Relevant bibliographies by topics / Nucleotide modification

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters

Academic literature on the topic 'Nucleotide modification'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Nucleotide modification"

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Ding, Hongxu, Andrew D. Bailey, Miten Jain, Hugh Olsen, and Benedict Paten. "Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts." Bioinformatics 36, no. 19 (2020): 4928–34. http://dx.doi.org/10.1093/bioinformatics/btaa601.

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Abstract Motivation Nucleotide modification status can be decoded from the Oxford Nanopore Technologies nanopore-sequencing ionic current signals. Although various algorithms have been developed for nanopore-sequencing-based modification analysis, more detailed characterizations, such as modification numbers, corresponding signal levels and proportions are still lacking. Results We present a framework for the unsupervised determination of the number of nucleotide modifications from nanopore-sequencing readouts. We demonstrate the approach can effectively recapitulate the number of modifications, the corresponding ionic current signal levels, as well as mixing proportions under both DNA and RNA contexts. We further show, by integrating information from multiple detected modification regions, that the modification status of DNA and RNA molecules can be inferred. This method forms a key step of de novo characterization of nucleotide modifications, shedding light on the interpretation of various biological questions. Availability and implementation Modified nanopolish: https://github.com/adbailey4/nanopolish/tree/cigar_output. All other codes used to reproduce the results: https://github.com/hd2326/ModificationNumber. Supplementary information Supplementary data are available at Bioinformatics online.
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Hoffmann, Anne, Lieselotte Erber, Heike Betat, Peter F. Stadler, Mario Mörl, and Jörg Fallmann. "Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum." Non-Coding RNA 7, no. 2 (2021): 32. http://dx.doi.org/10.3390/ncrna7020032.

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Dictyostelium discoideum is a social amoeba, which on starvation develops from a single-cell state to a multicellular fruiting body. This developmental process is accompanied by massive changes in gene expression, which also affect non-coding RNAs. Here, we investigate how tRNAs as key regulators of the translation process are affected by this transition. To this end, we used LOTTE-seq to sequence the tRNA pool of D. discoideum at different developmental time points and analyzed both tRNA composition and tRNA modification patterns. We developed a workflow for the specific detection of modifications from reverse transcriptase signatures in chemically untreated RNA-seq data at single-nucleotide resolution. It avoids the comparison of treated and untreated RNA-seq data using reverse transcription arrest patterns at nucleotides in the neighborhood of a putative modification site as internal control. We find that nucleotide modification sites in D. discoideum tRNAs largely conform to the modification patterns observed throughout the eukaroytes. However, there are also previously undescribed modification sites. We observe substantial dynamic changes of both expression levels and modification patterns of certain tRNA types during fruiting body development. Beyond the specific application to D. discoideum our results demonstrate that the developmental variability of tRNA expression and modification can be traced efficiently with LOTTE-seq.
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Jang, Eui Kyoung, Ryeo Gang Son, and Seung Pil Pack. "Novel enzymatic single-nucleotide modification of DNA oligomer: prevention of incessant incorporation of nucleotidyl transferase by ribonucleotide-borate complex." Nucleic Acids Research 47, no. 17 (2019): e102-e102. http://dx.doi.org/10.1093/nar/gkz612.

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Abstract Terminal deoxynucleotidyl transferase (TdT), which mediates template-independent polymerization with low specificity for nucleotides, has been used for nucleotide extension of DNA oligomers. One concern is that it is difficult to control the number of incorporated nucleotides, which is a limitation on the use of TdT for single-nucleotide incorporation of DNA oligomers. Herein, we uncovered an interesting inhibitory effect on TdT when ribonucleotide substrates (rNTPs) were employed in a borate buffer. On the basis of unique inhibitory effects of the ribonucleotide–borate complex, we developed a novel enzymatic method for single-nucleotide incorporation of a DNA oligomer with a modified rNTP by TdT. Single-nucleotide incorporation of a DNA oligomer with various modified rNTPs containing an oxanine, biotin, aminoallyl or N6-propargyl group was achieved with a high yield. The ‘TdT in rNTP-borate’ method is quite simple and efficient for preparing a single-nucleotide modified DNA oligomer, which is useful for the design of functional DNA-based systems.
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Price, Neil P. J., Michael A. Jackson, Karl E. Vermillion, Judith A. Blackburn, and Trina M. Hartman. "Rhodium-catalyzed reductive modification of pyrimidine nucleosides, nucleotide phosphates, and sugar nucleotides." Carbohydrate Research 488 (February 2020): 107893. http://dx.doi.org/10.1016/j.carres.2019.107893.

