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Journal articles on the topic 'Template-Directed polymerization'

Author: Grafiati

Published: 5 April 2023

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1

G. Lynn, David, Xiaoyu Li, Andres F. Hernandez, Martha A. Grover, and Nicholas V. Hud. "Step-Growth Control in Template-Directed Polymerization." HETEROCYCLES 82, no. 2 (2010): 1477. http://dx.doi.org/10.3987/com-10-s(e)99.

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2

Lin, Tao, Xue Song Shang, Jinne Adisoejoso, Pei Nian Liu, and Nian Lin. "Steering On-Surface Polymerization with Metal-Directed Template." Journal of the American Chemical Society 135, no. 9 (February 26, 2013): 3576–82. http://dx.doi.org/10.1021/ja311890n.

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3

Kanaya, Eiko, and Hiroshi Yanagawa. "Template-directed polymerization of oligoadenylates using cyanogen bromide." Biochemistry 25, no. 23 (November 18, 1986): 7423–30. http://dx.doi.org/10.1021/bi00371a026.

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4

Wang, Cheng-Xin, Jian-Le Chen, Chen-Hui Shu, Ke-Ji Shi, and Pei-Nian Liu. "On-surface synthesis of 2D COFs on Cu(111) via the formation of thermodynamically stable organometallic networks as the template." Physical Chemistry Chemical Physics 21, no. 24 (2019): 13222–29. http://dx.doi.org/10.1039/c9cp01843c.

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Template-directed polymerization is an effective approach used to afford regular 2D covalent organic frameworks (COFs), thus the regularity of the template is crucial for the quality of the resulting 2D COFs.

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5

Khan, Afzal, David M. Haddleton, Michael J. Hannon, Dax Kukulj, and Andrew Marsh. "Hydrogen Bond Template-Directed Polymerization of Protected 5‘-Acryloylnucleosides." Macromolecules 32, no. 20 (October 1999): 6560–64. http://dx.doi.org/10.1021/ma990283j.

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6

Lehman, Niles, and Eric J. Hayden. "Template-Directed RNA Polymerization: The Taming of the Milieu." ChemBioChem 12, no. 18 (October 26, 2011): 2727–28. http://dx.doi.org/10.1002/cbic.201100611.

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7

SHARMA, AJEET K., and DEBASHISH CHOWDHURY. "TEMPLATE-DIRECTED BIOPOLYMERIZATION: TAPE-COPYING TURING MACHINES." Biophysical Reviews and Letters 07, no. 03n04 (December 2012): 135–75. http://dx.doi.org/10.1142/s1793048012300083.

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DNA, RNA and proteins are among the most important macromolecules in a living cell. These molecules are polymerized by molecular machines. These natural nano-machines polymerize such macromolecules, adding one monomer at a time, using another linear polymer as the corresponding template. The machine utilizes input chemical energy to move along the template which also serves as a track for the movements of the machine. In the Alan Turing year 2012, it is worth pointing out that these machines are "tape-copying Turing machines". We review the operational mechanisms of the polymerizer machines and their collective behavior from the perspective of statistical physics, emphasizing their common features in spite of the crucial differences in their biological functions. We also draw the attention of the physics community to another class of modular machines that carry out a different type of template-directed polymerization. We hope this review will inspire new kinetic models for these modular machines.

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8

Li, Heng, Han Miao, Yong Gao, Huaming Li, and Daoyong Chen. "Efficient synthesis of narrowly dispersed amphiphilic double-brush copolymers through the polymerization reaction of macromonomer micelle emulsifiers at the oil–water interface." Polymer Chemistry 7, no. 27 (2016): 4476–85. http://dx.doi.org/10.1039/c6py00705h.

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9

Yang, Guangjie, Tianli Ning, Wei Zhao, Wenxiu Deng, and Xikui Liu. "Robust ambient pressure dried polyimide aerogels and their graphene oxide directed growth of 1D–2D nanohybrid aerogels using water as the only solvent." RSC Advances 7, no. 26 (2017): 16210–16. http://dx.doi.org/10.1039/c7ra01751k.

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Through soft/hard template directed hydrothermal polymerization, we reported the first green approach to the morpho-controlled synthesis of monolithic polyimide aerogels and their graphene nanohybrid aerogel using nothing but water.

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10

Gu, Siyi, Shizhang Fu, Caimei Gong, Sihao Li, Xiaoqing Liu, Yan Lu, Zhongping Wang, and Li Wang. "Directing on-surface polymerization via a substrate-directed molecular template." Physical Chemistry Chemical Physics 24, no. 5 (2022): 3030–34. http://dx.doi.org/10.1039/d1cp04911a.

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11

Blain, J. Craig, Alonso Ricardo, and Jack W. Szostak. "Synthesis and Nonenzymatic Template-Directed Polymerization of 2′-Amino-2′-deoxythreose Nucleotides." Journal of the American Chemical Society 136, no. 5 (January 22, 2014): 2033–39. http://dx.doi.org/10.1021/ja411950n.

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12

Walton, Travis, Saurja DasGupta, Daniel Duzdevich, Seung Soo Oh, and Jack W. Szostak. "In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole–activated substrates." Proceedings of the National Academy of Sciences 117, no. 11 (March 2, 2020): 5741–48. http://dx.doi.org/10.1073/pnas.1914367117.

