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Journal articles on the topic 'Trinucleotides'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Michel, Christian J., and Giuseppe Pirillo. "Strong Trinucleotide Circular Codes." International Journal of Combinatorics 2011 (August 25, 2011): 1–14. http://dx.doi.org/10.1155/2011/659567.

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Recently, we identified a hierarchy relation between trinucleotide comma-free codes and trinucleotide circular codes (see our previous works). Here, we extend our hierarchy with two new classes of codes, called DLD and LDL codes, which are stronger than the comma-free codes. We also prove that no circular code with 20 trinucleotides is a DLD code and that a circular code with 20 trinucleotides is comma-free if and only if it is a LDL code. Finally, we point out the possible role of the symmetric group ∑4 in the mathematical study of trinucleotide circular codes.

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2

Suchsland, Ruth, Bettina Appel, Matthäus Janczyk, and Sabine Müller. "Solid Phase Assembly of Fully Protected Trinucleotide Building Blocks for Codon-Based Gene Synthesis." Applied Sciences 9, no. 11 (2019): 2199. http://dx.doi.org/10.3390/app9112199.

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The use of pre-formed trinucleotides, representing codons of the 20 canonical amino acids, for oligonucleotide-directed mutagenesis offers the advantage of controlled randomization and generation of “smart libraries”. We here present a method for the preparation of fully protected trinucleotides on solid phase. The key issue of our strategy is the linkage of the starting nucleoside to the solid support via a traceless disulfide linker. Upon trinucleotide assembly, the disulfide bridge is cleaved under reducing conditions, and the fully protected trinucleotide is released with a terminal 3′-OH

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3

Benard, Emmanuel, and Christian J. Michel. "Transition and Transversion on the Common Trinucleotide Circular Code." Computational Biology Journal 2013 (May 29, 2013): 1–10. http://dx.doi.org/10.1155/2013/795418.

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In 1996, a trinucleotide circular code which is maximum, self-complementary, and , called , was identified statistically on a large gene population of eukaryotes and prokaryotes (Arquès and Michel (1996)). Transition and transversions I and II are classical molecular evolution processes. A comprehensive computer analysis of these three evolution processes in the code shows some new results; in particular (i) transversion I on the 2nd position of any subset of trinucleotides of generates trinucleotide circular codes which are always and (ii) transversion II on the three positions of any subset

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4

Suchsland, Ruth, Bettina Appel, Pasi Virta, and Sabine Müller. "Synthesis of fully protected trinucleotide building blocks on a disulphide-linked soluble support." RSC Advances 11, no. 7 (2021): 3892–96. http://dx.doi.org/10.1039/d0ra10941j.

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Fully protected trinucleotides are synthesized on a tetrapodal soluble support using a disulphide linkage that upon reductive cleavage allows release of the trinucleotide with free 3′-OH group for further conversion to a phosphoramidite.

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5

McClellan, James, and Sarah Newbury. "Inexpressible trinucleotides." Nature 379, no. 6564 (1996): 396. http://dx.doi.org/10.1038/379396a0.

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6

Piwowar, Monika, Jan Meus, Piotr Piwowar, Zdzisław Wiśniowski, Justyna Stefaniak, and Irena Roterman. "Tandemly repeated trinucleotides - comparative analysis." Acta Biochimica Polonica 53, no. 2 (2006): 279–87. http://dx.doi.org/10.18388/abp.2006_3340.

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Characteristics of 64 possible tandem trinucleotide repeats (TSSR) from Homo sapiens (hs), Mus musculus (mm) and Rattus norvegicus (rn) genomes are presented. Comparative analysis of TSSR frequency depending on their repetitiveness and similarity of the TSSR length distributions is shown. Comparative analysis of TSSR sequence motifs and association between type of motif and its length (n) using rho-coefficient method (quantitatively measuring the association between variables in contingency tables) is presented. These analyses were carried out in the context of neurodegenerative diseases based

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7

Polyansky, Anton A., Mathias Kreuter, John D. Sutherland, and Bojan Zagrovic. "Direct interplay between stereochemistry and conformational preferences in aminoacylated oligoribonucleotides." Nucleic Acids Research 47, no. 21 (2019): 11077–89. http://dx.doi.org/10.1093/nar/gkz902.