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Behm-Ansmant, Isabelle, Mark Helm, and Yuri Motorin. "Use of Specific Chemical Reagents for Detection of Modified Nucleotides in RNA." Journal of Nucleic Acids 2011 (2011): 1–17. http://dx.doi.org/10.4061/2011/408053.

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Naturally occurring cellular RNAs contain an impressive number of chemically distinct modified residues which appear posttranscriptionally, as a result of specific action of the corresponding RNA modification enzymes. Over 100 different chemical modifications have been identified and characterized up to now. Identification of the chemical nature and exact position of these modifications is typically based on 2D-TLC analysis of nucleotide digests, on HPLC coupled with mass spectrometry, or on the use of primer extension by reverse transcriptase. However, many modified nucleotides are silent in reverse transcription, since the presence of additional chemical groups frequently does not change base-pairing properties. In this paper, we give a summary of various chemical approaches exploiting the specific reactivity of modified nucleotides in RNA for their detection.
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Mullally, Grace, Kara van Aelst, Mohsin M. Naqvi, et al. "5′ modifications to CRISPR–Cas9 gRNA can change the dynamics and size of R-loops and inhibit DNA cleavage." Nucleic Acids Research 48, no. 12 (2020): 6811–23. http://dx.doi.org/10.1093/nar/gkaa477.

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Abstract A key aim in exploiting CRISPR–Cas is gRNA engineering to introduce additional functionalities, ranging from individual nucleotide changes that increase efficiency of on-target binding to the inclusion of larger functional RNA aptamers or ribonucleoproteins (RNPs). Cas9–gRNA interactions are crucial for complex assembly, but several distinct regions of the gRNA are amenable to modification. We used in vitro ensemble and single-molecule assays to assess the impact of gRNA structural alterations on RNP complex formation, R-loop dynamics, and endonuclease activity. Our results indicate that RNP formation was unaffected by any of our modifications. R-loop formation and DNA cleavage activity were also essentially unaffected by modification of the Upper Stem, first Hairpin and 3′ end. In contrast, we found that 5′ additions of only two or three nucleotides could reduce R-loop formation and cleavage activity of the RuvC domain relative to a single nucleotide addition. Such modifications are a common by-product of in vitro transcribed gRNA. We also observed that addition of a 20 nt RNA hairpin to the 5′ end of a gRNA still supported RNP formation but produced a stable ∼9 bp R-loop that could not activate DNA cleavage. Consideration of these observations will assist in successful gRNA design.
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Munoz-Tello, Paola, Lional Rajappa, Sandrine Coquille, and Stéphane Thore. "Polyuridylation in Eukaryotes: A 3′-End Modification Regulating RNA Life." BioMed Research International 2015 (2015): 1–12. http://dx.doi.org/10.1155/2015/968127.

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In eukaryotes, mRNA polyadenylation is a well-known modification that is essential for many aspects of the protein-coding RNAs life cycle. However, modification of the 3′ terminal nucleotide within various RNA molecules is a general and conserved process that broadly modulates RNA function in all kingdoms of life. Numerous types of modifications have been characterized, which are generally specific for a given type of RNA such as the CCA addition found in tRNAs. In recent years, the addition of nontemplated uridine nucleotides or uridylation has been shown to occur in various types of RNA molecules and in various cellular compartments with significantly different outcomes. Indeed, uridylation is able to alter RNA half-life both in positive and in negative ways, highlighting the importance of the enzymes in charge of performing this modification. The present review aims at summarizing the current knowledge on the various processes leading to RNA 3′-end uridylation and on their potential impacts in various diseases.
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Stepanov, Grigory, Evgenii Zhuravlev, Victoria Shender, et al. "Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs." Genes 9, no. 11 (2018): 531. http://dx.doi.org/10.3390/genes9110531.