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The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5′-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide–activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3′-5′ phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.

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13

Marsella, Michael J., Heather D. Maynard, and Robert H. Grubbs. "Template-Directed Ring-Closing Metathesis: Synthesis and Polymerization of Unsaturated Crown Ether Analogs." Angewandte Chemie International Edition in English 36, no. 10 (May 15, 1997): 1101–3. http://dx.doi.org/10.1002/anie.199711011.

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14

van Dijk, Alberdina A., Eugene V. Makeyev, and Dennis H. Bamford. "Initiation of viral RNA-dependent RNA polymerization." Journal of General Virology 85, no. 5 (May 1, 2004): 1077–93. http://dx.doi.org/10.1099/vir.0.19731-0.

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This review summarizes the combined insights from recent structural and functional studies of viral RNA-dependent RNA polymerases (RdRPs) with the primary focus on the mechanisms of initiation of RNA synthesis. Replication of RNA viruses has traditionally been approached using a combination of biochemical and genetic methods. Recently, high-resolution structures of six viral RdRPs have been determined. For three RdRPs, enzyme complexes with metal ions, single-stranded RNA and/or nucleoside triphosphates have also been solved. These advances have expanded our understanding of the molecular mechanisms of viral RNA synthesis and facilitated further RdRP studies by informed site-directed mutagenesis. What transpires is that the basic polymerase right hand shape provides the correct geometrical arrangement of substrate molecules and metal ions at the active site for the nucleotidyl transfer catalysis, while distinct structural elements have evolved in the different systems to ensure efficient initiation of RNA synthesis. These elements feed the template, NTPs and ions into the catalytic cavity, correctly position the template 3′ terminus, transfer the products out of the catalytic site and orchestrate the transition from initiation to elongation.

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15

Hwang, Sohee, Seungho Lee, and Jong-Sung Yu. "Template-directed synthesis of highly ordered nanoporous graphitic carbon nitride through polymerization of cyanamide." Applied Surface Science 253, no. 13 (April 2007): 5656–59. http://dx.doi.org/10.1016/j.apsusc.2006.12.032.

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16

Monnard, Pierre-Alain, and Jack W. Szostak. "Metal-ion catalyzed polymerization in the eutectic phase in water–ice: A possible approach to template-directed RNA polymerization." Journal of Inorganic Biochemistry 102, no. 5-6 (May 2008): 1104–11. http://dx.doi.org/10.1016/j.jinorgbio.2008.01.026.

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17

Dorr, Mark, Philipp Loffler, and Pierre-Alain Monnard. "Non-enzymatic Polymerization of Nucleic Acids from Monomers: Monomer Self- Condensation and Template-Directed Reactions." Current Organic Synthesis 9, no. 6 (November 1, 2012): 735–63. http://dx.doi.org/10.2174/157017912803901691.

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18

Wang, F. J., and L. S. Ripley. "DNA sequence effects on single base deletions arising during DNA polymerization in vitro by Escherichia coli Klenow fragment polymerase." Genetics 136, no. 3 (March 1, 1994): 709–19. http://dx.doi.org/10.1093/genetics/136.3.709.

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Abstract Most single base deletions detected after DNA polymerization in vitro directed by either Escherichia coli DNA polymerase I or its Klenow fragment are opposite Pu in the template. The most frequent mutations were previously found to be associated with the consensus template context 5'-PyTPu-3'. In this study, the predictive power of the consensus sequence on single base deletion frequencies was directly tested by parallel comparison of mutations arising in four related DNAs differing by a single base. G, a deletion hotspot within the template context 5'-TTGA-3', was substituted by each of the 3 other bases. Previous studies had shown that deletions opposite the G were frequent but that deletions opposite its neighboring A were never detected. Based on the predictions of the consensus, the substitution of T for G should produce frequent deletions opposite the neighboring A due to its new 5'-TTTA-3' template context. This prediction was fulfilled; no deletions of this A were detected in the other templates. The consensus further predicted that deletions opposite template C would be lower than those opposite either A or G at the same site and this prediction was also fulfilled. The C substitution also produced a new hotspot for 1 bp deletions 14 bp away. The new hotspot depends on quasi-palindromic misalignment of the newly synthesized DNA strand during polymerization; accurate, but ectopically templated synthesis is responsible for this mutagenesis. Mutations templated by quasi-palindromic misalignments have previously been recognized when they produced complex sequence changes; here we show that this mechanism can produce frequent single base deletions. The unique stimulation of misalignment mutagenesis by the C substitution in the template is consistent with the singular ability of C at that site to contribute to extended complementary pairing during the DNA misalignment that precedes mutagenesis.

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19

Jin, Xin, Shunsheng Cao, Xinhua Yuan, Weiwei Wu, Jie Hu, and Weichen Sheng. "The Preparation of Monodisperse Cationic Polystyrene and its Application to the Synthesis of Hollow Silica Spheres." Australian Journal of Chemistry 63, no. 10 (2010): 1418. http://dx.doi.org/10.1071/ch10093.

