxyribonucleic acid (DNA) sequencing has led to low-cost, fast, reliable, controlled, and amplified or label-free and high-resolution recognition and identification of DNA nucleotides. Solid-state materials and biological nanopores have a low signal-to-noise ratio (SNR) and generally are too thick to read at single-nucleotide resolution. The issue with solid-state nanopores is that the DNA strands stick to the nanopore sides and on the surface during the translocation process. The coexistence of DNA nucleotides on the surface and the nanopore sides will complicate the ionic current signals, making nucleotide detection difficult. Therefore, different sized nanogaps can be promising to overcome some of these issues. Using all-atom molecular dynamics (MD) simulations, we have studied the translocation of single-stranded (ss) DNA through solid-state nanogaps embedded in a graphene membrane device. A nucleotide-specific DNA sequencing technique is proposed based on unique differences in the ionic current responses for all the four ssDNA nucleotides (dAMP16, dGMP16, dTMP16, and dCMP16). As the individual homogeneous ssDNA translocate through the nanogaps, characteristic changes are observed in the ionic current. Our results show that ssDNA nucleotides can translocate through the proposed graphene nanogap devices by applying an external electric field. In addition, the sticking issue can be resolved using graphene nanogaps during the ssDNA translocation processes. Therefore, the significant difference in ionic current sensitivity and the translocation event/time yielded by the graphene nanogap-based devices reveal possibilities for utilizing it for ultrafast nanogap-based DNA sequencing.

Social distance teaching and learning: An online DNA nucleotide binding lab experience for health sciences and non-major students.

DNA analysis is a common diagnostic tool in healthcare: ranging from microbial typing (e.g. DNA strands of viral, bacterial and even fungal pathogens), oncological screen (e.g. Breast cancer detection via DNA analysis of any BRCA gene mutations), genetic amniocentesis test (a medical technique used in determining chromosomal conditions such as down syndrome in the fetus) and a host of other medical diagnostics based on the knowledge of deoxyribonucleic acid (DNA) and the genetic information carried in this macromolecule. However, such a wide-range of medical diagnostic mechanisms using DNA begs the question: How much does the undergraduate health sciences and/or non-major students understand about the basic biochemical properties of DNA? Here, a virtual lab module was used (with the addition of Pre and Post Lab Questions and a Discussion Topic relating DNA to Healthcare) along with a learning management system, to help undergraduate health sciences students visualize the biochemical properties of DNA molecule, such as binding constant and Gibbs free energy of binding. This lab was adapted to offer a platform on which an Instructor can design steps for students to explore the DNA nucleotide binding module during a time in which social distance curricula is necessary.

An efficient image encryption scheme based on chaotic and Deoxyribonucleic acid sequencing

In this research article, we have designed a novel image encryption scheme based on Deoxyribonucleic acid (DNA) and chaotic sequencing. We have studied sequences of different genes consisting of four bases, Adenine (A), Cytosine (C), Thymine (T) and Guanine (G), also known as nucleotides which are the fundamental code of life. The purpose of DNA is to store, copy and transmit the genetic information of the living organism. The proposed image encryption scheme uses the chaotic system to generate random sequences and to choose between two or more options. The image is totally transformed by first encoding it into DNA nucleotides, shuffling to achieve diffusion and then substitution is performed to achieve confusion. Then later the DNA fusion operation is performed on the DNA image and the DNA complements are applied on the resulting DNA image, a random number of times to break the residual correlation between the pixels. The cipher image has been tested to fulfill all the standard benchmarks to be categorized as a good ciphered image which includes entropy, correlation coefficient, Pearson’s chi square, peak signal to noise ratio, mean square error, mean absolute error, structure similarity indexed measures, differential analysis and histogram uniformity test.

Probing the Interaction between a DNA Nucleotide (Adenosine-5'-Monophosphate Disodium) and Surface Active Ionic Liquids by Rotational Relaxation Measurement and Fluorescence Correlation Spectroscopy.

