Adenine Cytosine Research Articles

Tunneling Effect in Proton Transfer: Transfer Matrix Approach

The transfer matrix (TM) method was applied to calculate the transmission probability (TP) for proton transfer reactions. The tunneling factors in the reaction rate constants were also evaluated using the TPs. To test this method, TPs for the Eckart potentials modeled as a guanine-cytosine base pair were calculated by the TM method and compared to TPs by the analytical solution. As a result, the errors in the TPs by the TM method were quite small. The tunneling factors for the guanine-thymine (G-T) and adenine-cytosine (A-C) mispair reactions were then evaluated by the TM method. A shoulder appears on each potential for these reactions [Odai, K.; Umesaki,K. J. Phys. Chem. A. 2021, 125, 8196-8204]. As a result, the shoulder for the G-T mispair reaction contributes significantly to the tunneling, while the shoulder for the A-C mispair reaction contributes little to the tunneling. These results are difficult to obtain with methods such as Wigner's tunneling factor.

Dinucleotide (AC)n Repeat Polymorphism (rs36213840) in the Promoter Region of IL18R1 Gene and Genetic Susceptibility to Severe Malaria

Background: Cytokines are key regulator s of human immune response to malaria but polymorphisms within the regulatory or coding regions of their genes may lead to differences in expression levels which may consequently influence disease susceptibility. In this study, we characterized an adeninecytosine (AC)n dinucleotide repeat polymorphism (rs36213840) at the promoter region of the Interleukin 18 Receptor 1 (IL18R1) gene and investigated its association with severe malaria. Methods: We utilised the case-control study design to enrol a total of 207 children including 87 severe malaria cases and 120 asymptomatic controls. DNA was extracted from blood spot on filter paper using QIAamp® DNA Mini Kit (Qiagen, Hilden, Germany). Genotyping for dinucleotide repeat polymorphisms was done by PCR and capillary electrophoresis of sequenced products on ABI PRISM® 3100 DNA sequencer (PE Applied Biosystems). Results: The genotype frequencies of the dinucleotide repeats differed significantly between the two groups (χ2 = 8.69, P=0.026). We found a significantly higher frequency of the 14bp (AC)7 allele in severe malaria patients than in asymptomatic controls (odds ratio 1.945, 95% CI: 1.23 – 3.09, P = 0.005) while the frequency of the 16bp (AC)8 allele was significant higher in the asymptomatic controls than in severe cases (odds ratio 0.431, 95% CI: 0.244 – 0.761, P = 0.004). Conclusion: Results of this suggest that the 14bp (AC)7 dinucleotide repeats might be a genetic risk factor for susceptibility to severe malaria while the 16bp (AC)8 dinucleotide repeats might be a protective factor against severe malaria

DFT study of adenine–cytosine mismatch in quaternary systems involving DNA bases

In the present work, the adenine–cytosine mismatch is theoretically investigated in quaternary systems involving DNA bases. The calculations, in gas phase, are performed at M06-2X/6-311++G(d,p) level. The results indicate that the quaternary systems involving G–C base pair are more stable than those containing A–T. Moreover, in the presence of A–T or G–C base pairs, the absolute values of formation energy in quaternary systems involving imino tautomer of adenine (A*) are higher than those including imino form of cytosine (C*). A comparison between systems having A* indicates that the absolute value of formation energy in quaternary systems increases when A* stacks with pyrimidine bases (C or T). In the case of systems containing C*, this behavior is observed when C* stacks with purine bases (G or A). Similar to binary systems, the quaternary systems involving A*–C thermodynamically prefer to transform their geometries into systems containing A–C*. The base pairs are stabilized by hydrogen bonds. The strength of hydrogen bonds in binary and quaternary systems is also examined using atoms in molecules (AIM) and natural bond orbital (NBO) analyses.

Molecular survey of ITS1 spacer and Rickettsia infection in human flea, Pulex irritans.