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Short nuclear regulatory RNAs play a key role in the main stages of maturation of the precursors of the major RNA species. Small nuclear RNAs (snRNAs) form the core of the spliceosome and are responsible for the splicing of pre-mRNA molecules. Small nucleolar RNAs (snoRNAs) direct post-transcriptional modification of pre-rRNAs. A promising strategy for the development of non-coding RNA (ncRNAs) mimicking molecules is the introduction of modified nucleotides, which are normally present in natural ncRNAs, into the structure of synthetic RNAs. We have created a set of snoRNAs and snRNA analogs and studied the effect of base modifications, specifically, pseudouridine (Ψ) and 5-methylcytidine (m5C), on the immune-stimulating and cytotoxic properties of these RNAs. Here, we performed a whole-transcriptome study of the influence of synthetic snoRNA analogs with various modifications on gene expression in human cells. Moreover, we confirmed the role of PKR in the recognition of snoRNA and snRNA analogs using the short hairpin RNA (shRNA) technique. We believe that the data obtained will contribute to the understanding of the role of nucleotide modification in ncRNA functions, and can be useful for creating the agents for gene regulation based on the structure of natural snoRNAs and snRNAs.
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Yip, W. S. Vincent, Nicholas G. Vincent, and Susan J. Baserga. "Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification." Archaea 2013 (2013): 1–14. http://dx.doi.org/10.1155/2013/614735.

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Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.
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MILLER, Richard W., Robert R. EADY, Carol GORMAL, Shirley A. FAIRHURST, and Barry E. SMITH. "Covalent modification of nitrogenase MoFe protein by ADP." Biochemical Journal 322, no. 3 (1997): 737–44. http://dx.doi.org/10.1042/bj3220737.

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MgADP- reacted with the nitrogenase molybdenum–iron (MoFe) protein of Klebsiella pneumoniae (Kp1) over a period of 2 h to yield a stable, catalytically active conjugate. The isolated protein exhibited a new, broad 31P NMR resonance at -1 p.p.m. lacking phosphorus J coupling. The adenine ring of [8-14C]ADP remained associated with the conjugate. A covalently bound nucleotide was identified as AMP by NMR and TLC. Extended dialysis of Kp1 against MgADP- resulted in further AMP binding at the protein surface. ADP was initially bound tightly to Kp1 at a site distinct from the AMP sites. ATP did not replace ADP. The time course of the formation of the Kp1-AMP was altered by the nitrogenase iron protein (Kp2) and was dependent on redox potential. Kp1-AMP was stable to concentration and oxidation with ferricyanide ion at -350 mV. Slow hydrolysis of Kp1-AMP over a period of 6 h yielded AMP and unaltered Kp1. The adenine ring of ADP exchanged with adenine of MgATP2- during reductant-limited turnover of nitrogenase under N2, indicating reversibility of ATP hydrolysis at 15 °C. [32P]Pi exchanged with the terminal phosphate group of both ADP and ATP on incubation with Kp1. 32P exchange and the catalytic activity of Kp1 were inhibited by a 20-fold molar excess of the lysine-modifying reagent, o-phthalaldehyde (OPT). Preincubation with MgADP- protected against OPT inactivation. Two potentially reactive lysine residues on the α chain of the MoFe protein near a putative hydrophobic docking site for the nitrogenase Fe protein are proposed as sites of OPT and nucleotide binding. Azotobacter vinelandiiMoFe protein (Av1) also formed an AMP adduct but Kp2 did not. Catalase did not interact with ADP. The reactions of the nitrogenase MoFe protein with adenine nucleotides have no counterpart in known protein–nucleotide interactions.
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Dissertations / Theses on the topic "Nucleotide modification"

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Gao, Enoch N. (Enoch Nuo). "Post-translational lipid modification and nucleotide binding of Myelin 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase (CNP)." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=23889.