This article demonstrates the interaction of a deoxyribonucleic acid (DNA) nucleotide, adenosine-5'-monophosphate disodium (AMP) with a cationic surface active ionic liquid (SAIL) 1-dodecyl-3-methylimidazoium chloride (C12mimCl), and an anionic SAIL, 1-butyl-3-methylimidazolium n-octylsulfate ([C4mim][C8SO4]). Dynamic light scattering (DLS) measurements and 1H NMR (nuclear magnetic resonance) studies indicate that substantial interaction is taking place among the DNA nucleotide (AMP) and the SAILs. Moreover, cryogenic transmission electron microscopy (cryo-TEM) suggests that SAILs containing micellar assemblies are transformed into larger micellar assemblies in the presence of DNA nucleotides. Additionally, the rotational motion of two oppositely charged molecules, rhodamine 6G perchlorate (R6G) and fluorescein sodium salt (Fl-Na), have been monitored in these aggregates. The rotational motion of R6G and Fl-Na differs significantly between SAILs micelles and SAILs-AMP containing larger micellar aggregates. The effect of negatively charged DNA nucleotide (AMP) addition into the cationic and anionic SAILs is more prominent for the cationic charged molecule R6G than that of anionic probe Fl-Na due to the favorable electrostatic interaction between the AMP and cationic R6G. Moreover, the influence of the anionic DNA nucleotide on the cationic and anionic SAIL micelles is monitored through the variation of the lateral diffusion motion of oppositely charged probe molecules (R6G and Fl-Na) inside these aggregates. This variation in diffusion coefficient values also suggests that the interaction pattern of these oppositely charged probes are different within the SAILs-nucleotide containing aggregates. Therefore, both rotational and translational diffusion measurements confirm that the DNA nucleotide (AMP) renders more rigid microenvironment within the micellar solution of SAILs.

A new biochemical dye molecule and nuclear stain formulation in histotechnology diagnostics as an alternative to hematoxylin

In this study, a novel molecule, a nucleotide permanent marker for nuclear staining from Papaver rhoeas (common poppy), and a sustainable stain formulation is disclosed. The molecule appears to penetrate tissue layers aggressively, and specifically attaches deoxyribonucleic acid nucleotides, staining the nucleus and revealing microscopic details. Various hematoxylin nuclear stain formulations have been presented for diagnostics, in the relative absence of viable alternatives. Millions of surgical microscopic diagnostic tests (2.5–3 million slides every day) are processed with hematoxylin, throughout the world. Apparently, hematoxylin is the most commonly used nuclear stain for histopathology diagnostics in the world, although the present cost – financial and ecological – of hematoxylin protocols is substantial and not well appreciated, even by pathologists and histologists. The origin of the hematoxylin is the Logwood tree (Haematoxylum campechianum), a species indigenous to the tropical rainforests of Central and South America, which sources the worldwide demand for a nuclear stain in medicine and raw material for other industrial disciplines. In the past, hematoxylin shortages placed hematoxylin medical diagnostics practices at risk, resulting not only in higher costs to health care, but also to the environment: increasing consumption of logwood trees deteriorated local rainforest ecology, producing negative global ecologic consequences over at least a 100-year period. Herein, a sustainable nuclear stain formulation featuring a highly complex and functional molecule, which reveals the nuclear morphology properly, is presented and the proposed nuclear staining is discussed as a promising potential substitute for hematoxylin in routine microscopic diagnostics in histology and pathology.

Choi-Williams Distribution to Describe Coding and Non-coding Regions in Primary Transcript Pre-mRNA

Deoxyribonucleic acid (DNA) information is discrete in both ”time” (sequence positions) and ”amplitude” (nucleotide values). This permits the use of signal processing techniques for its characterization. The conversion of DNA nucleotide symbols into discrete numerical values enables signal processing to be employed to solve problems related to sequence analysis, such as finding coding sequences. In this work, a numerical conversion method was chosen based on the thermodynamic data of free energy changes (∆G°) of the formation of a duplex structure of DNA or ribonucleic acid (RNA), associated with the nucleotide sequence pre-mRNA (messenger RNA). The aim of this work was to characterize coding regions (exons) from non-coding regions (introns) using a methodology based on time-frequency representation (TFR). This permits the observation of the evolution of the periodicity and frequency components with time, introducing more variables related to the gene sequences compared to those used in traditional fast Fourier transform analysis. The parameters calculated from TFR are instantaneous frequency and instantaneous power. It was found that instantaneous frequency and power variables in different frequency bands allowed the correct classification between exons and introns with a prediction accuracy of more than 85%.

BioMe: biologically relevant metals

In this article, we introduce BioMe (biologically relevant metals), a web-based platform for calculation of various statistical properties of metal-binding sites. Users can obtain the following statistical properties: presence of selected ligands in metal coordination sphere, distribution of coordination numbers, percentage of metal ions coordinated by the combination of selected ligands, distribution of monodentate and bidentate metal-carboxyl, bindings for ASP and GLU, percentage of particular binuclear metal centers, distribution of coordination geometry, descriptive statistics for a metal ion–donor distance and percentage of the selected metal ions coordinated by each of the selected ligands. Statistics is presented in numerical and graphical forms. The underlying database contains information about all contacts within the range of 3 Å from a metal ion found in the asymmetric crystal unit. The stored information for each metal ion includes Protein Data Bank code, structure determination method, types of metal-binding chains [protein, ribonucleic acid (RNA), deoxyribonucleic acid (DNA), water and other] and names of the bounded ligands (amino acid residue, RNA nucleotide, DNA nucleotide, water and other) and the coordination number, the coordination geometry and, if applicable, another metal(s). BioMe is on a regular weekly update schedule. It is accessible at http://metals.zesoi.fer.hr.