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Abstract To address the structural and dynamical consequences of amino-acid attachment at 2′- or 3′-hydroxyls of the terminal ribose in oligoribonucleotides, we have performed an extensive set of molecular dynamics simulations of model aminoacylated RNA trinucleotides. Our simulations suggest that 3′-modified trinucleotides exhibit higher solvent exposure of the aminoacylester bond and may be more susceptible to hydrolysis than their 2′ counterparts. Moreover, we observe an invariant adoption of well-defined collapsed and extended conformations for both stereoisomers. We show that the average

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8

Houlston, C. E., M. Cummings, H. Lindsay, S. Pradhan, and R. L. P. Adams. "DNA substrate specificity of pea DNA methylase." Biochemical Journal 293, no. 3 (1993): 617–24. http://dx.doi.org/10.1042/bj2930617.

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DNA methylase, present in low-salt extracts of nuclei prepared from Pisum sativum shoot tips, methylates model DNA substrates containing CNG trinucleotides or CI dinucleotides only. The binding to the hemimethylated trinucleotide substrates is very much stronger and more persistent than the binding to the unmethylated substrates or to the hemimethylated dinucleotide substrate. When the DNA concentration is limiting, the rate of methyl-group transfer with the hemimethylated CNG substrate is much greater than that with the unmethylated CNG. However, the Vmax. is similar for the two CNG substrate

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9

Fimmel, Elena, Christian J. Michel, and Lutz Strüngmann. "n -Nucleotide circular codes in graph theory." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 374, no. 2063 (2016): 20150058. http://dx.doi.org/10.1098/rsta.2015.0058.

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The circular code theory proposes that genes are constituted of two trinucleotide codes: the classical genetic code with 61 trinucleotides for coding the 20 amino acids (except the three stop codons { TAA , TAG , TGA }) and a circular code based on 20 trinucleotides for retrieving, maintaining and synchronizing the reading frame. It relies on two main results: the identification of a maximal C 3 self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses (Michel 2015 J. Theor. Biol. 380, 156–177. ( doi:10.1016/j.jtbi.2015.04.009 ); Arquès & Miche

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10

Suchsland, Ruth, Bettina Appel, and Sabine Müller. "Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries." Beilstein Journal of Organic Chemistry 14 (February 13, 2018): 397–406. http://dx.doi.org/10.3762/bjoc.14.28.

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The preparation of protein libraries is a key issue in protein engineering and biotechnology. Such libraries can be prepared by a variety of methods, starting from the respective gene library. The challenge in gene library preparation is to achieve controlled total or partial randomization at any predefined number and position of codons of a given gene, in order to obtain a library with a maximum number of potentially successful candidates. This purpose is best achieved by the usage of trinucleotide synthons for codon-based gene synthesis. We here review the strategies for the preparation of f

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11

Gusella, James F., and Marcy E. MacDonald. "Huntington's Disease and Repeating Trinucleotides." New England Journal of Medicine 330, no. 20 (1994): 1450–51. http://dx.doi.org/10.1056/nejm199405193302011.

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12

Pirillo, Giuseppe. "SOME PROPERTIES OF TRINUCLEOTIDES AND TETRANUCLEOTIDES." Journal of the Siena Academy of Sciences 4, no. 1 (2012): 59. http://dx.doi.org/10.4081/jsas.2012.59.

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13

Homchan, Somjit, Pradeep Bhadola, and Yash Munnalal Gupta. "Statistical Analysis of Simple Sequence Repeats in Genome Sequence: A Case of Acheta Domesticus (Orthoptera: Gryllidae)." ECS Transactions 107, no. 1 (2022): 14799–806. http://dx.doi.org/10.1149/10701.14799ecst.

