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Journal of Biomolecular Structure &... Apr 2009The molecular structure and deformability (with respect to average geometry) of methyl ethers of canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (mTMP),...
The molecular structure and deformability (with respect to average geometry) of methyl ethers of canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (mTMP), 2-deoxycytidine-5'-phosphate (mCMP), 2-deoxyadenosine-5'-phosphate (mAMP) and 2'-deoxyguanosine-5'-phosphate (mGMP) in different types of DNA have been calculated using B3LYP/cc-pvdz method. Comparison of energy at equilibrium conformations of nucleotides and conformations with torsion angles of backbone fixed to average values for different types of DNA reveals that incorporation of nucleotides to A-DNA macromolecules requires the minimum amount of deformation energy. Therefore, this type of DNA should be the least strained from viewpoint of intramolecular deformations of monomers. Modeling of environmental effects within the PCM approach reveals that the immersion of nucleotides in polar medium results in significant decrease of energy differences between anti conformers of all DNTs and syn conformers of mGMP. This also leads to reduction by almost a half nucleotides' deformation energy facilitating formation of DNA macromolecule. Change of DNTs conformation causes switch between different types of intramolecular H bonds. Every type of DNA possesses unique set of intramolecular hydrogen bonds in nucleotides.
Topics: Computer Simulation; Deoxyribonucleotides; Hydrogen Bonding; Molecular Structure; Nucleic Acid Conformation
PubMed: 19236114
DOI: 10.1080/07391102.2009.10507279 -
The Journal of Biological Chemistry Feb 1978The 29-residue ribonucleotide primer formed by primase at the origin of phage G4 DNA replication (Bouché, J.-P, Rowen, L., and Kornberg, A. (1978) J. Biol. Chem. 253,...
The 29-residue ribonucleotide primer formed by primase at the origin of phage G4 DNA replication (Bouché, J.-P, Rowen, L., and Kornberg, A. (1978) J. Biol. Chem. 253, 765-769) was shorter in the presence of deoxynucleoside triphosphates (dNTPs). At 50 micrometer dNTPs and 20 micrometer rNTPs, RNA trancripts no longer than 6 residues were synthesized and these were still effective in priming replication by the DNA polymerase III holoenzyme. Primer synthesis was initiated with ATP; adenosine 5'-O-(3-thiotriphosphate) (Appp(S)), adenosine 5'-tetraphosphate, adenylyl imidodiphosphate (App(NH)p), and ADP were able to substitute for ATP. dATP and GTP were ineffective in initiating replication. DNA replication was stimulated by GTP, suggesting that incorporation of this nucleotide into the second position of the primer trancript by primase produces a more efficient primer. Each of the dNTPs can be incorporated into a hybrid ribonucleotide-deoxyribonucleotide transcript, indicating that primase is able to add either a ribonucleotide or deoxyribonucleotide to the 3'-OH of either of ribo residue or a deoxy residue of the primer terminus. Incorporation of an individual dNTP was less efficient than that of the corresponding rNTP, and the presence of all four dNTPs profoundly depressed RNA synthesis by primase.
Topics: Adenosine Triphosphate; Coliphages; DNA Replication; Deoxyribonucleotides; Escherichia coli; RNA Nucleotidyltransferases; Ribonucleotides; Transcription, Genetic
PubMed: 340459
DOI: No ID Found -
Journal of Biomolecular Structure &... Feb 2004The molecular structure and relative stability of north and south conformers of 2'-deoxyribonucleotides containing pyrimidine nucleic acid bases ( 2'-deoxythymidilic...
The molecular structure and relative stability of north and south conformers of 2'-deoxyribonucleotides containing pyrimidine nucleic acid bases ( 2'-deoxythymidilic (pdT), 2'-deoxycytidilic (pdC) acids and their mono- and dianions) have been obtained and analyzed at the DFT/B3LYP level using the standard 6-31G(d) basis set. We have revealed that, when the nucleobase moiety is incorporated into the nucleotides, it maintains a nonplanar and nonrigid conformation due to out-of-plane deformation of the amino group and pyrimidine ring. It has been demonstrated that an increase of negative charge of the phosphate group results in increase of amino group pyramidalization, discrimination between conformers with syn and anti orientation of base with respect to sugar, strengthening of intramolecular C-H.O hydrogen bonds leading to deformation and fixation of geometry of nucleotides, and weakening of phosphodiester bond. These results allow to make suggestions about sources of twist and buckle deformations of base pairs, mechanisms of repaire of DNA via change of base orientation, and conditions for breakage of the P-O bonds during hydrolysis.