DNA-Based Data Encryption and Hiding Using Playfair and Insertion Techniques

In this paper, we propose a novel algorithm to communicate data securely. The proposed technique is a composition of both encryption and data hiding using some properties of Deoxyribonucleic Acid (DNA) sequences. Hence, the proposed scheme consists mainly of two phases. In the first phase, the secret data is encrypted using a DNA and Amino Acids-Based Playfair cipher. While in the second phase the encrypted data is steganographically hidden into some reference DNA sequence using an insertion technique.The proposed algorithm can successfully work on any binary data since it is actually transformed into a sequence of DNA nucleotides using some binary conversion rule. Subsequently, these nucleotides are represented as an amino acids structure in order to pass through the specially designed Playfair Cipher and encrypt it into another DNA sequence. Then, this encrypted DNA data is randomly inserted into some reference DNA sequence to produce a faked DNA sequence with the encrypted data hidden. In order to recover the embedded secret data, the receiver can carry out the inverse process with the help of the both the secret key and the reference DNA sequence.

A Novel Dual-Core Architecture for the Analysis of DNA Microarray Images

A deoxyribonucleic acid (DNA) microarray is a collection of microscopic DNA spots attached to a solid surface, such as a glass, plastic, or silicon chip forming an array. DNA microarray technologies are an essential part of modern biomedical research. DNA microarray allows compressing hundreds of thousands of different DNA nucleotide sequences in a little microscope glass and permits having all this information on a single image. The analysis of DNA microarray images allows the identification of gene expressions to draw biological conclusions for applications ranging from genetic profiling to diagnosis of cancer. Unfortunately, DNA microarray technology has a high variation of data quality. Therefore, to obtain reliable results, complex and extensive image analysis algorithms should be applied before the actual DNA microarray information can be used for biomedical purposes. In this paper, we present a novel hardware architecture that is specifically designed to analyze DNA microarray images. The architecture is based on a dual-core system that implements several units working in a single-instruction/multiple-data fashion. A field-programmable-gate-array (FPGA)-based prototypal implementation of the proposed architecture is presented. The effectiveness of the novel dual-core architecture is demonstrated by several analyses performed on original DNA microarray images, showing that the capability of detecting DNA spots increases by more than the 30% with respect to that of previously developed software techniques.

Tyrimo lygiai genetikoje ir geno sąvoka

Straipsnyje analizuojami genetikos mokslo raidoje aptinkami tyrimo lygiai, besiskiriantys metodologiniu požiūriu. Tyrimo lygis – tai metodologinė kategorija, apimanti klausimų grupę, tyrimo metodų arsenalą, būtiną tiems klausimams atsakyti, patogius tyrimo objektus. Tyrimo lygio negalima tapatinti su istoriniu etapu. Kiekvieną tyrimo lygį charakterizuoja tyrimo objektas ir jo vertinimo kriterijus. Genetikoje tyrimo objektas yra genetinis aparatas: plačiąja prasme – organizmas, siaurąja – ląstelė, chromosoma, DBR molekulė. Genetikoje objekto vertinimo kriterijus yra požymis. Pirmajame tyrimo lygyje į organizmą žiūrima kaip į požymių visumą: požymiai nulemia organizmo vietą sistematikos hierarchijoje. Šiame tyrimo lygyje sukurta rūšies sąvoka, tiriamas rūšies pastovumas ir naujų rūšių atsiradimas, požymio-individo-populiacijos santykis. Antrojo tyrimo lygio pagrindas yra tai, kad organizmui pradžią duoda viena ląstelė, trečiojo tyrimo lygio bruožas – požymių paveldėjimo kartose sugretinimas su chromosomų persitvarkymais, ketvirtojo – genetiniai tyrimai atliekami su gryna žinomos cheminės sudėties bei struktūros genetine medžiaga, penktojo lygio – DBR arba RBR nukleotidų seka – funkcija.

Detection of 8-Hydroxy-2'-deoxyguanosine in Deoxyribonucleic Acid by the 32P-Postlabeling Method.