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Herein, we have described genome wide screening of microsatellites (Simple Sequence Repeats: SSRs) and their distribution in the Acheta domesticus genome using a custom python script. A total of 232,179 microsatellites were identified, in which trinucleotide repeats were found to be the most abundant repeats in the genome, representing 60 % of the total microsatellite, followed by dinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides. Among trinucleotides, dinucleotides, and tetranucleotides, the most prevalent microsatellite motifs were AAT/ATT, TG/CA, and AAAT/ATTT, respecti

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14

Liao, Wei, Yong Tang, Yu-liang Kuo, Bao-Ying Liu, Chi-Jie Xu, and Chou-Zen Giam. "Kaposi's Sarcoma-Associated Herpesvirus/Human Herpesvirus 8 Transcriptional Activator Rta Is an Oligomeric DNA-Binding Protein That Interacts with Tandem Arrays of Phased A/T-Trinucleotide Motifs." Journal of Virology 77, no. 17 (2003): 9399–411. http://dx.doi.org/10.1128/jvi.77.17.9399-9411.2003.

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ABSTRACT Kaposi's sarcoma associated herpesvirus (KSHV)/human herpesvirus 8 (HHV-8) encodes an immediate early transcriptional activator, Rta, which mediates viral reactivation from latency and lytic viral replication. Here we report the purification and characterizations of HHV-8 Rta and its interaction with Rta-responsive DNA elements. The Rta response element (RtaRE) in the promoter of the KSHV/HHV-8 K8 open reading frame was mapped to a 47-bp sequence (RtaRE1) and a 60-bp sequence (RtaRE2) upstream of the TATA motif. A comparison of the K8 RtaREs with other viral RtaREs revealed a pattern

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15

Debiais, Mégane, Alejandro Gimenez Molina, Sabine Müller, et al. "Design and NMR characterization of reversible head-to-tail boronate-linked macrocyclic nucleic acids." Organic & Biomolecular Chemistry 20, no. 14 (2022): 2889–95. http://dx.doi.org/10.1039/d2ob00232a.

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16

Westphal, K., J. Wiczk, J. Miloch, G. Kciuk, K. Bobrowski, and J. Rak. "Irreversible electron attachment – a key to DNA damage by solvated electrons in aqueous solution." Organic & Biomolecular Chemistry 13, no. 41 (2015): 10362–69. http://dx.doi.org/10.1039/c5ob01542a.

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17

Xu, Pengning, Feng Pan, Christopher Roland, Celeste Sagui, and Keith Weninger. "Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts." Nucleic Acids Research 48, no. 5 (2020): 2232–45. http://dx.doi.org/10.1093/nar/gkaa036.

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Abstract DNA trinucleotide repeats (TRs) can exhibit dynamic expansions by integer numbers of trinucleotides that lead to neurodegenerative disorders. Strand slipped hairpins during DNA replication, repair and/or recombination may contribute to TR expansion. Here, we combine single-molecule FRET experiments and molecular dynamics studies to elucidate slipping dynamics and conformations of (CAG)n TR hairpins. We directly resolve slipping by predominantly two CAG units. The slipping kinetics depends on the even/odd repeat parity. The populated states suggest greater stability for 5′-AGCA-3′ tetr

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18

Urretavizcaya, G., and E. J. Baran. "Wechselwirkung des Vanadyl(IV)-Kations mit Nucleotiden in wäßriger Lösung / Interaction of the Vanadyl(IV) Cation with Nucleotides in Aqueous Solution." Zeitschrift für Naturforschung B 42, no. 12 (1987): 1537–42. http://dx.doi.org/10.1515/znb-1987-1208.

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AbstractThe interaction of VO2+ with mono-, di- and trinucleotides and with some of the related nucleosides and bases, was investigated spectrophotometrically at pH = 4.9. The results point to a preferential interaction of the cation with the phosphate groups of all the nucleotides whereas no interaction with the nucleosides and bases was detected. The vanadyl coordination sphere shows some distortive effects in the case of mononucleotides whereas it appears more regular in the case of di- and trinucleotides. At high pH-values the cation interacts with the deprotonated OH-groups of the ribose

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19

Makarov, Dmitry, and Anastasia Kharlamova. "Peculiarities of Scattering of Ultrashort Laser Pulses on DNA and RNA Trinucleotides." International Journal of Molecular Sciences 23, no. 23 (2022): 15417. http://dx.doi.org/10.3390/ijms232315417.