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The fabrication of hollow spheres with well defined size and morphology has been attracting much attention due to their unique structures and related physicochemical properties. Among the synthetic methods, the template-directed method is particularly interesting and extensively employed to fabricate hollow spheres due to templates available of essentially any size, shape, and chemistry. As a result, a new monodispersed cationic polystyrene (PS) template in this paper was fabricated by using 2-(methacryloyloxy) ethyltrimethylammonium chloride as co-monomer via emulsifier-free polymerization. The template not only can easily be tuned to the size, but can combine the advantages of hard-templating and soft-templating methods. Subsequently, we used cationic PS particles as templates to prepare hollow silica spheres – the results indicated that cationic templates can attract the assembly of tetraethylorthosilicate hydrolyzate on their surface and that the dissolution of templates can be done in the system of silica encapsulation by modification of the reaction conditions.

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20

Chamanian, Pouyan, and Paul G. Higgs. "Computer simulations of Template-Directed RNA Synthesis driven by temperature cycling in diverse sequence mixtures." PLOS Computational Biology 18, no. 8 (August 24, 2022): e1010458. http://dx.doi.org/10.1371/journal.pcbi.1010458.

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We present simulations of non-enzymatic template-directed RNA synthesis that incorporate primer extension, ligation, melting, and reannealing. Strand growth occurs over multiple heating/cooling cycles, producing strands of several hundred nucleotides in length, starting with random oligomers of 4 to 10 nucleotides. A strand typically grows by only 1 or 2 nucleotides in each cycle. Therefore, a strand is copied from many different templates, not from one specific complementary strand. A diverse sequence mixture is produced, and there is no exact copying of sequences, even if single base additions are fully accurate (no mutational errors). It has been proposed that RNA systems may contain a virtual circular genome, in which sequences partially overlap in a way that is mutually catalytic. We show that virtual circles do not emerge naturally in our simulations, and that a system initiated with a virtual circle can only maintain itself if there are no mutational errors and there is no input of new sequences formed by random polymerization. Furthermore, if a virtual sequence and its complement contain repeated short words, new sequences can be produced that were not on the original virtual circle. Therefore the virtual circle sequence cannot maintain itself. Functional sequences with secondary structures contain complementary words on opposite sides of stem regions. Both these words are repeated in the complementary sequence; hence, functional sequences cannot be encoded on a virtual circle. Additionally, we consider sequence replication in populations of protocells. We suppose that functional ribozymes benefit the cell which contains them. Nevertheless, scrambling of sequences occurs, and the functional sequence is not maintained, even when under positive selection.

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21

Klarmann, G. J., C. A. Schauber, and B. D. Preston. "Template-directed pausing of DNA synthesis by HIV-1 reverse transcriptase during polymerization of HIV-1 sequences in vitro." Journal of Biological Chemistry 268, no. 13 (May 1993): 9793–802. http://dx.doi.org/10.1016/s0021-9258(18)98417-6.

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22

Zhang, Zhuang, Guangming Chen, Hanfu Wang, and Xin Li. "Template-Directed In Situ Polymerization Preparation of Nanocomposites of PEDOT:PSS-Coated Multi-Walled Carbon Nanotubes with Enhanced Thermoelectric Property." Chemistry - An Asian Journal 10, no. 1 (October 22, 2014): 149–53. http://dx.doi.org/10.1002/asia.201403100.

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23

Job, C., D. Shire, V. Sure, and D. Job. "A DNA-dependent RNA synthesis by wheat-germ RNA polymerase II insensitive to the fungal toxin α-amanitin." Biochemical Journal 285, no. 1 (July 1, 1992): 85–90. http://dx.doi.org/10.1042/bj2850085.

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Wheat-germ RNA polymerase II is able to catalyse a DNA-dependent reaction of RNA synthesis in the presence of a high concentration (1 mg/ml) of the fungal toxin alpha-amanitin. This anomalous reaction is specifically directed by single-stranded or double-stranded homopolymer templates, such as poly(dC) or poly(dC).poly(dG), and occurs in the presence of either Mn2+ or Mg2+ as the bivalent metal cofactor. In contrast, the transcription of other synthetic templates, such as poly(dT), poly(dA).poly(dT) or poly[d(A-T)] is completely abolished in the presence of 1 microgram of alpha-amanitin/ml, in agreement with well-established biochemical properties of class II RNA polymerases. Size analysis of reaction products resulting from transcription of (dC)n templates of defined lengths suggests that polymerization of RNA chains proceeds through a slippage mechanism. The fact that alpha-amanitin does not impede this synthetic reaction implies that the amatoxin interferes with the translocation of wheat-germ RNA polymerase II along the DNA template.

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24

LOYA, Shoshana, Amira RUDI, Yoel KASHMAN, and Amnon HIZI. "Polycitone A, a novel and potent general inhibitor of retroviral reverse transcriptases and cellular DNA polymerases." Biochemical Journal 344, no. 1 (November 8, 1999): 85–92. http://dx.doi.org/10.1042/bj3440085.