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The myelin protein CNP $(2 sp prime,3 sp prime$-Cyclic Nucleotide 3$ sp prime$-Phosphodiesterase) is thio-palmitoylated. Since acylation plays an important role in the protein-membrane interaction, CNP palmitoylation was further investigated. Seven cysteine residues in CNP were individually converted into serines and the palmitoylation was analyzed in either COS-7 cells or an in vitro acylation reaction. No single Cys to Ser mutation could reduce substantially the level of palmitoylation, which may indicate that the turnover of palmitate on CNP is high and that there are multiple palmitoylation sites. Immunostaining and subcellular fractionation showed that isoprenylation is the major factor to control the membrane association of CNP while palmitoylation may serve as a fine tuning mechanism. A double mutation of Cys 231 to Ser and Thr 374 to Pro greatly reduced CNPase activity and the level of palmitoylation. CNP was expressed in Sf9 cells and the mutant C397S was purified to near homogeneity. Since CNP contains several ATPase consensus motifs, we investigated in a preliminary way its ATPase/ATP-binding properties. CNP was affinity-photolabeled by $ lbrack alpha- sp{32}$P) 8-azido ATP in a specific and saturable way, although no apparent ATPase activity was detected. The binding of 8N3 ATP could be competed by ATP, GTP and CTP at different concentrations.
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Elmore, Calvin Lee. "MODIFICATION OF THE NUCLEOTIDE COFACTOR-BINDING SITE OF CYTOCHROME P450 REDUCTASE TO ENHANCE TURNOVER WITH NADH IN VIVO." UKnowledge, 2003. http://uknowledge.uky.edu/gradschool_diss/467.

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NADPH-cytochrome P450 reductase is the electron transfer partner for the cytochromes P450, heme oxygenase, and squalene monooxygenase, and is a component of the nitric oxide synthases and methionine synthase reductase. P450 reductase shows very high selectivity for NADPH and uses NADH only poorly. Substitution of tryptophan 677 with alanine (W677A) has been shown by others to yield a 3-fold increase in turnover with NADH, but profound inhibition by NADP+ makes the enzyme unsuitable for in vivo applications. In the present study site-directed mutagenesis of amino acids in the 2'-phosphate-binding site of the NADPH domain, coupled with the W677A substitution, was used to generate a reductase that was able to use NADH efficiently in vivo without inhibition by NADP+. Of 11 single, double, and triple mutant proteins, two (R597M/W677A and R597M/K602W/W677A) showed up to a 500-fold increase in catalytic efficiency (kcat/Km) with NADH. Inhibition by NADP+ was reduced by up to four orders of magnitude relative to the W677A protein and was equal to or less than that of the wild-type reductase. Both proteins were 2- to 3-fold more active than wild-type reductase with NADH in reconstitution assays with cytochrome P450 1A2 and with squalene monooxygenase. In a recombinant cytochrome P450 2E1 Ames bacterial mutagenicity assay the R597M/W677A protein increased the sensitivity to dimethylnitrosamine by approximately 2-fold, suggesting that the ability to use NADH afforded a significant advantage in this in vivo assay. In addition to providing a valuable tool for understanding the determinants of nucleotide cofactor specificity in this and related enzymes, these mutants might also lend themselves to creation of bioremediation schemes with increased enzymatic activity and robustness in situ, as well as cost-effective reconstitution of enzyme systems in vitro that do not require the use of expensive reducing equivalents from NADPH.
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Grodsky, Neil B. "Probing cooperative interactions between nucleotide binding sites in the F₁-ATPases by site-directed mutagenesis and chemical modification /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1998. http://wwwlib.umi.com/cr/ucsd/fullcit?p9820885.

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Kshetri, Man B. "N-TERMINAL DOMAIN OF rRNA METHYLTRANSFERASE ENZYME RsmC IS IMPORTANT FOR ITS BINDING TO RNA AND RNA CHAPERON ACTIVITY." Kent State University Honors College / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1621007414429417.

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Durbin, Ann M. "Nucleotide Modifications of RNA Suppress RIG-I Antiviral Signaling by Unique Mechanisms." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493466.

