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Journal articles on the topic 'DNA Substrates'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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1

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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2

Lu, Yue, and Piero Bianco. "High-yield purification of exceptional-quality, single-molecule DNA substrates." Journal of Biological Methods 8, no. 1 (2021): e145. http://dx.doi.org/10.14440/jbm.2021.350.

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Single-molecule studies involving DNA or RNA, require homogeneous preparations of nucleic acid substrates of exceptional quality. Over the past several years, a variety of methods have been published describing different purification methods but these are frustratingly inconsistent with variable yields even in the hands of experienced bench scientists. To address these issues, we present an optimized and straightforward, column-based approach that is reproducible and produces high yields of substrates or substrate components of exceptional quality. Central to the success of the method presente

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3

Deng, Chuyun, Wanyun Ma та Jia-Lin Sun. "Fabrication of Highly Rough Ag Nanobud Substrates and Surface-Enhanced Raman Scattering ofλ-DNA Molecules". Journal of Nanomaterials 2012 (2012): 1–5. http://dx.doi.org/10.1155/2012/820739.

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Raman scattering signals can be enhanced by several orders of magnitude on surface-enhanced Raman scattering (SERS) substrates made from noble metal nanostructures. Some SERS substrates are even able to detect single-molecule Raman signals. A novel silver nanobud (AgNB) substrate with superior SERS activity was fabricated with a solid-state ionics method. The AgNB substrate was formed by tightly collocated unidirectional 100 nm size silver buds, presenting a highly rough surface topography. Distinct SERS signals of singleλ-DNA molecules in water were detected on AgNB substrates. AgNB substrate

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4

Hsieh, C. L., R. P. McCloskey, E. Radany, and M. R. Lieber. "V(D)J recombination: evidence that a replicative mechanism is not required." Molecular and Cellular Biology 11, no. 8 (1991): 3972–77. http://dx.doi.org/10.1128/mcb.11.8.3972-3977.1991.

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We examined a series of extrachromosomal DNA substrates for V(D)J recombination under replicating and nonreplicating conditions. Complete and partial replications were examined by monitoring the loss of prokaryote-specific adenine methylation at 14 to 22 MboI-DpnI restriction sites (GATC) on the substrates. Some of these sites are within 2 bases of the signal sequence ends. We found that neither coding joint nor signal joint formation requires substrate replication. After ruling out replication as a substrate requirement, we determined whether replication had any effect on the efficiency of V(

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5

Hsieh, C. L., R. P. McCloskey, E. Radany, and M. R. Lieber. "V(D)J recombination: evidence that a replicative mechanism is not required." Molecular and Cellular Biology 11, no. 8 (1991): 3972–77. http://dx.doi.org/10.1128/mcb.11.8.3972.

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We examined a series of extrachromosomal DNA substrates for V(D)J recombination under replicating and nonreplicating conditions. Complete and partial replications were examined by monitoring the loss of prokaryote-specific adenine methylation at 14 to 22 MboI-DpnI restriction sites (GATC) on the substrates. Some of these sites are within 2 bases of the signal sequence ends. We found that neither coding joint nor signal joint formation requires substrate replication. After ruling out replication as a substrate requirement, we determined whether replication had any effect on the efficiency of V(

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6

Craggs, Timothy D., Marko Sustarsic, Anne Plochowietz, et al. "Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase." Nucleic Acids Research 47, no. 20 (2019): 10788–800. http://dx.doi.org/10.1093/nar/gkz797.

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Abstract DNA-binding proteins utilise different recognition mechanisms to locate their DNA targets; some proteins recognise specific DNA sequences, while others interact with specific DNA structures. While sequence-specific DNA binding has been studied extensively, structure-specific recognition mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I Klenow Fragment (Pol) substrates both alone and in DNA–Pol complexes. Using a docking approach based on a network of 73 distances collected using single-molecule FRET

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7

Burke, Cassandra R., and Andrej Lupták. "DNA synthesis from diphosphate substrates by DNA polymerases." Proceedings of the National Academy of Sciences 115, no. 5 (2018): 980–85. http://dx.doi.org/10.1073/pnas.1712193115.