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Polycitone A, an aromatic alkaloid isolated from the ascidian Polycitorsp. exhibits potent inhibitory capacity of both RNA- and DNA-directed DNA polymerases. The drug inhibits retroviral reverse transcriptase (RT) [i.e. of human immunodeficiency virus type 1 (HIV), murine leukaemia virus (MLV) and mouse mammary tumour virus (MMTV)] as efficiently as cellular DNA polymerases (i.e. of both DNA polymerases α and β and Escherichia coliDNA polymerase I). The mode and mechanism of inhibition of the DNA-polymerase activity associated with HIV-1 RT by polycitone A have been studied. The results suggest that the inhibitory capacity of the DNA polymerase activity is independent of the template-primer used. The RNase H function, on the other hand, is hardly affected by this inhibitor. Polycitone A has been shown to interfere with DNA primer extension as well as with the formation of the RT-DNA complex. Steady-state kinetic studies demonstrate that this inhibitor can be considered as an allosteric inhibitor of HIV-1 RT. The target site on the enzyme may be also spatially related to the substrate binding site, since this inhibitor behaves competitively with respect to dTTP with poly(rA)˙oligo(dT) as template primer. Chemical transformations of the five phenol groups of polycitone A by methoxy groups have a determinant effect on the inhibitory potency. Thus, the pentamethoxy derivative which is devoid of all hydroxy moieties, loses significantly, by 40-fold, the ability to inhibit the DNA polymerase function. Furthermore, this analogue lacks the ability to inhibit DNA primer extension as well as the formation of the RT-DNA complex. Indeed, inhibition of the first step in DNA polymerization, the formation of the RT-DNA complex, and hence, of the overall process, could serve as a model for a universal inhibitor of the superfamily of DNA polymerases.

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25

Li, Zhi, and D. Lorne J. Tyrrell. "Expression of an enzymatically active polymerase of human hepatitis B virus in a coupled transcription-translation system." Biochemistry and Cell Biology 77, no. 2 (June 20, 1999): 119–26. http://dx.doi.org/10.1139/o99-024.

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Genome replication of hepadnavirus proceeds by reverse transcription from a viral pregenomic RNA template by a virally encoded polymerase that possesses protein-priming, reverse transcriptase, DNA polymerase, and RNase H activities. Characterization of this enzyme has been hampered by failure to purify an active enzyme from virions and difficulties in expressing an active polymerase in heterologous systems. In this study, we constructed human hepatitis B virus polymerase cDNA under the control of a phage T7 promoter and expressed it in a rabbit reticulocyte lysate-coupled transcription-translation system. In vitro site-directed mutagenesis confirmed that the recombinant polymerase cDNA produced three products: a full-length protein (~94 kDa), an internally initiated protein (~81 kDa), and an N-terminal protein (~40 kDa). The in vitro expressed polymerase possessed protein priming activity, as demonstrated by32P-dGTP-labeling of the full size polymerase and the N-terminal portion of the molecule in an in vitro priming assay. The polymerase also exhibited polymerization activity, as detected in an in vitro polymerase assay by incorporation of radionucleotides into acid-precipitable polynucleotides and by synthesis of human hepatitis B virus (HBV) specific DNA with product lengths between 100 and 500 nucleotides. In addition, the polymerase was found to use an RNA sequence bearing HBV DR1/epsilon stem-loop motif as a template for DNA synthesis. Both the protein-priming and the reverse transcription activities of this recombinant polymerase are dependent on the RNA fragment containing the HBV DR1/epsilon stem-loop sequence known to be required for the polymerase activities. The in vitro systems used in this study will be applicable to further functional and biochemical studies of this enzyme.Key words: hepadnavirus, HBV polymerase, protein priming, reverse transcription, rabbit reticulocyte lysate.

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26

Filipowsky, Mark E., Mary L. Kopka, Michelle Brazil-Zison, J. William Lown, and Richard E. Dickerson. "Linked Lexitropsins and thein VitroInhibition of HIV-1 Reverse Transcriptase RNA-Directed DNA Polymerization: A Novel Induced-Fit of 3,5m-Pyridyl Bisdistamycin to Enzyme-Associated Template-Primer†." Biochemistry 35, no. 48 (January 1996): 15397–410. http://dx.doi.org/10.1021/bi961604b.

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27

Edelsztein, Valeria C., Andrea S. Mac Cormack, Matías Ciarlantini, and Pablo H. Di Chenna. "Self-assembly of 2,3-dihydroxycholestane steroids into supramolecular organogels as a soft template for the in-situ generation of silicate nanomaterials." Beilstein Journal of Organic Chemistry 9 (September 9, 2013): 1826–36. http://dx.doi.org/10.3762/bjoc.9.213.

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Supramolecular gels are an important and interesting class of soft materials that show great potential for many applications. Most of them have been discovered serendipitously, and understanding the supramolecular self-assembly that leads to the formation of the gel superstructure is the key to the directed design of new organogels. We report herein the organogelating property of four stereoisomers of the simple steroid 2,3-dihydroxycholestane. Only the isomer with the trans-diaxial hydroxy groups had the ability to gelate a broad variety of liquids and, thus, to be a super-organogelator for hydrocarbons. The scope of solvent gelation was analysed with regard to two solvent parameters, namely the Kamlet–Taft and the Hansen solubility parameters. The best correlation was observed with the Hansen approach that revealed the existence of two clear gelation zones. We propose a general model of self-assembly through multiple intermolecular hydrogen bonds between the 1,2-dihydroxy system, which is based on experimental data and computational simulations revealing the importance of the di-axial orientation of the hydroxy groups for the one-dimensional self-assembly. Under controlled conditions, the fibrillar superstructure of the organogel was successfully used as a template for the in-situ sol–gel polymerization of tetraethoxysilane and the further preparation of silica nanotubes. We propose that the driving forces for templating are hydrogen bonding and electrostatic interactions between the anionic silicate intermediate species and the self-assembled fibrillar network.