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In order to counter pathogen infection while preventing autoimmune responses, the human innate immune system must be precisely regulated to distinguish “self” from “non-self”. Pattern recognition receptors detect “non-self” pathogen RNAs and initiate antiviral signaling. Accumulated evidence suggests that host “self” RNAs contain modified nucleotides that evade or suppress immune signaling; however, the precise mechanisms are not understood. Defining these mechanisms is relevant toward understanding the biology of immunity as well as the applied use of RNAs as therapeutic molecules, where reducing ligand immunogenicity is essential. Evidence from our lab and others’ suggests that the cytosolic RNA helicase RIG-I (retinoic acid inducible gene-I) detects not only the 5’ terminus and double-stranded nature of RNA, but also the presence/absence of modified nucleotides. In the present study, we use a model RNA ligand (polyU/UC), derived from the 3’ untranslated region of the hepatitis C virus RNA, to dissect the mechanisms by which RNAs containing nucleotide modifications suppress or evade RIG-I signaling. Five assays were developed to test our hypothesis that eight different nucleotide modifications, both natural and synthetic, share a common mechanism of innate immune evasion. In vitro transcribed 5’-triphosphate polyU/UC RNA containing canonical nucleotides potently activates the RIG-I signaling pathway in transfected cells, culminating in an antiviral state. When transcribed with any of eight modified nucleotides, the polyU/UC RNA suppressed the RIG-I antiviral response. Unexpectedly, the modified nucleotides had different effects on RIG-I:RNA binding affinity, as well as RIG-I conformational change. The data suggest that multiple RIG-I evasion/suppression mechanisms associated with different modified nucleotides may have evolved to effect a common result of interrupting innate immune signaling responses to “self” RNA. Our findings hold implications for understanding the co-evolution of the innate immune response and RNA modification pathways across domains of life, as well as for defining approaches for testing the multitude of naturally occurring and synthetic nucleotides that may have utility in the design of therapeutic RNAs.<br>Medical Sciences
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Alexander, Katie. "The synthesis, detection and repair of nucleotides containing the 8-nitroguanine modification." Thesis, University of Liverpool, 2014. http://livrepository.liverpool.ac.uk/2006939/.

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There is accumulating evidence that reactive nitrogen species derived from nitric oxide metabolism are involved in cancer as they are able to damage DNA largely through oxidation or nitration of the guanine base. The 8-nitroguanine lesion is increasingly associated with cancers that result from chronic inflammation; however due to its instability, very little is known about this base modification. Consequently this thesis focuses upon establishing methods to detect and quantify the lesion and investigate enzymes potentially involved in repair systems directed against 8-nitroguanine in DNA. The approach outlined in this thesis utilises ribonucleoside analogues of the lesion which sufficiently stabilised the labile glycosidic bond. The 8-nitroguanine nucleosides were prepared prior to incorporation into the oligodeoxynucleotide sequences using the traditional 3’- to 5’-solid-phase phosphoramidite chemistry. A number of oligodeoxynucleotides of varying lengths containing a single modification, and dinucleotides containing two modifications were prepared. A variety of reactions of the 8-nitroguanine base both in nucleosides and oligodeoxynucleotides have been investigated. Studies revealed a different pattern of alkylation for the modified base when compared to results reported in the literature for the natural nucleoside. Thus demonstrating the dramatic effect that nitration has on the intrinsic reactivity of the nucleoside. In view of the susceptibility of nitro group to reaction with thiol nucleophiles, displacement of the nitro group from within nucleosides and oligodeoxynucleotides has been achieved. In particular a fluorescent nucleophile has been developed which stabilises the lesion and could enable direct detection of the levels of 8-nitroguanine in DNA. Using a variety of substrates prepared in this thesis, detection of the 8-nitroguanine base in oligodeoxynucleotides has been investigated using surface enhanced Raman spectroscopy in collaboration with Professor Steven Bell at Queen’s University, Belfast. The unique absorption profile of the 8-nitroguanine derivatives allows for signals exclusively associated with the lesion to be identified using this highly sensitive technique. The synthesis of 8-nitroguanosine triphosphate was investigated using a number of different approaches. Although the initial aim was not successful, the principles for the phosphorylation of a nucleoside have been shown. The problems encountered were attributed to the conformational constraints of the molecule.
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Chitale, Shalaka [Verfasser]. "Nucleotide excision repair: interplay between nuclear compartmentalization, histone modifications and signaling / Shalaka Chitale." Mainz : Universitätsbibliothek Mainz, 2017. http://d-nb.info/1137859040/34.

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Roy, Snigdha. "Cleavage and Ligation Studies in Hairpin and Hammerhead Ribozymes Using Site Specific Nucleotide Modifications." ScholarWorks @ UVM, 2008. http://scholarworks.uvm.edu/graddis/203.

