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Proceedings of the National Academy of... Feb 1977DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments...
DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments then identify the positions of that base. We describe reactions that cleave DNA preferentially at guanines, at adenines, at cytosines and thymines equally, and at cytosines alone. When the products of these four reactions are resolved by size, by electrophoresis on a polyacrylamide gel, the DNA sequence can be read from the pattern of radioactive bands. The technique will permit sequencing of at least 100 bases from the point of labeling.
Topics: Adenine; Base Sequence; Biochemical Phenomena; Biochemistry; Cytosine; DNA; DNA Restriction Enzymes; Guanine; Hydrazines; Methods; Nucleic Acid Hybridization; Thymine
PubMed: 265521
DOI: 10.1073/pnas.74.2.560 -
Proceedings of the National Academy of... Feb 2021In this study, absorption, fluorescence, synchronous fluorescence, and Raman spectra of nonirradiated and ultraviolet (UV)-irradiated thymine solutions were recorded in...
In this study, absorption, fluorescence, synchronous fluorescence, and Raman spectra of nonirradiated and ultraviolet (UV)-irradiated thymine solutions were recorded in order to detect thymine dimer formation. The thymine dimer formation, as a function of irradiation dose, was determined by Raman spectroscopy. In addition, the formation of a mutagenic (6-4) photoproduct was identified by its synchronous fluorescence spectrum. Our spectroscopic data suggest that the rate of conversion of thymine to thymine dimer decreases after 20 min of UV irradiation, owing to the formation of an equilibrium between the thymine dimers and monomers. However, the formation of the (6-4) photoproduct continued to increase with UV irradiation. In addition, the Raman spectra of nonirradiated and irradiated calf thymus DNA were recorded, and the formation of thymine dimers was detected. The spectroscopic data presented make it possible to determine the mechanism of thymine dimer formation, which is known to be responsible for the inhibition of DNA replication that causes bacteria inactivation.
Topics: Animals; Cattle; DNA; DNA Damage; Pyrimidine Dimers; Spectrometry, Fluorescence; Spectrum Analysis, Raman; Thymine; Ultraviolet Rays
PubMed: 33526704
DOI: 10.1073/pnas.2025263118 -
Nucleic Acids Research Dec 1987Evidence is summarized showing that thymine methyls are as important in the recognition of specific sequences by proteins as are the more widely recognized hydrogen... (Review)
Review
Evidence is summarized showing that thymine methyls are as important in the recognition of specific sequences by proteins as are the more widely recognized hydrogen bonding sites of bases in the major groove (1). Strongest evidence has come from experiments using functional group mutagenesis (2) in which thymines in a specific recognition sequence (e.g., promoters, operators and restriction sites) are replaced by oligonucleotide synthesis with methyl-free uracil or cytosine and 5-methylcytosine. Such experiments have shown that thymine methyls can provide contact points via van der Waals interactions with amino acid side chains of specific DNA binding proteins. Actual contact between a thymine methyl and carbons of a glutamine side chain has been observed in a cocrystal of the phage 434 repressor and its operator by X-ray analysis. The issue of why thymine occurs in DNA is discussed in light of these findings.
Topics: Bacterial Proteins; Base Sequence; DNA (Cytosine-5-)-Methyltransferases; DNA, Bacterial; DNA-Binding Proteins; Methylation; Thymine
PubMed: 3320959
DOI: 10.1093/nar/15.23.9975 -
Photochemistry and Photobiology May 20225-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage.... (Review)
Review
5-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage. In DNA strands, the uracil radical generated from 5-halouracil causes DNA damage via a hydrogen-abstraction reaction. We analyzed the photoreaction of 5-halouracil in various DNA structures and revealed that the reaction is DNA structure-dependent. In this review, we summarize the results of the analysis of the reactivity of 5-halouracil in various DNA local structures. Among the 5-halouracil molecules, 5-bromouracil has been used as a probe in the analysis of photoinduced electron transfer through DNA. The analysis of groove-binder/DNA and protein/DNA complexes using a 5-bromouracil-based electron transfer system is also described.