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28

Lelyveld, Victor S., Wen Zhang, and Jack W. Szostak. "Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase." Proceedings of the National Academy of Sciences 117, no. 13 (March 18, 2020): 7276–83. http://dx.doi.org/10.1073/pnas.1922400117.

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All known polymerases copy genetic material by catalyzing phosphodiester bond formation. This highly conserved activity proceeds by a common mechanism, such that incorporated nucleoside analogs terminate chain elongation if the resulting primer strand lacks a terminal hydroxyl group. Even conservatively substituted 3′-amino nucleotides generally act as chain terminators, and no enzymatic pathway for their polymerization has yet been found. Although 3′-amino nucleotides can be chemically coupled to yield stable oligonucleotides containing N3′→P5′ phosphoramidate (NP) bonds, no such internucleotide linkages are known to occur in nature. Here, we report that 3′-amino terminated primers are, in fact, slowly extended by the DNA polymerase from B. stearothermophilus in a template-directed manner. When its cofactor is Ca2+ rather than Mg2+, the reaction is fivefold faster, permitting multiple turnover NP bond formation to yield NP-DNA strands from the corresponding 3′-amino-2′,3′-dideoxynucleoside 5′-triphosphates. A single active site mutation further enhances the rate of NP-DNA synthesis by an additional 21-fold. We show that DNA-dependent NP-DNA polymerase activity depends on conserved active site residues and propose a likely mechanism for this activity based on a series of crystal structures of bound complexes. Our results significantly broaden the catalytic scope of polymerase activity and suggest the feasibility of a genetic transition between native nucleic acids and NP-DNA.

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29

Kurz, Markus, Karin Schütz, and Michael Göbel. "Looking for catalysis in the template-directed non-enzymatic polymerization of RNA: Acridine-labelled oligonucleotides as a tool for the rapid and precise determination of chain elongation kinetics." Origins of Life and Evolution of the Biosphere 26, no. 3-5 (October 1996): 263–64. http://dx.doi.org/10.1007/bf02459748.

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30

Bastian, Caleb Deen, and Hershel Rabitz. "Hitting Times of Some Critical Events in RNA Origins of Life." Life 11, no. 12 (December 17, 2021): 1419. http://dx.doi.org/10.3390/life11121419.

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Can a replicase be found in the vast sequence space by random drift? We partially answer this question through a proof-of-concept study of the times of occurrence (hitting times) of some critical events in the origins of life for low-dimensional RNA sequences using a mathematical model and stochastic simulation studies from Python software. We parameterize fitness and similarity landscapes for polymerases and study a replicating population of sequences (randomly) participating in template-directed polymerization. Under the ansatz of localization where sequence proximity correlates with spatial proximity of sequences, we find that, for a replicating population of sequences, the hitting and establishment of a high-fidelity replicator depends critically on the polymerase fitness and sequence (spatial) similarity landscapes and on sequence dimension. Probability of hitting is dominated by landscape curvature, whereas hitting time is dominated by sequence dimension. Surface chemistries, compartmentalization, and decay increase hitting times. Compartmentalization by vesicles reveals a trade-off between vesicle formation rate and replicative mass, suggesting that compartmentalization is necessary to ensure sufficient concentration of precursors. Metabolism is thought to be necessary to replication by supplying precursors of nucleobase synthesis. We suggest that the dynamics of the search for a high-fidelity replicase evolved mostly during the final period and, upon hitting, would have been followed by genomic adaptation of genes and to compartmentalization and metabolism, effecting degree-of-freedom gains of replication channel control over domain and state to ensure the fidelity and safe operations of the primordial genetic communication system of life.

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31

Gao, S. "Building Fluorescent Sensors for Carbohydrates Using Template-Directed Polymerizations." Bioorganic Chemistry 29, no. 5 (October 2001): 308–20. http://dx.doi.org/10.1006/bioo.2001.1219.

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32

Higgs, Paul G. "When Is a Reaction Network a Metabolism? Criteria for Simple Metabolisms That Support Growth and Division of Protocells." Life 11, no. 9 (September 14, 2021): 966. http://dx.doi.org/10.3390/life11090966.