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Currently, X-ray diffraction analysis (XRD) with high spatial and time resolution (TR-XRD) is based on the known theory of X-ray scattering, where the main parameter of USP—its duration—is not taken into account. In the present work, it is shown that, for scattering of attosecond USPs on DNA and RNA trinucleotides, the pulse length is the most important scattering parameter. The diffraction pattern changes considerably in comparison with the previously known scattering theory. The obtained results are extremely important in TR-XRD when using attosecond pulses to study trinucleotides of DNA and

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20

Michel, Christian J. "Single-Frame, Multiple-Frame and Framing Motifs in Genes." Life 9, no. 1 (2019): 18. http://dx.doi.org/10.3390/life9010018.

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We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif SF has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon AAACAA is SF as the trinucleotides AAA and CAA do not occur in a shifted frame. A motif which is not single-frame SF is multiple-frame MF. Several classes of MF motifs are defined and analysed. The distributions of single-frame SF motifs (associated with an unambiguous trinucleotide decoding in the two 5'–3' and 3'–5' directions) and 5′ unambi

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21

Pan, Zhengzheng, Jinquan Chen, Wolfgang J. Schreier, Bern Kohler, and Frederick D. Lewis. "Thymine Dimer Photoreversal in Purine-Containing Trinucleotides." Journal of Physical Chemistry B 116, no. 1 (2011): 698–704. http://dx.doi.org/10.1021/jp210575g.

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22

Bussoli, Lorenzo, Christian J. Michel, and Giuseppe Pirillo. "On Conjugation Partitions of Sets of Trinucleotides." Applied Mathematics 03, no. 01 (2012): 107–12. http://dx.doi.org/10.4236/am.2012.31017.

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23

Skorski, Patricia, Prune Leroy, Olivier Fayet, Marc Dreyfus, and Sylvie Hermann-Le Denmat. "The Highly Efficient Translation Initiation Region from the Escherichia coli rpsA Gene Lacks a Shine-Dalgarno Element." Journal of Bacteriology 188, no. 17 (2006): 6277–85. http://dx.doi.org/10.1128/jb.00591-06.

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ABSTRACT The translational initiation region (TIR) of the Escherichia coli rpsA gene, which encodes ribosomal protein S1, shows a number of unusual features. It extends far upstream (to position −91) of the initiator AUG, it lacks a canonical Shine-Dalgarno sequence (SD) element, and it can fold into three successive hairpins (I, II, and III) that are essential for high translational activity. Two conserved GGA trinucleotides, present in the loops of hairpins I and II, have been proposed to form a discontinuous SD. Here, we have tested this hypothesis with the “specialized ribosome” approach.

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24

Pedrosa, Andre, and Leoncio Rabelo Borges Filho. "EXPANSION OF TRINUCLEOTIDE REPEATS IN HUMAN DNA AND MOLECULAR DIAGNOSIS OF TRINUCLEOTIDE EXPANSION DISORDERS: INTEGRATIVE REVIEW." Acta Biologica Brasiliensia 7, no. 2 (2024): 279–91. https://doi.org/10.18554/acbiobras.v7i2.8007.

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Trinucleotide repeat (TNR) expansions are increases in the number of repeated trinucleotides in the genome. TNR expansions have been confirmed as the molecular etiology of various neurodegenerative disorders, such as Huntington's Disease, Fragile X Syndrome, and Friedreich's Ataxia. Due to the potential achieved by molecular diagnostic technology, new disorders related to TNR expansions are being elucidated more rapidly, as high-throughput technologies for analyzing DNA are described every year. Thus, we carried out an integrative review on the importance of improving DNA analysis methods for

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25

Takeuchi, Fumihiko, Yasuhiro Futamura, Hiroshi Yoshikura, and Kenji Yamamoto. "Statistics of trinucleotides in coding sequences and evolution." Journal of Theoretical Biology 222, no. 2 (2003): 139–49. http://dx.doi.org/10.1016/s0022-5193(03)00021-3.