Topics: Bromouracil; DNA; Thymine; Uracil
PubMed: 34543451
DOI: 10.1111/php.13521 -
Topics in Current Chemistry 2015Laboratory experiments have shown that the UV photo-irradiation of low-temperature ices of astrophysical interest leads to the formation of organic molecules, including... (Review)
Review
Laboratory experiments have shown that the UV photo-irradiation of low-temperature ices of astrophysical interest leads to the formation of organic molecules, including molecules important for biology such as amino acids, quinones, and amphiphiles. When pyrimidine is introduced into these ices, the products of irradiation include the nucleobases uracil, cytosine, and thymine, the informational sub-units of DNA and RNA, as well as some of their isomers. The formation of these compounds, which has been studied both experimentally and theoretically, requires a succession of additions of OH, NH₂, and CH₃groups to pyrimidine. Results show that H₂O ice plays key roles in the formation of the nucleobases, as an oxidant, as a matrix in which reactions can take place, and as a catalyst that assists proton abstraction from intermediate compounds. As H₂O is also the most abundant icy component in most cold astrophysical environments, it probably plays the same roles in space in the formation of biologically relevant compounds. Results also show that although the formation of uracil and cytosine from pyrimidine in ices is fairly straightforward, the formation of thymine is not. This is mostly due to the fact that methylation is a limiting step for its formation, particularly in H₂O-rich ices, where methylation must compete with oxidation. The relative inefficiency of the abiotic formation of thymine to that of uracil and cytosine, together with the fact that thymine has not been detected in meteorites, are not inconsistent with the RNA world hypothesis. Indeed, a lack of abiotically produced thymine delivered to the early Earth may have forced the choice for an RNA world, in which only uracil and cytosine are needed, but not thymine.
Topics: Absorption, Radiation; Cytosine; Extraterrestrial Environment; Ice; Models, Theoretical; Nucleic Acids; Photons; Photosynthesis; Prebiotics; Radiation, Ionizing; Thymine; Ultraviolet Rays; Uracil
PubMed: 24500331
DOI: 10.1007/128_2013_499 -
Molecules (Basel, Switzerland) Jun 2020A series of TMPK (TMPK) inhibitors based on a reported compound were synthesized and evaluated for their capacity to inhibit TMPK catalytic activity and the growth of...
A series of TMPK (TMPK) inhibitors based on a reported compound were synthesized and evaluated for their capacity to inhibit TMPK catalytic activity and the growth of a virulent strain (H37Rv). Modifications of the scaffold of failed to afford substantial improvements in TMPK inhibitory activity and antimycobacterial activity. Optimization of the substitution pattern of the D ring of resulted in compound with improved TMPK inhibitory potency (three-fold) and H37Rv growth inhibitory activity (two-fold). Moving the 3-chloro substituent of to the -position afforded isomer , which, despite a 10-fold increase in IC-value, displayed promising whole cell activity (minimum inhibitory concentration (MIC) = 12.5 μM).
Topics: Antitubercular Agents; Bacterial Proteins; Enzyme Inhibitors; Humans; Models, Molecular; Molecular Structure; Mycobacterium tuberculosis; Nucleoside-Phosphate Kinase; Structure-Activity Relationship; Thymine
PubMed: 32560578
DOI: 10.3390/molecules25122805 -
Scientific Reports Jul 2022Understanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and...
Understanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and clinical efforts are put into combining chemotherapy and immunotherapy to combat cancer. Single-cell RNA sequencing (scRNA-seq) has proved to be a powerful technique with a broad range of applications, studies evaluating drug effects in co-cultures of tumor and immune cells are however scarce. We treated a co-culture comprised of human colorectal cancer (CRC) cells and peripheral blood mononuclear cells (PBMCs) with the nucleoside analogue trifluridine (FTD) and used scRNA-seq to analyze posttreatment gene expression profiles in thousands of individual cancer and immune cells concurrently. ScRNA-seq recapitulated major mechanisms of action previously described for FTD and provided new insight into possible treatment-induced effects on T-cell mediated antitumor responses.