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With the aim of better understanding the nature of metabolism in the first cells and the relationship between the origin of life and the origin of metabolism, we propose three criteria that a chemical reaction system must satisfy in order to constitute a metabolism that would be capable of sustaining growth and division of a protocell. (1) Biomolecules produced by the reaction system must be maintained at high concentration inside the cell while they remain at low or zero concentration outside. (2) The total solute concentration inside the cell must be higher than outside, so there is a positive osmotic pressure that drives cell growth. (3) The metabolic rate (i.e., the rate of mass throughput) must be higher inside the cell than outside. We give examples of small-molecule reaction systems that satisfy these criteria, and others which do not, firstly considering fixed-volume compartments, and secondly, lipid vesicles that can grow and divide. If the criteria are satisfied, and if a supply of lipid is available outside the cell, then continued growth of membrane surface area occurs alongside the increase in volume of the cell. If the metabolism synthesizes more lipid inside the cell, then the membrane surface area can increase proportionately faster than the cell volume, in which case cell division is possible. The three criteria can be satisfied if the reaction system is bistable, because different concentrations can exist inside and out while the rate constants of all the reactions are the same. If the reaction system is monostable, the criteria can only be satisfied if there is a reason why the rate constants are different inside and out (for example, the decay rates of biomolecules are faster outside, or the formation rates of biomolecules are slower outside). If this difference between inside and outside does not exist, a monostable reaction system cannot sustain cell growth and division. We show that a reaction system for template-directed RNA polymerization can satisfy the requirements for a metabolism, even if the small-molecule reactions that make the single nucleotides do not.

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33

LOYA, Shoshana, Amira RUDI, Yoel KASHMAN, and Amnon HIZI. "Mode of inhibition of HIV-1 reverse transcriptase by polyacetylenetriol, a novel inhibitor of RNA- and DNA-directed DNA polymerases." Biochemical Journal 362, no. 3 (March 8, 2002): 685–92. http://dx.doi.org/10.1042/bj3620685.

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Polyacetylenetriol (PAT), a natural marine product from the Mediterranean sea sponge Petrosia sp., was found to be a novel general potent inhibitor of DNA polymerases. It inhibits equally well the RNA- and DNA-dependent DNA polymerase activities of retroviral reverse transcriptases (RTs) (i.e. of HIV, murine leukaemia virus and mouse mammary tumour virus) as well as cellular DNA polymerases (i.e. DNA polymerases α and β and Escherichia coli polymerase I). A study of the mode and mechanism of the polymerase inhibition by PAT has been conducted with HIV-1 RT. PAT was shown to be a reversible non-competitive inhibitor. PAT binds RT independently and at a site different from that of the primer-template and dNTP substrates with high affinity (Ki = 0.51μM and Ki = 0.53μM with dTTP and with dGTP as the variable substrates respectively). Blocking the polar hydroxy groups of PAT has only a marginal effect on the inhibitory capacity, thus hydrophobic interactions are likely to play a major role in inhibiting RT. Preincubation of RT with the primer-template substrate prior to the interaction with PAT reduces substantially the inhibition capacity, probably by preventing these contacts. PAT does not interfere with the first step of polymerization, the binding of RT to DNA, nor does the inhibitor interfere with the binding of dNTP to RT/DNA complex, as evident from the steady-state kinetic study, whereby Km remains unchanged. We assume, therefore, that PAT interferes with subsequent catalytic steps of DNA polymerization. The inhibitor may alter the optimal stereochemistry of the polymerase active site relative to the primer terminus, bound dNTP and the metal ions that are crucial for efficient catalysis or, alternatively, may interfere with the thumb sub-domain movement and, thus, with the translocation of the primer-template following nucleotide incorporation.

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34

Abdi, Mahnaz, Paridah Md Tahir, Rawaida Liyana, and Ramin Javahershenas. "A Surfactant Directed Microcrystalline Cellulose/Polyaniline Composite with Enhanced Electrochemical Properties." Molecules 23, no. 10 (September 26, 2018): 2470. http://dx.doi.org/10.3390/molecules23102470.

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In this study a cationic surfactant, cetyltrimethylammonium bromide (CTAB), was used as a soft template for in situ chemical polymerization of aniline on the surface of microcrystalline cellulose (MCC). The morphology of the wire-like and porous nanostructure of the resulting composite was highly dependent on the MCC and CTAB concentrations. The effect of the MCC and CTAB concentrations on the electrochemical and morphological properties of the polyaniline (PAni) nanocomposite was studied. Cyclic voltammograms of modified PAni/MCC/CTAB electrode displayed a high current response and the effect of scan rate on the current response confirmed a diffusion controlled process on the surface of the electrode that makes it suitable for sensor applications. The overlapping characteristic peaks of pure PAni and MCC caused peak broadening at 3263 cm−1 in the IR spectra of PAni/MCC/CTAB nanocomposite that revealed the interaction between NH of PAni and OH group of MCC via electrostatic interactions. The addition of MCC to PAni through chemical polymerization decreased the thermal stability of composite compared to pure PAni. Lower crystallinity was observed in the XRD diffractogram, with 2 theta values of 22.8, 16.5, and 34.6 for PAni/MCC, confirming the formation of PAni on the MCC surface.

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35

Stribling, Roscoe, and Stanley L. Miller. "Attempted non-enzymatic template-directed polymerizations of uridine and uridine analogs on polyadenosine: Implications for the nature of the first genetic material." Origins of Life and Evolution of the Biosphere 19, no. 3-5 (May 1989): 329–30. http://dx.doi.org/10.1007/bf02388875.

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36

Matsubara, Yoshiya J., Nobuto Takeuchi, and Kunihiko Kaneko. "Avoidance of error catastrophe via proofreading innate to template-directed polymerization." Physical Review Research 5, no. 1 (March 13, 2023). http://dx.doi.org/10.1103/physrevresearch.5.013170.