Topics: Anions; Deoxycytosine Nucleotides; Deoxyuracil Nucleotides; Hydrogen Bonding; Models, Molecular; Thymine Nucleotides
PubMed: 14692798
DOI: 10.1080/07391102.2004.10506947 -
Postepy Biochemii Jun 2019High replication fidelity, understood as the DNA polymerases’ ability to select nucleotides with both correct base and sugar, is of critical importance for maintaining... (Review)
Review
High replication fidelity, understood as the DNA polymerases’ ability to select nucleotides with both correct base and sugar, is of critical importance for maintaining the genetic stability. Due to the fact that the cellular levels of ribonucleotides are much higher than the concentrations of deoxyribonucleotides, replicative polymerases are able to incorporate ribonucleotides with up to 1000-fold higher frequency than mismatched deoxyribonucleotides. The ability to discriminate against ribonucleotides by the DNA polymerases relies on the steric gate residue in the enzyme’s catalytic centre. Despite the fact that ribonucleotides are the most abundantly inserted incorrect nucleotides in DNA, they are not observed in properly functioning cells. The major pathway responsible for the recognition and removal of ribonucleotides from DNA is called Ribonucleotide Excision Repair. The impairment of ribonucleotide removal pathways can cause increased mutation rate, replication stress, DNA breakage, problems with transcription, chromatin structure maintenance, genetic disorders and cell death. In spite of that, ribonucleotide incorporation into DNA may have some positive biological impact, stimulating mismatch repair and non-homologous end joining.
Topics: DNA; DNA Repair; DNA Replication; DNA-Directed DNA Polymerase; Deoxyribonucleotides; Genomic Instability; Ribonucleotides
PubMed: 31642653
DOI: 10.18388/pb.2019_247 -
Current Biology : CB Apr 2019The egg contains maternal RNAs and proteins, which have instrumental functions in patterning and morphogenesis. Besides these, the egg also contains metabolites, whose...
The egg contains maternal RNAs and proteins, which have instrumental functions in patterning and morphogenesis. Besides these, the egg also contains metabolites, whose developmental functions have been little investigated. For example, the rapid increase of DNA content during the fast embryonic cell cycles poses high demands on the supply of deoxyribonucleotides (dNTPs), which may be synthesized in the embryo or maternally provided [1, 2]. Here, we analyze the role of dNTP in early Drosophila embryos. We found that dNTP levels initially decreased about 2-fold before reaching stable levels at the transition from syncytial to cellular blastoderm. Employing a mutant of the metabolic enzyme serine hydroxymethyl transferase (SHMT), which is impaired in the embryonic synthesis of deoxythymidine triphosphate (dTTP), we found that the maternal supply of dTTP was specifically depleted by interphase 13. SHMT mutants showed persistent S phase, replication stress, and a checkpoint-dependent cell-cycle arrest in NC13, depending on the loss of dTTP. The cell-cycle arrest in SHMT mutants was suppressed by reduced zygotic transcription. Consistent with the requirement of dTTP for cell-cycle progression, increased dNTP levels accelerated the cell cycle in embryos lacking zygotic transcription. We propose a model that both a limiting dNTP supply and interference of zygotic transcription with DNA replication [3] elicit DNA replication stress and checkpoint activation. Our study reveals a specific mechanism of how dNTP metabolites contribute to the embryonic cell-cycle control.
Topics: Animals; Cell Cycle Checkpoints; Deoxyribonucleotides; Drosophila; Embryo, Nonmammalian
PubMed: 30880011
DOI: 10.1016/j.cub.2019.02.021 -
Journal of the American Chemical Society Jul 2019Previously, we reported the creation of a semi-synthetic organism (SSO) that stores and retrieves increased information by virtue of stably maintaining an unnatural base...
Previously, we reported the creation of a semi-synthetic organism (SSO) that stores and retrieves increased information by virtue of stably maintaining an unnatural base pair (UBP) in its DNA, transcribing the corresponding unnatural nucleotides into the codons and anticodons of mRNAs and tRNAs, and then using them to produce proteins containing noncanonical amino acids (ncAAs). Here we report a systematic extension of the effort to optimize the SSO by exploring a variety of deoxy- and ribonucleotide analogues. Importantly, this includes the first in vivo structure-activity relationship (SAR) analysis of unnatural ribonucleoside triphosphates. Similarities and differences between how DNA and RNA polymerases recognize the unnatural nucleotides were observed, and remarkably, we found that a wide variety of unnatural ribonucleotides can be efficiently transcribed into RNA and then productively and selectively paired at the ribosome to mediate the synthesis of proteins with ncAAs. The results extend previous studies, demonstrating that nucleotides bearing no significant structural or functional homology to the natural nucleotides can be efficiently and selectively paired during replication, to include each step of the entire process of information storage and retrieval. From a practical perspective, the results identify the most optimal UBP for replication and transcription, as well as the most optimal unnatural ribonucleoside triphosphates for transcription and translation. The optimized SSO is now, for the first time, able to efficiently produce proteins containing multiple, proximal ncAAs.