The human flea is an important ectoparasite causing serious public health problems worldwide. Planning and monitoring the control programs against this vector require the knowledge of population structure and vector competence. This study was carried out to identify molecular structure of internal transcribed spacer 1 (ITS1) of ribosomal gene and its capability in the survey of Pulex irritans populations as well as to investigate Rickettsia infection in these populations. Flea samples were collected via human baits from animal farms in two districts of Zanjan Province, northwest of Iran. The ITS1 region and the partial Rickettsia gltA gene were amplified from the samples of human flea, and 30 amplicons were sequenced. The 1136 collected fleas consisted of 1079 (94.98%) P. irritans, 36 (3.17%) Ctenocephalides canis, and 21 (1.85%) Ctenocephalides felis. Molecular investigation of 182 human fleas detected the infection of Rickettsia sp. in 4.9%. The ITS1 region covered 957bp and contained three tandem units of 98-99bp, starting at positions 145, 245, and 331. Multiple alignments of ITS1 sequences showed single-nucleotide polymorphism at position 798, which caused the substitution of cytosine for adenine in the novel haplotype. High frequency of P. irritans and its Rickettsia infection requires the application of vector control measures, and full characterization of Rickettsia sp. and its potential to cause disease in humans. Regarding the consistency of ITS1 region and its ability to differentiate insect communities, further investigations are recommended to identify the role of selective factors in maintenance of this spacer.

The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine–cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.

CD4(+) T Cells Modified by the Endoribonuclease MazF Are Safe and Can Persist in SHIV-infected Rhesus Macaques.

MazF, an endoribonuclease encoded by Escherichia coli, specifically cleaves the ACA (adenine–cytosine–adenine) sequence of single-stranded RNAs. Conditional expression of MazF under the control of the HIV-1 LTR promoter rendered CD4+ T cells resistant to HIV-1 replication without affecting cell growth. To investigate the safety, persistence and efficacy of MazF-modified CD4+ T cells in a nonhuman primate model in vivo, rhesus macaques were infected with a pathogenic simian/human immunodeficiency virus (SHIV) and transplanted with autologous MazF-modified CD4+ T cells. MazF-modified CD4+ T cells were clearly detected throughout the experimental period of more than 6 months. The CD4+ T cell count values increased in all four rhesus macaques. Moreover, the transplantation of the MazF-modified CD4+ T cells was not immunogenic, and did not elicit cellular or humoral immune responses. These data suggest that the autologous transplantation of MazF-modified CD4+ T cells in the presence of SHIV is effective, safe and not immunogenic, indicating that this is an attractive strategy for HIV-1 gene therapy.

The Effect of Interfacial Design on the Electrochemical Detection of DNA and MicroRNA Using Methylene Blue at Low‐Density DNA Films

AbstractHerein, we study the effect of interfacial design, specifically the orientation of a DNA probe strand, the length of the diluent and the type of target (DNA vs. microRNA), on the electrochemical response from methylene blue (MB) at low‐density DNA films. The probe DNA interfaces are formed from mixed self‐assembled monolayers of single‐stranded DNA (ss‐DNA) and a hydroxyl terminated alkanethiol diluents on gold surfaces. Variation in the current from the DNA–MB complex after hybridization with complementary and single adenine–cytosine mismatch DNA target is shown to depend on whether the 3′ or 5′ end is tethered to the electrode and the length of the diluent (6‐mercapto‐1‐hexanol vs. 9‐mercapto‐1‐nonanol). The sensors show better mismatch discrimination of single base pairs when both the duplexes are tethered from the 5′ end to the electrode and with a longer‐chain (9‐mercapto‐1‐nonanol) diluent. Of particular note is our demonstration that the DNA/microRNA duplex exhibits greater single adenine–cytosine mismatch discrimination when compared to the corresponding DNA/DNA duplex. This study contributes to the development of selective DNA and microRNA biosensors.

Modeling hole transfer in DNA: Low-lying excited states of oxidized cytosine homodimer and cytosine–adenine heterodimer

Charge transport in DNA strands has been studied by characterizing on theoretical grounds the lowest doublet states of the oxidized cytosine homodimer (CC +) and adenine–cytosine heterodimer (CA +) along the intermolecular separation of the monomers. The high-level quantum-chemical ab initio CASPT2 method and accurate one-electron basis sets have been employed. Both cationic species are found to be bound with comparable binding energies as those of neutral CC and reduced CC −. The results suggest that charge transport in DNA and the distinct photophysical attributes related to the polymer can be described within the framework of a unified theory. A cooperative micro-hopping mechanism involving consecutively two-by-two adjacent π-stacked nucleobases is proposed for hole transport along single strands of only dCMP or alternate dAMP and dCMP oligonucleotides. This model could be extrapolated to other combinations of deoxynucleotides and even to double stranded DNA and is expected to be similar for the transport of an excess electron. It is suggested that the efficiency of the process is controlled by the presence and relative location of conical intersections connecting the relevant hypersurfaces.

Pyrimidine transporters of trypanosomes – a class apart?

Pyrimidine transporters of trypanosomes – a class apart?