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RNA catalysis is of fundamental importance in many biological functions, such as the peptidyl transferase activity of the ribosome and genetic control by riboswitches, among others. Small ribozymes are a convenient system to increase our understanding about the structure, folding and catalytic mechanism of ribozymes. This dissertation includes analysis of certain aspects of the catalytic mechanism in the hairpin and hammerhead ribozyme. In the hairpin ribozyme, we studied the functional consequences of molecular substitutions at two conserved positions, A9 and A10. These nucleotides are located close to the scissile phosphate but their exact function is unclear since they do not appear to be making any essential interactions with other nucleotides in the catalytic core. G, C, U, 2-aminopurine, 2, 6-diaminopurine, purine, and inosine were substituted at A9 and A10 and their effects on cleavage and ligation rates were analyzed. The effect of the variations on tertiary structure and docking was monitored by hydroxyl radical footprinting and native gel electrophoresis. It was observed that all the variants that exhibited poor docking and/or tertiary structure formation were also ligation challenged whereas they performed normally in the cleavage reaction. We found a unique variant, A10G that cleaved five times faster than A10 but did not exhibit any ligation. Results suggested that ligation required a more kinetically stable core than that needed to carry out cleavage. The hammerhead ribozyme field featured extensive disagreements between the crystal structure of the minimal hammerhead released in the mid 90s and the accumulating biochemical data. Much of the conflict was resolved with the new crystal structure of the extended hammerhead ribozyme. This structure confirmed many of the biochemical findings and brought out some new interactions, notably the G8·C3 base pair. We studied numerous base substitutions to establish the importance of the base pair for cleavage and ligation. Catalysis requires the formation of the base pair but even the fastest base paired variant was 10-fold slower than G8·C3 base pair. Docking and tertiary structure analysis by hydroxyl radical footprinting and native gel electrophoresis emphasized the importance of having a purine at position 8 and a pyrimidine at 3. Catalysis in the unmodified ribozyme was uniquely accompanied by hydrolysis of the 2′, 3′- cyclic phosphate ring present on one of the cleavage products, leading to the generation of non-ligatable products during a ligation assay. We determined the ligation rate-pH profile for unmodified ribozyme that differed from the cleavage rate-pH profile only at high pH.
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Hayward, Laura E. "Identification of Functional Single Nucleotide Polymorphisms Associated with Breast Cancer Based on Chromatin Modifications." Scholarship @ Claremont, 2016. http://scholarship.claremont.edu/cmc_theses/1312.

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Breast cancer affects 1 in 8 women and can be deadly; yet when detected early enough it is often treatable. Thus, early detection of breast cancer is imperative to save lives. The success of early detection depends, in part, on being able to stratify risk. A new approach to determining risk involves identifying genetic variants that alter an individual’s risk for developing breast cancer. This thesis identified key functional candidates involved in breast cancer development, some of which have been verified by other studies. For a few of the functional candidates, further research needs to be done in order to determine the biological significance they play in the development of breast cancer. The functional candidates were identified by comparing SNPs in Linkage Disequilibrium with high risk SNPS—determined by GWAS—using histone modification markers to identify functional genomic elements in breast cell lines. The results yielded three top tier candidates and multiple second tier candidates. Further research should be done in order to assess the risk involved with these variants and the underlying biological mechanism. As genetic testing becomes more accessible to the public, the identification and understanding of these high risk variants will be an essential tool in preventing and treating breast cancer.
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Krull, Matthias. "Synthesis of rare nucleobases and artificial nucleotides for investigation of catalytic enzyme activity." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://hdl.handle.net/21.11130/00-1735-0000-0005-1287-E.

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Books on the topic "Nucleotide modification"

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H, Grosjean, Buckingham R, Centre national de la recherche scientifique., European Molecular Biology Organization, and EMBO-CNRS Workshop on Nucleotide Modification and Base Conversion of RNA (1994 : Aussois,Savoie, France), eds. Nucleotide modification and base conversion of RNA: Part 1. Elsevier, 1994.

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2

Kapdi, Anant R., Debabrata Maiti, and Yogesh S. Sanghvi. Palladium-Catalyzed Modification of Nucleosides, Nucleotides and Oligonucleotides. Elsevier Science & Technology Books, 2018.

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Palladium-Catalyzed Modification of Nucleosides, Nucleotides and Oligonucleotides. Elsevier, 2018. http://dx.doi.org/10.1016/c2016-0-00656-3.

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Mastroeni, Diego F. An Epigenetics Perspective on Diseases of the Central Nervous System. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780190233563.003.0011.