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37

Zhang, Wen, Seohyun Chris Kim, Chun Pong Tam, Victor S. Lelyveld, Saikat Bala, John C. Chaput, and Jack W. Szostak. "Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization." Nucleic Acids Research, December 21, 2020. http://dx.doi.org/10.1093/nar/gkaa1215.

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Abstract The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3′-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.

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Gudkov, Maksim V., Peter N. Brevnov, Maxim K. Rabchinskii, Marina V. Baidakova, Dina Yu Stolyarova, Grigorii A. Antonov, Maria A. Yagovkina, et al. "Template-Directed Polymerization Strategy for Producing rGO/UHMWPE Composite Aerogels with Tunable Properties." ACS Applied Materials & Interfaces, January 17, 2023. http://dx.doi.org/10.1021/acsami.2c19649.

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39

Poudyal, Raghav R., Rebecca M. Guth-Metzler, Andrew J. Veenis, Erica A. Frankel, Christine D. Keating, and Philip C. Bevilacqua. "Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates." Nature Communications 10, no. 1 (January 30, 2019). http://dx.doi.org/10.1038/s41467-019-08353-4.

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40

Takahashi, Shuntaro, Saki Matsumoto, Pallavi Chilka, Saptarshi Ghosh, Hiromichi Okura, and Naoki Sugimoto. "Dielectricity of a molecularly crowded solution accelerates NTP misincorporation during RNA-dependent RNA polymerization by T7 RNA polymerase." Scientific Reports 12, no. 1 (January 21, 2022). http://dx.doi.org/10.1038/s41598-022-05136-8.

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AbstractIn biological systems, the synthesis of nucleic acids, such as DNA and RNA, is catalyzed by enzymes in various aqueous solutions. However, substrate specificity is derived from the chemical properties of the residues, which implies that perturbations of the solution environment may cause changes in the fidelity of the reaction. Here, we investigated non-promoter-based synthesis of RNA using T7 RNA polymerase (T7 RNAP) directed by an RNA template in the presence of polyethylene glycol (PEG) of various molecular weights, which can affect polymerization fidelity by altering the solution properties. We found that the mismatch extensions of RNA propagated downstream polymerization. Furthermore, PEG promoted the polymerization of non-complementary ribonucleoside triphosphates, mainly due to the decrease in the dielectric constant of the solution. These results indicate that the mismatch extension of RNA-dependent RNA polymerization by T7 RNAP is driven by the stacking interaction of bases of the primer end and the incorporated nucleotide triphosphates (NTP) rather than base pairing between them. Thus, proteinaceous RNA polymerase may display different substrate specificity with changes in dielectricity caused by molecular crowding conditions, which can result in increased genetic diversity without proteinaceous modification.

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Wang, Luyao, Qingbo Wang, Emil Rosqvist, Jan‐Henrik Smått, Qiwen Yong, Lippo Lassila, Jouko Peltonen, et al. "Template‐Directed Polymerization of Binary Acrylate Monomers on Surface‐Activated Lignin Nanoparticles in Toughening of Bio‐Latex Films." Small, March 15, 2023, 2207085. http://dx.doi.org/10.1002/smll.202207085.

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42

Sivashankari, Ramamoorthi M., Maierwufu Mierzati, Yuki Miyahara, Shoji Mizuno, Christopher T. Nomura, Seiichi Taguchi, Hideki Abe, and Takeharu Tsuge. "Exploring Class I polyhydroxyalkanoate synthases with broad substrate specificity for polymerization of structurally diverse monomer units." Frontiers in Bioengineering and Biotechnology 11 (February 21, 2023). http://dx.doi.org/10.3389/fbioe.2023.1114946.

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Polyhydroxyalkanoate (PHA) synthases (PhaCs) are key enzymes in PHA polymerization. PhaCs with broad substrate specificity are attractive for synthesizing structurally diverse PHAs. In the PHA family, 3-hydroxybutyrate (3HB)-based copolymers are industrially produced using Class I PhaCs and can be used as practical biodegradable thermoplastics. However, Class I PhaCs with broad substrate specificities are scarce, prompting our search for novel PhaCs. In this study, four new PhaCs from the bacteria Ferrimonas marina, Plesiomonas shigelloides, Shewanella pealeana, and Vibrio metschnikovii were selected via a homology search against the GenBank database, using the amino acid sequence of Aeromonas caviae PHA synthase (PhaCAc), a Class I enzyme with a wide range of substrate specificities, as a template. The four PhaCs were characterized in terms of their polymerization ability and substrate specificity, using Escherichia coli as a host for PHA production. All the new PhaCs were able to synthesize P(3HB) in E. coli with a high molecular weight, surpassing PhaCAc. The substrate specificity of PhaCs was evaluated by synthesizing 3HB-based copolymers with 3-hydroxyhexanoate, 3-hydroxy-4-methylvalerate, 3-hydroxy-2-methylbutyrate, and 3-hydroxypivalate monomers. Interestingly, PhaC from P. shigelloides (PhaCPs) exhibited relatively broad substrate specificity. PhaCPs was further engineered through site-directed mutagenesis, and the variant resulted in an enzyme with improved polymerization ability and substrate specificity.