The role of Ag(I) ions in the electronic spectroscopy of adenine–cytosine mispairs: A MS-CASPT2 theoretical study

Adenine–cytosine (AC) mispairs have been theoretically studied with MS-CASPT2//CASSCF methods in the presence and absence of Ag ions. The electronically excited states of the most stable AC mispair in the reverse-Wobble (RW) conformation have been compared with those of different Ag(I)–AC complexes, including (i) metalated RW conformations, and (ii) the most stable structures in gas phase which contain the Ag ion bridging A and C. The spectra of these complexes are characterized by charge-transfer (CT) and strong locally excited (LE) states. The metal-to-metal, metal-to-ligand, and Rydberg transitions are very weak in comparison to the nucleobase transitions. Attending to the LE and CT states, and except for the shifts induced by the presence of the Ag, the electronic spectrum of metalated AC mispairs resembles the one of the RW, showing two intense LE bands around 4.5 and 5.5 eV, corresponding to transitions within the adenine and cytosine π-system, respectively. Additionally TD-DFT results obtained with the B3LYP functional are compared with MS-CASPT2//CASSCF calculations. The results clearly evidence the weakness of TD-DFT to describe long range exchange interactions leading to strongly underestimated CT states.

A1166C polymorphism of the angiotensin II type 1 receptor gene and essential hypertension in Han, Tibetan and Yi populations.

Our aim was to clarify whether substitution of cytosine for adenine at position 1166 (A1166C) polymorphism of the angiotensin II type 1 receptor (AT1R) gene is associated with susceptibility to essential hypertension in Han, Tibetan and Yi populations in China. This study involved 302 normotensive and 446 hypertensive subjects. The polymorphism was detected by polymelase chain reaction of genomic DNA and restriction fragment length polymorphism (PCR-RFLP) in genomic DNA. The data were analyzed by analysis of covariance (ANCOVA), X2 test, and multiple logistic regression. In normotensive controls, the A1166 allele frequencies were 0.979, 0.939 and 0.965 in Han, Tibetan and Yi participants, respectively. There was no significant intergroup variation in frequency of the allele in normotensives (X2=4.166, p=0.125). The frequency of the A1166 allele was significantly higher in Tibetan male hypertensives than that in normotensives (X2=11.46, p=0.001). There was no significant difference in A1166C genotype distribution and allele frequency between normotensives and hypertensives either in the Han (p=0.465) or Yi (p=0.357) populations. Body mass index in the Han and Yi populations (p=0.0001), age in the Tibetan and Yi populations (p=0.0001), and AA genotype in the Tibetan male population (p=0.0034) all were independent risk factors for hypertension. Diastolic blood pressure levels were significantly higher in Tibetan male subjects with the AA genotype than in those with the AC+CC genotype (p=0.0040). We concluded that the A1166 allele is very common in Han, Tibetan and Yi populations, approximately 1.35-fold more common than in Caucasians. The A1166 allele of the AT1R gene may be a predisposing factor for essential hypertension in Tibetan males. A1166C polymorphism of the AT1R gene is probably not involved in the pathogenesis of essential hypertension in Han or Yi populations.

A Novel Nonsense Mutation of the Sedlin Gene in a Family with Spondyloepiphyseal Dysplasia Tarda

We report a new nonsense mutation in the human sedlin (SEDL) gene in a family with X-linked spondyloepiphyseal dysplasia tarda. A substitution of cytosine for adenine at nucleotide position 329 causing a nonsense mutation (S110X) in exon 6 was identified in the affected patient in the family.

Strand displacement recognition of mixed adenine–cytosine sequences in double stranded DNA by thymine–Guanine PNA (Peptide nucleic acid)

Mixed pyrimidine–purine peptide nucleic acids (PNAs) composed of thymines and guanines are shown to form a PNA 2–DNA triplex with Watson–Crick complementary adenine–cytosine oligonucleotides and to bind complementary adenine–cytosine targets in double stranded DNA by helix invasion. These results for the first time demonstrate binding of an unmodified PNA oligomer to a mixed pyrimidine–purine target in double stranded DNA and illustrate a novel binding mode of PNA.

Molecular genetic heterogeneity of myophosphorylase deficiency (McArdle's disease).