Using synthesized 8-hydroxy-2'-deoxyguanosine 3'-monophosphate as a marker, the 32P-postlabeling method was adapted with minimum modifications for the analysis of 8-hydroxy-2'-deoxyguanosine (8-OH-dG) content in deoxyribonucleic acid (DNA). This method allows the analysis of one 8-OH-dG per 10(4) DNA nucleotides with only 10 pmoles of nucleotides required. The amounts of 8-OH-dG in DNA detected by the postlabeling method correlated well with the electrochemical detection method but were consistently lower.

Deoxyribonucleic Acid Base Compositions and Nucleotide Distributions of 65 Strains of Budding Bacteria

A total of 65 strains of appendaged or prosthecate, budding bacteria from our culture collection were selected for a study of deoxyribonucleic acid (DNA) base composition and nucleotide distribution. These strains represented 11 genera, including 4 genera of hyphal, budding bacteria which have not been formally described yet. The DNA species were thermally denatured, and absorbance-temperature profiles were recorded. The midpoints, widths, and asymmetries of the melting transitions were determined. When the DNA base compositions and nucleotide distributions were plotted on a dissimilarity map, it became evident that the strains of each genus occupied a distinct area. The distribution of strains within such an area indicated the degree of heterogeneity of a genus. When 16 Hyphomicrobium strains were analyzed, they formed five clusters within their generic area. These clusters correlated well with groups which had been previously established by DNA base composition analyses, by DNA-DNA homology studies, and by numerical taxonomy. Nine of the strains investigated were distinguished by melting profiles which were skewed uniquely to the left.

The Reaction of Hydrogen Atoms with DNA

The reactions of hydrogen atoms with samples of calf and salmon deoxyribonucleic acid (DNA) have been investigated by an electron spin resonance technique. The reactions with component DNA nucleotides and deoxyribose were also investigated to aid in the interpretation of the DNA results. Analysis of the resultant ESR spectra was facilitated by use of a computer spectrum simulation technique. The results showed that hydrogen atoms react mainly by addition to purine (49%) and thymine (23%) base groups in DNA. The extent of attack on each base is roughly in proportion to the percentage of the base present in DNA. This result is in contrast to radiolysis where preferential attack on the thymine base occurs. Approximately 20% of the hydrogen atoms react with the deoxyribose groups in the backbone of the DNA molecule. The presence of histones in the samples is shown to inhibit hydrogen atom addition. It is expected that the presence of histones in vivo will protect DNA from hydrogen atom attack during radiolysis.

HYDRATION OF PURINES, PYRIMIDINES, NUCLEOSIDES, AND NUCLEOTIDES

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Metabolic studies on the sugars of nucleic acids: II. 14C-labelling of ribose and deoxyribose and its comparison with 32P incorporation into ribonucleic acid and deoxyribonucleic acid of rat-thymus cells

1. 1. Rat-thymus cells were incubate with [ 14C 6]glucose. Ribose and deoxyribose moieties bound to the different bases of nucleic acids were isolated and the incorporation of 14C into these sugars was determined. 2. 2. Among the ribose moieties, those bound to adenine and guanine had the highest specific activities; that of uracil-bound ribose was lower, while the specific activity of the cytosine-bound ribose was the lowest, amounting to only a few per cent of that of the purine-ribose. 3. 3. In deoxyribonucleic acid, similarly, the specific activity of the purine-deoxyribose was much higher (about 20 times) than that of the pyrimidine-deoxyribose. 4. 4. On the other hand, when 32P was used as a precursor, no such differences were observed in its uptake into the 5′-nucleotides derived from ribonucleic acid, nor in its uptake into the deoxyribonucleic acid nucleotides. 5. 5. These results are discussed in relation to the comparative utilization of the purine and pyrimidine nucleosides as precursors in the formation of nucleic acids.

P32 uptake in DNA nucleotides after partial hepatectomy and after unilateral nephrectomy

Deoxyribonucleic acid (DNA) synthesis as reflected in the specific activity of DNA nucleotides 12 hr after intraperitoneal injection of P32 has been compared after partial hepatectomy and after unilateral nephrectomy. Thirty-six hours after partial hepatectomy, a maximum uptake 11-fold greater than in controls was found. The maximum after unilateral nephrectomy occurred 48 hr after operation and was twofold greater than in controls. Subsequent to these maxima, P32 uptake declined after both operations to a minimum eight days postoperatively which was followed by a second rise on the 9th day. These data support the concept that similar basic mechanisms regulate growth and cell division after the two types of operation. In another experiment, P32 uptake in kidney DNA nucleotides showed no increase after partial hepatectomy; this lends weight to the hypothesis that the mitosis-stimulating substances which appear in the serum after partial hepatectomy and after unilateral nephrectomy are organ specific.