Topics: Base Pairing; Deoxyribonucleotides; Genetic Code; Nucleotides; Protein Biosynthesis; Synthetic Biology; Transcription, Genetic
PubMed: 31241334
DOI: 10.1021/jacs.9b02075 -
Scientific Reports Jun 2021Deoxyribonucleotide biosynthesis from ribonucleotides supports the growth of active cancer cells by producing building blocks for DNA. Although ribonucleotide reductase...
Deoxyribonucleotide biosynthesis from ribonucleotides supports the growth of active cancer cells by producing building blocks for DNA. Although ribonucleotide reductase (RNR) is known to catalyze the rate-limiting step of de novo deoxyribonucleotide triphosphate (dNTP) synthesis, the biological function of the RNR large subunit (RRM1) in small-cell lung carcinoma (SCLC) remains unclear. In this study, we established siRNA-transfected SCLC cell lines to investigate the anticancer effect of silencing RRM1 gene expression. We found that RRM1 is required for the full growth of SCLC cells both in vitro and in vivo. In particular, the deletion of RRM1 induced a DNA damage response in SCLC cells and decreased the number of cells with S phase cell cycle arrest. We also elucidated the overall changes in the metabolic profile of SCLC cells caused by RRM1 deletion. Together, our findings reveal a relationship between the deoxyribonucleotide biosynthesis axis and key metabolic changes in SCLC, which may indicate a possible link between tumor growth and the regulation of deoxyribonucleotide metabolism in SCLC.
Topics: Animals; Cell Line, Tumor; Cell Proliferation; DNA Damage; Deoxyribonucleotides; Female; Humans; Lung Neoplasms; Mice; Mice, Nude; Neoplasm Proteins; Ribonucleoside Diphosphate Reductase; Small Cell Lung Carcinoma
PubMed: 34188151
DOI: 10.1038/s41598-021-92948-9 -
Acta Biochimica Polonica 1996The results obtained in our laboratory on investigating of substrate properties of a large number of compounds towards different DNA polymerases have been summarized. On... (Review)
Review
The results obtained in our laboratory on investigating of substrate properties of a large number of compounds towards different DNA polymerases have been summarized. On the basis of systematic analysis a directed synthesis of nucleotides with antiviral properties was performed.
Topics: Antiviral Agents; DNA-Directed DNA Polymerase; Deoxyribonucleotides; Drug Design; HIV; Humans; Nucleic Acid Synthesis Inhibitors; Retroviridae; Reverse Transcriptase Inhibitors; Simplexvirus; Virus Replication
PubMed: 8790718
DOI: No ID Found -
Biochimica Et Biophysica Acta Oct 1973
Topics: Chemical Phenomena; Chemistry; Chromatography, DEAE-Cellulose; Chromatography, Ion Exchange; Chromatography, Paper; Deoxyribonucleotides; Methods; Oligonucleotides; Phosphorus Radioisotopes; Pressure
PubMed: 4762420
DOI: 10.1016/0005-2787(73)90288-8 -
Trends in Biochemical Sciences Oct 1995In addition to its induction by DNA damage, p53 is induced by drugs that starve cells for DNA and RNA precursors, or by inhibitors of DNA or RNA polymerase. In normal... (Review)
Review
In addition to its induction by DNA damage, p53 is induced by drugs that starve cells for DNA and RNA precursors, or by inhibitors of DNA or RNA polymerase. In normal cells, the induction of p53 by dNTP starvation serves a protective role, mediating rapid, reversible cell-cycle arrest without DNA damage. In most cell lines, this first line of defense is missing, so that starvation for dNTPs causes DNA to break, thus increasing the probability of genomic instability, chromosome deletions and gene amplification. The mechanism of how p53 is induced remains unclear.
Topics: Animals; Cell Cycle; DNA; DNA Damage; Deoxyribonucleotides; Gene Amplification; Gene Expression Regulation; Genes, p53; Humans; Models, Genetic; RNA
PubMed: 8533158
DOI: 10.1016/s0968-0004(00)89094-5