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The activity of DNA polymerase underlies numerous biotechnologies, cell division, and therapeutics, yet the enzyme remains incompletely understood. We demonstrate that both thermostable and mesophilic DNA polymerases readily utilize deoxyribonucleoside diphosphates (dNDPs) for DNA synthesis and inorganic phosphate for the reverse reaction, that is, phosphorolysis of DNA. For Taq DNA polymerase, the KMs of the dNDP and phosphate substrates are ∼20 and 200 times higher than for dNTP and pyrophosphate, respectively. DNA synthesis from dNDPs is about 17 times slower than from dNTPs, and DNA phosph

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8

Victorova, Lyubov, Vasily Sosunov, Alexander Skoblov, Alexander Shipytsin, and Alexander Krayevsky. "New substrates of DNA polymerases." FEBS Letters 453, no. 1-2 (1999): 6–10. http://dx.doi.org/10.1016/s0014-5793(99)00615-8.

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9

Chiriboga, Matthew, Christopher M. Green, Divita Mathur, et al. "Structural and optical variation of pseudoisocyanine aggregates nucleated on DNA substrates." Methods and Applications in Fluorescence 11, no. 1 (2023): 014003. http://dx.doi.org/10.1088/2050-6120/acb2b4.

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Abstract Coherently coupled pseudoisocyanine (PIC) dye aggregates have demonstrated the ability to delocalize electronic excitations and ultimately migrate excitons with much higher efficiency than similar designs where excitations are isolated to individual chromophores. Here, we report initial evidence of a new type of PIC aggregate, formed through heterogeneous nucleation on DNA oligonucleotides, displaying photophysical properties that differ significantly from previously reported aggregates. This new aggregate, which we call the super aggregate (SA) due to the need for elevated dye excess

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10

AHN, Jinwoo, Vadim S. KRAYNOV, Xuejun ZHONG, Brian G. WERNEBURG та Ming-Daw TSAI. "DNA polymerase β: effects of gapped DNA substrates on dNTP specificity, fidelity, processivity and conformational changes1". Biochemical Journal 331, № 1 (1998): 79–87. http://dx.doi.org/10.1042/bj3310079.

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Pre-steady-state kinetic analysis was used to compare the catalytic properties of DNA polymerase β (Pol β) for single-base gap-filling and regular duplex DNA synthesis. The rate of polymerization (kpol) and the apparent equilibrium dissociation constant of dNTP (Kd) were determined with single-nucleotide gapped DNA substrates for all four possible correct base pairs and twelve possible incorrect base pairs, and the results were compared with those obtained previously with non-gapped primer/template duplex DNA substrates. For correct dNTP incorporation, the use of single-nucleotide gapped DNA l

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11

Maekawa, Masashi, and Shigeki Higashiyama. "The Roles of SPOP in DNA Damage Response and DNA Replication." International Journal of Molecular Sciences 21, no. 19 (2020): 7293. http://dx.doi.org/10.3390/ijms21197293.

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Speckle-type BTB/POZ protein (SPOP) is a substrate recognition receptor of the cullin-3 (CUL3)/RING type ubiquitin E3 complex. To date, approximately 30 proteins have been identified as ubiquitinated substrates of the CUL3/SPOP complex. Pathologically, missense mutations in the substrate-binding domain of SPOP have been found in prostate and endometrial cancers. Prostate and endometrial cancer-associated SPOP mutations lose and increase substrate-binding ability, respectively. Expression of these SPOP mutants, thus, causes aberrant turnovers of the substrate proteins, leading to tumor formatio

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12

Whitaker, Neal, Yuqing Chen, Simon J. Jakubowski, Mayukh K. Sarkar, Feng Li, and Peter J. Christie. "The All-Alpha Domains of Coupling Proteins from the Agrobacterium tumefaciens VirB/VirD4 and Enterococcus faecalis pCF10-Encoded Type IV Secretion Systems Confer Specificity to Binding of Cognate DNA Substrates." Journal of Bacteriology 197, no. 14 (2015): 2335–49. http://dx.doi.org/10.1128/jb.00189-15.