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26

Cvekl, Aleš, Květa Horská, Karel Šebesta, Ivan Rosenberg, and Antonín Holý. "Trinucleotide AUA and UAU formation catalyzed by wheat germ RNA polymerase II." Collection of Czechoslovak Chemical Communications 54, no. 3 (1989): 811–18. http://dx.doi.org/10.1135/cccc19890811.

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The elongation of dinucleotides ApU and UpA to trinucleotides ApUpA and UpApU by wheat germ RNA polymerase II was studied at a medium ionic strength (60 mM-KCl). The catalytic mechanism of the first internucleotide bond formation consists in the binding of the primer dinucleotide followed by the binding of NTP ("ordered bibi" reaction), i.e. by an analogous mechanism as found for RNA polymerase holoenzyme from E. coli. In further experiments phosphonate analogues of dinucleotides ApU and UpA were used as the priming dinucleotides. It was shown that analogues U(c)pA and Up(c)A are very poor pri

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Li, Jie, Jingfang Liu, Ligang Zhou, Huadong Pei, Jian Zhou, and Hua Xiang. "Two Distantly Homologous DnaG Primases from Thermoanaerobacter tengcongensis Exhibit Distinct Initiation Specificities and Priming Activities." Journal of Bacteriology 192, no. 11 (2010): 2670–81. http://dx.doi.org/10.1128/jb.01511-09.

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ABSTRACT Primase, encoded by dnaG in bacteria, is a specialized DNA-dependent RNA polymerase that synthesizes RNA primers de novo for elongation by DNA polymerase. Genome sequence analysis has revealed two distantly related dnaG genes, TtdnaG and TtdnaG 2, in the thermophilic bacterium Thermoanaerobacter tengcongensis. Both TtDnaG (600 amino acids) and TtDnaG2 (358 amino acids) exhibit primase activities in vitro at a wide range of temperatures. Interestingly, the template recognition specificities of these two primases are quite distinctive. When trinucleotide-specific templates were tested,

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Faidah, A. N., and H. Shabrina. "Expressed sequence tag simple sequence repeats (EST-SSRs) mining and marker development from Leucaena leucocephala root transcriptome." IOP Conference Series: Earth and Environmental Science 959, no. 1 (2022): 012022. http://dx.doi.org/10.1088/1755-1315/959/1/012022.

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Abstract Leucaena leucocephala is a nitrogen-fixing legume and a fast-growing species used for various purposes, including food, medicine, and most recently, energy-source wood. Compared to other commonly planted legumes, this species has a high-stress tolerance, and only one recorded insect infestation. The transcriptome analysis revealed genes involved in the production of stress tolerance compounds in the root. In this study, we attempted to extract simple sequence repeats (SSRs) from the transcriptome data of L. leucocephala root to establish molecular markers. The SSRs mined from L. leuco

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van Eijk, Erika, Vasileios Paschalis, Matthew Green, et al. "Primase is required for helicase activity and helicase alters the specificity of primase in the enteropathogen Clostridium difficile." Open Biology 6, no. 12 (2016): 160272. http://dx.doi.org/10.1098/rsob.160272.

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DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by subtle mechanistic differences and limited understanding of DNA replication in pathogenic microorganisms. Clostridium difficile is the main cause of healthcare-associated diarrhoea and its DNA replication machinery is virtually uncharacterized. We identify and characterize the mechanistic details of the putative replicative helicase (CD3657), helicase-loader ATPase (CD3654) and primase (CD1454) of C. diffici

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30

Xiao, Jiajing, Binghua Nie, Meng-En Chen, Danfeng Ge, and Renyi Liu. "Discovery and Genomic Analysis of Three Novel Viruses in the Order Mononegavirales in Leafhoppers." Viruses 16, no. 8 (2024): 1321. http://dx.doi.org/10.3390/v16081321.

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Leafhoppers are economically important pests and may serve as vectors for pathogenic viruses that cause substantial crop damage. In this study, using deep transcriptome sequencing, we identified three novel viruses within the order Mononegavirales, including two viruses belonging to the family Rhabdoviridae and one to the family Lispiviridae. The complete genome sequences were obtained via the rapid amplification of cDNA ends and tentatively named Recilia dorsalis rhabdovirus 1 (RdRV1, 14,251 nucleotides, nt), Nephotettix virescens rhabdovirus 1 (NvRV1, 13,726 nt), and Nephotettix virescens li

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31

Ahmed, Ahmed, Gabriel Frey, and Christian J. Michel. "Frameshift Signals in Genes Associated with the Circular Code." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 7, no. 2 (2007): 155–68. https://doi.org/10.3233/isb-00286.