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Pauszek, Raymond F., Rajan Lamichhane, Arishma Rajkarnikar Singh, and David P. Millar. "Single-molecule view of coordination in a multi-functional DNA polymerase." eLife 10 (March 11, 2021). http://dx.doi.org/10.7554/elife.62046.

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Replication and repair of genomic DNA requires the actions of multiple enzymatic functions that must be coordinated in order to ensure efficient and accurate product formation. Here, we have used single-molecule FRET microscopy to investigate the physical basis of functional coordination in DNA polymerase I (Pol I) from Escherichia coli, a key enzyme involved in lagging-strand replication and base excision repair. Pol I contains active sites for template-directed DNA polymerization and 5’ flap processing in separate domains. We show that a DNA substrate can spontaneously transfer between polymerase and 5’ nuclease domains during a single encounter with Pol I. Additionally, we show that the flexibly tethered 5’ nuclease domain adopts different positions within Pol I-DNA complexes, depending on the nature of the DNA substrate. Our results reveal the structural dynamics that underlie functional coordination in Pol I and are likely relevant to other multi-functional DNA polymerases.

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44

Palanivelu, Peramachi. "Eukaryotic Multi-subunit DNA dependent RNA Polymerases: An Insight into Their Active Sites and Catalytic Mechanism." International Journal of Biochemistry Research & Review, July 17, 2019, 1–60. http://dx.doi.org/10.9734/ijbcrr/2019/v26i330097.

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Aim: To analyze the most complex multi-subunit (MSU) DNA dependent RNA polymerases (RNAPs) of eukaryotic organisms and find out conserved motifs, metal binding sites and catalytic regions and propose a plausible mechanism of action for these complex eukaryotic MSU RNAPs, using yeast (Saccharomyces cerevisiae) RNAP II, as a model enzyme. Study Design: Bioinformatics, Biochemical, Site-directed mutagenesis and X-ray crystallographic data were analyzed. Place and Duration of Study: School of Biotechnology, Madurai Kamaraj University, Madurai, India, between 2007- 2013. Methodology: Bioinformatics, Biochemical, Site-directed mutagenesis (SDM) and X-ray crystallographic data of the enzyme were analyzed. The advanced version of Clustal Omega was used for protein sequence analysis of the MSU DNA dependent RNAPs from various eukaryotic sources. Along with the conserved motifs identified by the bioinformatics analysis, the data already available by biochemical and SDM experiments and X-ray crystallographic analysis of these enzymes were used to confirm the possible amino acids involved in the active sites and catalysis. Results: Multiple sequence alignment (MSA) of RNAPs from different eukaryotic organisms showed a large number of highly conserved motifs among them. Possible catalytic regions in the catalytic subunits of the yeast Rpb2 (= β in eubacteria) and Rpb1 (= β’ in eubacteria) consist of an absolutely conserved amino acid R, in contrast to a K that was reported for DNA polymerases and single subunit (SSU) RNAPs. However, the invariant ‘gatekeeper/DNA template binding’ YG pair that was reported in all SSU RNAPs, prokaryotic MSU RNAPs and DNA polymerases is also highly conserved in eukaryotic Rpb2 initiation subunits, but unusually a KG pair is found in higher eukaryotes including the human RNAPs. Like the eubacterial initiation subunits of MSU RNAPs, the eukaryotic initiation subunits, viz. Rpb2, exhibit very similar active site and catalytic regions but slightly different distance conservations between the template binding YG/KG pair and the catalytic R. In the eukaryotic initiation subunits, the proposed catalytic R is placed at the -9th position from the YG/KG pair and an invariant R is placed at -5 which are implicated to play a role in nucleoside triphosphate (NTP) selection as reported for SSU RNAPs (viral family) and DNA polymerases. Similarly, the eukaryotic elongation subunits (Rpb1) are also found to be very much homologous to the elongation subunits (β’) of prokaryotes. Interestingly, the catalytic regions are highly conserved, and the metal binding sites are absolutely conserved as in prokaryotic MSU RNAPs. In eukaryotes, the template binding YG pair is replaced with an FG pair. Another interesting observation is, similar to the prokaryotic β’ subunits, in the eukaryotic Rpb1 elongation subunits also, the proposed catalytic R is placed double the distance, i.e., -18 amino acids downstream from the FG pair unlike in the SSU RNAPs and DNA polymerases where the distance is only -8 amino acids downstream from the YG pair. Thus, the completely conserved FG pair, catalytic R with an invariant R, at -6th position are proposed to play a crucial role in template binding, NTP selection and polymerization reactions in the elongation subunits of eukaryotic MSU RNAPs. Moreover, the Zn binding motif with the three completely conserved Cs is also highly conserved in the eukaryotic elongation subunits. Another important difference is that the catalytic region is placed very close to the N-terminal region in eukaryotes. Conclusions: Unlike reported for the DNA polymerases and SSU RNA polymerases, the of eukaryotic MSU RNAPs use an R as the catalytic amino acid and exhibit a different distance conservation in the initiation and elongation subunits. An invariant Zn2+ binding motif found in the Rpb1 elongation subunits is proposed to participate in proof-reading function. Differences in the active sites of bacterial and human RNA polymerases may pave the way for the design of new and effective drugs for many bacterial infections, including the multidrug resistant strains which are a global crisis at present.

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