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ABSTRACTBacterial type IV coupling proteins (T4CPs) bind and mediate the delivery of DNA substrates through associated type IV secretion systems (T4SSs). T4CPs consist of a transmembrane domain, a conserved nucleotide-binding domain (NBD), and a sequence-variable helical bundle called the all-alpha domain (AAD). In the T4CP structural prototype, plasmid R388-encoded TrwB, the NBD assembles as a homohexamer resembling RecA and DNA ring helicases, and the AAD, which sits at the channel entrance of the homohexamer, is structurally similar to N-terminal domain 1 of recombinase XerD. Here, we defin

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13

Qi, Mingxuan, Peijun Shi, Xiaokang Zhang, et al. "Reconfigurable DNA triplex structure for pH responsive logic gates." RSC Advances 13, no. 15 (2023): 9864–70. http://dx.doi.org/10.1039/d3ra00536d.

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We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.

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14

Bullard, Desmond R., and Richard P. Bowater. "Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4." Biochemical Journal 398, no. 1 (2006): 135–44. http://dx.doi.org/10.1042/bj20060313.

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The genome of bacteriophage T4 encodes three polynucleotide ligases, which seal the backbone of nucleic acids during infection of host bacteria. The T4Dnl (T4 DNA ligase) and two RNA ligases [T4Rnl1 (T4 RNA ligase 1) and T4Rnl2] join a diverse array of substrates, including nicks that are present in double-stranded nucleic acids, albeit with different efficiencies. To unravel the biochemical and functional relationship between these proteins, a systematic analysis of their substrate specificity was performed using recombinant proteins. The ability of each protein to ligate 20 bp double-strande

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15

Raymond, Amy C., Bart L. Staker, and Alex B. Burgin. "Substrate Specificity of Tyrosyl-DNA Phosphodiesterase I (Tdp1)." Journal of Biological Chemistry 280, no. 23 (2005): 22029–35. http://dx.doi.org/10.1074/jbc.m502148200.

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Tyrosyl-DNA phosphodiesterase I (Tdp1) hydrolyzes 3′-phosphotyrosyl bonds to generate 3′-phosphate DNA and tyrosine in vitro. Tdp1 is involved in the repair of DNA lesions created by topoisomerase I, although the in vivo substrate is not known. Here we study the kinetic and binding properties of human Tdp1 (hTdp1) to identify appropriate 3′-phosphotyrosyl DNA substrates. Genetic studies argue that Tdp1 is involved in double and single strand break repair pathways; however, x-ray crystal structures suggest that Tdp1 can only bind single strand DNA. Separate kinetic and binding experiments show

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16

Jian, Jeffrey Y., and Neil Osheroff. "Telling Your Right Hand from Your Left: The Effects of DNA Supercoil Handedness on the Actions of Type II Topoisomerases." International Journal of Molecular Sciences 24, no. 13 (2023): 11199. http://dx.doi.org/10.3390/ijms241311199.

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Type II topoisomerases are essential enzymes that modulate the topological state of DNA supercoiling in all living organisms. These enzymes alter DNA topology by performing double-stranded passage reactions on over- or underwound DNA substrates. This strand passage reaction generates a transient covalent enzyme–cleaved DNA structure known as the cleavage complex. Al-though the cleavage complex is a requisite catalytic intermediate, it is also intrinsically dangerous to genomic stability in biological systems. The potential threat of type II topoisomerase function can also vary based on the nat

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17

Kim, Dongwook, Yixing Sun, Dan Xie, et al. "Application of a Substrate-Mediated Selection with c-Src Tyrosine Kinase to a DNA-Encoded Chemical Library." Molecules 24, no. 15 (2019): 2764. http://dx.doi.org/10.3390/molecules24152764.

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As aberrant activity of protein kinases is observed in many disease states, these enzymes are common targets for therapeutics and detection of activity levels. The development of non-natural protein kinase substrates offers an approach to protein substrate competitive inhibitors, a class of kinase inhibitors with promise for improved specificity. Also, kinase activity detection approaches would benefit from substrates with improved activity and specificity. Here, we apply a substrate-mediated selection to a peptidomimetic DNA-encoded chemical library for enrichment of molecules that can be pho

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18

Boule, J. B., and V. A. Zakian. "The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates." Nucleic Acids Research 35, no. 17 (2007): 5809–18. http://dx.doi.org/10.1093/nar/gkm613.