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Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshif

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Pan, Zhengzheng, Martin McCullagh, George C. Schatz, and Frederick D. Lewis. "Conformational Control of Thymine Photodimerization in Purine-Containing Trinucleotides." Journal of Physical Chemistry Letters 2, no. 12 (2011): 1432–38. http://dx.doi.org/10.1021/jz200532w.

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Severin, Geoffrey B., and Christopher M. Waters. "Pyrimidines and Cyclic Trinucleotides Join the Second Messenger Symphony." Cell Host & Microbe 25, no. 4 (2019): 471–73. http://dx.doi.org/10.1016/j.chom.2019.03.016.

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Ross, Samuel E., Allegra Angeloni, Fan-Suo Geng, Alex de Mendoza, and Ozren Bogdanovic. "Developmental remodelling of non-CG methylation at satellite DNA repeats." Nucleic Acids Research 48, no. 22 (2020): 12675–88. http://dx.doi.org/10.1093/nar/gkaa1135.

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Abstract In vertebrates, DNA methylation predominantly occurs at CG dinucleotides however, widespread non-CG methylation (mCH) has been reported in mammalian embryonic stem cells and in the brain. In mammals, mCH is found at CAC trinucleotides in the nervous system, where it is associated with transcriptional repression, and at CAG trinucleotides in embryonic stem cells, where it positively correlates with transcription. Moreover, CAC methylation appears to be a conserved feature of adult vertebrate brains. Unlike any of those methylation signatures, here we describe a novel form of mCH that o

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Chen, Jingchao, Hailan Cui, Hongjuan Huang, et al. "EST-SSR Markers’ Development Based on RNA-Sequencing and Their Application in Population Genetic Structure and Diversity Analysis of Eleusine indica in China." Current Issues in Molecular Biology 45, no. 1 (2022): 141–50. http://dx.doi.org/10.3390/cimb45010011.

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Goosegrass (Eleusine indica) is one of the worst agricultural weeds in China. Molecular markers were developed for genetic diversity and population structure analyses. In this study, we identified 8391 expressed sequence tag-simple sequence repeat (EST-SSR) markers from the de novo assembled unigenes of E. indica. Mononucleotides were the most abundant type of repeats (3591, 42.79%), followed by trinucleotides (3162, 37.68%). The most dominant mononucleotide and trinucleotide repeat motifs were A/T (3406, 40.59%) and AAT/ATT (103, 1.5%), respectively. Fourteen pairs of EST-SSR primers were ver

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Rosandić, Marija, Matko Glunčić, and Vladimir Paar. "Start/stop codon like trinucleotides extensions in primate alpha satellites." Journal of Theoretical Biology 317 (January 2013): 301–9. http://dx.doi.org/10.1016/j.jtbi.2012.09.022.

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Tulub, Alexander A. "Magnesium cations assist with unpairing hydrogen-bonded 2-deoxyribose trinucleotides." Archives of Biochemistry and Biophysics 607 (October 2016): 44–46. http://dx.doi.org/10.1016/j.abb.2016.08.013.

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38

Schweickhardt, C., I. Sabolic, D. Brown, and G. Burckhardt. "Ecto-adenosinetriphosphatase in rat small intestinal brush-border membranes." American Journal of Physiology-Gastrointestinal and Liver Physiology 268, no. 4 (1995): G663—G672. http://dx.doi.org/10.1152/ajpgi.1995.268.4.g663.