Myophosphorylase deficiency (McArdle's disease) is one of the most common causes of exercise intolerance, muscle cramps, and recurrent myoglobinuria. The myophosphorylase gene has been sequenced and assigned to chromosome 11, but the molecular basis of McArdle's disease is not known. We sequenced complementary DNA in 4 patients and studied genomic DNA by restriction-endonuclease analysis in 40 patients with McArdle's disease. Sequence analysis revealed three distinct point mutations: the substitution of thymine for cytosine at codon 49 in exon 1, changing an encoded arginine to a stop codon; the substitution of adenine for guanine at codon 204 in exon 5, changing glycine to serine; and the substitution of cytosine for adenine at codon 542 in exon 14, changing lysine to threonine. Analysis of restriction-fragment-length polymorphisms of appropriate fragments of genomic DNA after amplification with the polymerase chain reaction showed that 18 patients were homozygous for the stop-codon mutation, 6 had different mutations in the two alleles (compound heterozygotes), and 11 were presumed to be compound heterozygotes for a known mutation and an unknown one; only 5 patients had none of the three mutations. All three mutations were present in various combinations in five members of a family in which transmission appeared to be autosomal dominant. McArdle's disease is genetically heterogeneous, but the most common mutation is the substitution of thymine for cytosine at codon 49. These results suggest that in about 90 percent of patients the diagnosis of McArdle's disease can be made from a patient's leukocytes, thus avoiding the need for muscle biopsy.

Assessment of DNA fingerprinting for studies of small-mammal populations

We examined the use of DNA fingerprinting for determining degree of genetic relatedness and kin relationships of small mammals. We examined the utility of three DNA probes: a "mouse" probe, a repeat sequence from a Mus musculus genomic library; (CAC)5, a synthesized probe consisting of cytosine–adenine–cytosine repeated five times; and the SNAP probe, a synthesized probe containing a 22 base pair sequence. All three probes provided DNA fingerprints for montane voles (Microtus montanus), although the number of bands per individual varied among probes. We could obtain bands only with the snap probe for deer mice (Peromyscus maniculatus) and pocket mice (Perognathus parvus). Successful modifications of protocols for DNA extraction from small blood samples and for nonradioactive detection of bands suggest that DNA fingerprinting should be useful for in situ studies of natural populations by many research laboratories. To determine genetic similarity we calculated the probability of band sharing between individuals. The average probability varied among probes for the same unrelated M. montanus individuals and among species for the snap probe. For all probes the average probability of band sharing was significantly greater for related than for unrelated individuals of M. montanus. Unrelated individuals usually share an unpredictable number of bands, and the probability of band sharing may reach that of related individuals. Average band sharing for related M. montanus individuals was greater than the expected 0.5 only for (CAC)5. Average probability of band sharing between unrelated and related individuals and the variance of this value must be known before an attempt is made to determine general relationships in field populations. When maternity was known, paternity could be determined with a low probability of misassignment by identifying obligate paternal bands.

Changes of RNA base composition in nerve cells of monkeys subjected to visual discrimination and delayed alternation performance

Rhesus monkeys were subjected to visual discrimination and delayed alternation training. Controls were exposed to the same experimental conditions and training procedures, but with rewards given at random. The results of these active controls were compared with those of the learning animals. The amount of RNA per nerve cell and RNA base composition were determined in pyramidal nerve cells in the CA3 region of the hippocampus and in pyramidal nerve cells from the fifth layers of the inferior temporal gyrus and the gyrus principalis. With visual discrimination learning, significant RNA base ration changes occurred in the nerve cells of the inferior temporal gyrus, the integrity of which is a prerequisite for the monkey to resolve the task by a correct behavior. No changes were observed in the gyrus principalis. A different type of RNA base composition change occured on delayed alternation learning in the gyrus principalis which is known to be specifically involved in that type of behavior. During both these kinds of training the RNA of the hippocampal nerve cells responded with the same type of changes involving adenine cytosine, indicating a biochemical and functional response of the CA3 neurons whenever a new behavior is acquired. Thus, with the acquisition of different behavioral patterns, specific brain regions respond with different RNA changes induced by so far unknown mechanisms.

Study of the hydrogen bonding in the adenine-thymine, adenine-cytosine, and guanine-thymine base pairs.

The motion of the protons in the hydrogen bonds of the guanine—cytosine base pair has recently been studied by Rein and Harris, using a semiempirical LCAO MO SCF method. These investigations are extended to the adenine—thymine base pair and the ``rare'' base pairs adenine—cytosine and guanine—thymine. The total electronic energy of the ground states of the neutral base pairs and their positive and negative ions has been calculated for about 100 different configurations of the protons in the hydrogen bonds. The potential-energy surfaces obtained are reported together with the equilibrium distributions between different tautomeric forms of the base pairs.