Topics: Colorectal Neoplasms; Frontotemporal Dementia; Humans; Leukocytes, Mononuclear; Pyrrolidines; Single-Cell Analysis; Thymine; Trifluridine
PubMed: 35831404
DOI: 10.1038/s41598-022-16077-7 -
The Biochemical Journal May 2021G:T mismatches, the major mispairs generated during DNA metabolism, are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (MBD4)...
G:T mismatches, the major mispairs generated during DNA metabolism, are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). Mismatch-specific DNA glycosylases must discriminate the mismatches against million-fold excess correct base pairs. MBD4 efficiently removes thymine opposite guanine but not opposite adenine. Previous studies have revealed that the substrate thymine is flipped out and enters the catalytic site of the enzyme, while the estranged guanine is stabilized by Arg468 of MBD4. To gain further insights into the mismatch discrimination mechanism of MBD4, we assessed the glycosylase activity of MBD4 toward various base pairs. In addition, we determined a crystal structure of MBD4 bound to T:O6-methylguanine-containing DNA, which suggests the O6 and N2 of purine and the O4 of pyrimidine are required to be a substrate for MBD4. To understand the role of the Arg468 finger in catalysis, we evaluated the glycosylase activity of MBD4 mutants, which revealed the guanidinium moiety of Arg468 may play an important role in catalysis. D560N/R468K MBD4 bound to T:G mismatched DNA shows that the side chain amine moiety of the Lys stabilizes the flipped-out thymine by a water-mediated phosphate pinching, while the backbone carbonyl oxygen of the Lys engages in hydrogen bonds with N2 of the estranged guanine. Comparison of various DNA glycosylase structures implies the guanidinium and amine moieties of Arg and Lys, respectively, may involve in discriminating between substrate mismatches and nonsubstrate base pairs.
Topics: Catalysis; Catalytic Domain; Endodeoxyribonucleases; Guanine; Humans; Protein Conformation; Substrate Specificity; Thymine
PubMed: 33960375
DOI: 10.1042/BCJ20210017 -
Daru : Journal of Faculty of Pharmacy,... Jun 2014Mercury poisoning cases have been reported in many parts of the world, resulting in many deaths every year. Mercury compounds are classified in different chemical types... (Review)
Review
Mercury poisoning cases have been reported in many parts of the world, resulting in many deaths every year. Mercury compounds are classified in different chemical types such as elemental, inorganic and organic forms. Long term exposure to mercury compounds from different sources e.g. water, food, soil and air lead to toxic effects on cardiovascular, pulmonary, urinary, gastrointestinal, neurological systems and skin. Mercury level can be measured in plasma, urine, feces and hair samples. Urinary concentration is a good indicator of poisoning of elemental and inorganic mercury, but organic mercury (e.g. methyl mercury) can be detected easily in feces. Gold nanoparticles (AuNPs) are a rapid, cheap and sensitive method for detection of thymine bound mercuric ions. Silver nanoparticles are used as a sensitive detector of low concentration Hg2+ ions in homogeneous aqueous solutions. Besides supportive therapy, British anti lewisite, dimercaprol (BAL), 2,3-dimercaptosuccinic acid (DMSA. succimer) and dimercaptopropanesulfoxid acid (DMPS) are currently used as chelating agents in mercury poisoning. Natural biologic scavengers such as algae, azolla and other aquatic plants possess the ability to uptake mercury traces from the environment.
Topics: Chelating Agents; Humans; Mercury; Mercury Poisoning; Metal Nanoparticles; Thymine
PubMed: 24888360
DOI: 10.1186/2008-2231-22-46 -
Journal of Bacteriology Mar 2006
Review
Topics: Bacteria; Bacterial Physiological Phenomena; Bacteriological Techniques; Cell Division; Chromosomes, Bacterial; DNA, Bacterial; Mutation; Thymine
PubMed: 16484178
DOI: 10.1128/JB.188.5.1667-1679.2006