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Antibodies against the holo ecto-adenosinetriphosphatase (ATPase) of rat liver and antibodies against COOH-terminal peptides of the long isoform of this enzyme reacted in Western blots with a 105-kDa band from small intestinal brush-border membranes. Indirect immunofluorescence revealed reactive proteins predominantly at the apical surface of enterocytes with some staining of basolateral membranes and of vascular endothelium. Similar results were obtained with monoclonal antibodies against HA4, a protein from rat liver closely related to the ecto-ATPase. Since these results suggested the prese

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Gupta, S. K., and T. Gopalakrishna. "Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species." Genome 53, no. 7 (2010): 508–23. http://dx.doi.org/10.1139/g10-028.

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Unigene sequences available in public databases provide a cost-effective and valuable source for the development of molecular markers. In this study, the identification and development of unigene-based SSR markers in cowpea ( Vigna unguiculata (L.) Walp.) is presented. A total of 1071 SSRs were identified in 15 740 cowpea unigene sequences downloaded from the National Center for Biotechnology Information. The most frequent SSR motifs present in the unigenes were trinucleotides (59.7%), followed by dinucleotides (34.8%), pentanucleotides (4%), and tetranucleotides (1.5%). The copy number varied

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Mangin, Antoine, Laure de Pontual, Yu-Chih Tsai, et al. "Robust Detection of Somatic Mosaicism and Repeat Interruptions by Long-Read Targeted Sequencing in Myotonic Dystrophy Type 1." International Journal of Molecular Sciences 22, no. 5 (2021): 2616. http://dx.doi.org/10.3390/ijms22052616.

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Myotonic dystrophy type 1 (DM1) is the most complex and variable trinucleotide repeat disorder caused by an unstable CTG repeat expansion, reaching up to 4000 CTG in the most severe cases. The genetic and clinical variability of DM1 depend on the sex and age of the transmitting parent, but also on the CTG repeat number, presence of repeat interruptions and/or on the degree of somatic instability. Currently, it is difficult to simultaneously and accurately determine these contributing factors in DM1 patients due to the limitations of gold standard methods used in molecular diagnostics and resea

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Hüttel, Bruno, Peter Winter, Kurt Weising, Wafa Choumane, Franz Weigand, and Günter Kahl. "Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.)." Genome 42, no. 2 (1999): 210–17. http://dx.doi.org/10.1139/g98-122.

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Two small-insert genomic libraries of chickpea (Cicer arietinum L.) were screened with a set of microsatellite-specific oligonucleotide probes. A total of 121 positive clones were identified among 13 000 plated colonies. Thirty-nine clones were recognized by (TAA)5, 26 by (GA)8, 18 by (GT)8, 27 by a pool of AT-rich trinucleotide repeats [(CAA)5, (CAT)5, and (GAA)5], and 11 by a pool of GC-rich trinucleotides [(TCC)5, (CAC)5, (CAG)5, and (CGA)5]. Of 53 clones selected for sequencing, 43 carried a microsatellite. Flanking primer pairs were designed for 28 loci, and used on a small test-set compr

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Lee, Juna, Se Jin Jang, Nicole Benoit, et al. "Presence of 5-methylcytosine in CpNpG trinucleotides in the human genome." Genomics 96, no. 2 (2010): 67–72. http://dx.doi.org/10.1016/j.ygeno.2010.03.013.

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Han, Ye, Yuanning Liu, Hao Zhang, Fei He, Chonghe Shu, and Liyan Dong. "Utilizing Selected Di- and Trinucleotides of siRNA to Predict RNAi Activity." Computational and Mathematical Methods in Medicine 2017 (2017): 1–12. http://dx.doi.org/10.1155/2017/5043984.

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Small interfering RNAs (siRNAs) induce posttranscriptional gene silencing in various organisms. siRNAs targeted to different positions of the same gene show different effectiveness; hence, predicting siRNA activity is a crucial step. In this paper, we developed and evaluated a powerful tool named “siRNApred” with a new mixed feature set to predict siRNA activity. To improve the prediction accuracy, we proposed 2-3NTs as our new features. A Random Forest siRNA activity prediction model was constructed using the feature set selected by our proposed Binary Search Feature Selection (BSFS) algorith

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Børsting, Philip, Anders M. Sørensen, and Poul Nielsen. "A Ring-Closing Metathesis Strategy Towards Conformationally Restricted Di- and Trinucleotides." Synthesis 2002, no. 06 (2002): 797–801. http://dx.doi.org/10.1055/s-2002-25754.