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In the next two decades epigenetics could revolutionize understanding and treatment of diseases of the central nervous system. New research already demonstrates that manipulation of epigenetic mechanisms in vivo and in vitro can ameliorate a host of pathogenic processes associated with neurodegenerative disorders such as Alzheimer’s disease (AD), Parkinson’s (PD), amyotrophic lateral sclerosis (ALS), Huntington’s (HD), and multiple sclerosis (MS), among others. These advances have come relatively rapidly for a field that is still in its infancy compared to the much longer history of epigenetics in developmental biology. Epigenetic modifications are all-encompassing, from nucleotides to amino acids. They are capable of altering transcriptional to biochemical activity in a consistent manner across thousands of genes and hundreds of biologic pathways, yet they can do so differentially even in individuals or cells with identical gene codes. As such, epigenetic modifications are likely to touch on virtually all the mechanisms described in this book.
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Hamilton, Matthew Lloyd. COMT genotypes in pain responses. Edited by Paul Farquhar-Smith, Pierre Beaulieu, and Sian Jagger. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198834359.003.0080.

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The landmark study discussed in this chapter is ‘COMT val158met genotype affects μ‎-opioid neurotransmitter responses to a pain stressor’, published by Zubieta et al. in 2003. Catechol-O-methyl-transferase (COMT) is a key modulator of dopaminergic and noradrenergic neurotransmission. This study focused on a single nucleotide polymorphism of the COMT gene encoding the substitution of valine (val) by methionine (met) at Codon 158 (val158met), resulting in a three- to fourfold reduction in its activity. Individuals with the val/val genotype have the highest activity of COMT, val/met genotypes have intermediate activity, and met/met genotypes have the lowest activity of COMT. Using a mixture of PET imaging of the binding of μ‎-opioid receptors and correlation with clinical outcomes, this groundbreaking study provided evidence that confirmed their hypothesis and established the COMT val158met SNP as one of the first gene modifications with direct ramifications on human pain.
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Henri, Grosjean, ed. Fine-tuning of RNA functions by modification and editing. Springer, 2005.

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Book chapters on the topic "Nucleotide modification"

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Lennox, Kim A., Christopher A. Vakulskas, and Mark A. Behlke. "Non-nucleotide Modification of Anti-miRNA Oligonucleotides." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6563-2_3.

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Douthwaite, Stephen, Dominique Fourmy, and Satoko Yoshizawa. "Nucleotide methylations in rRNA that confer resistance to ribosome-targeting antibiotics." In Fine-Tuning of RNA Functions by Modification and Editing. Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/b105586.

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Gulzar, Naila, Hayley Dingerdissen, Cheng Yan, and Raja Mazumder. "Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins." In Protein Bioinformatics. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6783-4_8.

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Imaizumi, Y., Y. Takano, S. Kitadume, H. Ozaki, S. Obika, and M. Kuwahara. "Nucleotide Modification and Polymerase Engineering for Creating a Novel Class of Artificial Nucleic Acid Aptamers." In IFMBE Proceedings. Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-23508-5_266.

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Bickel-Sandkötter, S., and P. Strümper. "Characterization of Nucleotide Binding Sites on Isolated Chloroplast ATPase by Modification with 7-Chloro-4-Nitro-Benzofurazan." In Current Research in Photosynthesis. Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-0511-5_455.

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Auffinger, Pascal, and Eric Westhof. "Location and Distribution of Modified Nucleotides in tRNA." In Modification and Editing of RNA. ASM Press, 2014. http://dx.doi.org/10.1128/9781555818296.app5.

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Grosjean, Henri, Claude Houssier, Pascale Romby, and Roland Marquet. "Modulatory Role of Modified Nucleotides in RNA Loop-Loop Interaction." In Modification and Editing of RNA. ASM Press, 2014. http://dx.doi.org/10.1128/9781555818296.ch7.

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Marquet, Roland. "Importance of Modified Nucleotides in Replication of Retroviruses, Plant Pararetroviruses, and Retrotransposons." In Modification and Editing of RNA. ASM Press, 2014. http://dx.doi.org/10.1128/9781555818296.ch28.

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Grosjean, Henri, Gérard Keith, and Louis Droogmans. "Detection and Quantification of Modified Nucleotides in RNA Using Thin-Layer Chromatography." In RNA Interference, Editing, and Modification. Humana Press, 2004. http://dx.doi.org/10.1385/1-59259-775-0:357.

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Mason, Thomas L. "Functional Aspects of the Three Modified Nucleotides in Yeast Mitochondrial Large-Subunit rRNA." In Modification and Editing of RNA. ASM Press, 2014. http://dx.doi.org/10.1128/9781555818296.ch14.

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