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Horská, Květa, Aleš Cvekl, Ivan Rosenberg, Antonín Holý, and Karel Šebesta. "DNA-dependent RNA polymerase mediated formation of methylphosphonyl internucleotide linkage." Collection of Czechoslovak Chemical Communications 55, no. 8 (1990): 2100–2109. http://dx.doi.org/10.1135/cccc19902100.

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Analogues of ATP modified in the triphosphate moiety by introducing phosphonylmethyl ether residue(s) were used as substrates for bacterial DNA-dependent RNA polymerase. Although the analogues function as poor substrates they enter the initiation as well as the elongation site of the enzyme. The ATP analogue containing the phosphonylmethyl ether group in the α position in the presence of UTP and poly [d(A-T)] gives rise to alternating di- and trinucleotides with one anomalous internucleotide linkage per molecule.

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Rosandić, Marija, and Vladimir Paar. "The Supersymmetry Genetic Code Table and Quadruplet Symmetries of DNA Molecules Are Unchangeable and Synchronized with Codon-Free Energy Mapping during Evolution." Genes 14, no. 12 (2023): 2200. http://dx.doi.org/10.3390/genes14122200.

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The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: (1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all bases (purines [A, G) and pyrimidines (U, C)] and (2) of bases in the form of codons; (3) direct–complement like codon/anticodon symmetry in the sixteen alternating boxes of the genetic code columns; (4) A + T-rich and C + G-rich alternate codons in the same row between both columns of the genetic code; (5) the same position between divided and undivided codon boxes in relation to horizontal mirror

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Cvekl, Aleš, Květa Horská, and Karel Šebesta. "On the mechanism of rifampicin inhibition of DNA dependent RNA polymerase from Escherichia coli: A new hypothesis of the drug action." Collection of Czechoslovak Chemical Communications 53, no. 1 (1988): 181–85. http://dx.doi.org/10.1135/cccc19880181.

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The influence of rifampicin on the temperature dependent synthesis of trinucleotides ApUpA and UpApU was studied. Whereas the elongation of dinucleotide ApU is stimulated to a great extent, the elongation of UpA is inhibited to about 50%. These results cannot be explained in terms of different models proposed for the mechanism of inhibition of RNA synthesis caused by rifampicin. According to our hypothesis rifampicin inhibits internal rearrangement of the RNA polymerase which occurs during the transition of the initiation complex to the stable elongation complex.

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Wang, Qiang, Milen Raytchev, and Torsten Fiebig. "Ultrafast Energy Delocalization and Electron Transfer Dynamics in 2-Aminopurine-Containing Trinucleotides." Photochemistry and Photobiology 83, no. 3 (2007): 637–41. http://dx.doi.org/10.1111/j.1751-1097.2007.00115.x.

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Zenker, Andrea, Markus Galanski, Thomas L. Bereuter, Bernhard K. Keppler, and Wolfgang Lindner. "Capillary electrophoretic study of cisplatin interaction with nucleoside monophosphates, di- and trinucleotides." Journal of Chromatography A 852, no. 1 (1999): 337–46. http://dx.doi.org/10.1016/s0021-9673(99)00467-7.

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Slegtenhorst-Eegdeman, Karin E., Dirk G. de Rooij, Miriam Verhoef-Post, et al. "Macroorchidism in FMR1 Knockout Mice Is Caused by Increased Sertoli Cell Proliferation during Testicular Development*." Endocrinology 139, no. 1 (1998): 156–62. http://dx.doi.org/10.1210/endo.139.1.5706.

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Abstract The fragile X syndrome is the most frequent hereditary form of mental retardation. This X-linked disorder is, in most cases, caused by an unstable and expanding trinucleotide CGG repeat located in the 5′-untranslated region of the gene involved, the fragile X mental retardation 1 (FMR1) gene. Expansion of the CGG repeat to a length of more than 200 trinucleotides results in silencing of the FMR1 gene promoter and, thus, in an inactive gene. The clinical features of male fragile X patients include mental retardation, autistiform behavior, and characteristic facial features. In addition

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