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19

Yoshida, Toru, and Hideaki Tsuge. "Common Mechanism for Target Specificity of Protein- and DNA-Targeting ADP-Ribosyltransferases." Toxins 13, no. 1 (2021): 40. http://dx.doi.org/10.3390/toxins13010040.

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Many bacterial pathogens utilize ADP-ribosyltransferases (ARTs) as virulence factors. The critical aspect of ARTs is their target specificity. Each individual ART modifies a specific residue of its substrates, which could be proteins, DNA, or antibiotics. However, the mechanism underlying this specificity is poorly understood. Here, we review the substrate recognition mechanism and target residue specificity based on the available complex structures of ARTs and their substrates. We show that there are common mechanisms of target residue specificity among protein- and DNA-targeting ARTs.

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20

Yoshida, Toru, and Hideaki Tsuge. "Common Mechanism for Target Specificity of Protein- and DNA-Targeting ADP-Ribosyltransferases." Toxins 13, no. 1 (2021): 40. http://dx.doi.org/10.3390/toxins13010040.

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Many bacterial pathogens utilize ADP-ribosyltransferases (ARTs) as virulence factors. The critical aspect of ARTs is their target specificity. Each individual ART modifies a specific residue of its substrates, which could be proteins, DNA, or antibiotics. However, the mechanism underlying this specificity is poorly understood. Here, we review the substrate recognition mechanism and target residue specificity based on the available complex structures of ARTs and their substrates. We show that there are common mechanisms of target residue specificity among protein- and DNA-targeting ARTs.

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21

Takabayashi, Sadao, Shohei Kotani, Juan Flores-Estrada, et al. "Boron-Implanted Silicon Substrates for Physical Adsorption of DNA Origami." International Journal of Molecular Sciences 19, no. 9 (2018): 2513. http://dx.doi.org/10.3390/ijms19092513.

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DNA nanostructures routinely self-assemble with sub-10 nm feature sizes. This capability has created industry interest in using DNA as a lithographic mask, yet with few exceptions, solution-based deposition of DNA nanostructures has remained primarily academic to date. En route to controlled adsorption of DNA patterns onto manufactured substrates, deposition and placement of DNA origami has been demonstrated on chemically functionalized silicon substrates. While compelling, chemical functionalization adds fabrication complexity that limits mask efficiency and hence industry adoption. As an alt

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22

Wright, G. E. "Nucleotide probes of DNA polymerases." Acta Biochimica Polonica 43, no. 1 (1996): 115–24. http://dx.doi.org/10.18388/abp.1996_4522.

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The modified nucleotides, N2-(p-n-butylphenyl)dGTP and 2-(p-n-butylanilino) dATP and related compounds have been developed as inhibitor-probes of B family DNA polymerases. Synthetic approaches to these compounds are summarized. The nucleotides are potent, non-substrate inhibitors of DNA polymerase a. In contrast, they inhibit other members of the family with less potency but act as substrates for these enzymes. Modelling of the inhibitor: enzyme binding mechanism has been done based on the known structure of E. coli DNA polymerase I, and site-directed mutagenesis experiments to evaluate this m

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23

Ciubotaru, Mihai, and David G. Schatz. "Synapsis of Recombination Signal Sequences Located in cis and DNA Underwinding in V(D)J Recombination." Molecular and Cellular Biology 24, no. 19 (2004): 8727–44. http://dx.doi.org/10.1128/mcb.24.19.8727-8744.2004.

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ABSTRACT V(D)J recombination requires binding and synapsis of a complementary (12/23) pair of recombination signal sequences (RSSs) by the RAG1 and RAG2 proteins, aided by a high-mobility group protein, HMG1 or HMG2. Double-strand DNA cleavage within this synaptic, or paired, complex is thought to involve DNA distortion or melting near the site of cleavage. Although V(D)J recombination normally occurs between RSSs located on the same DNA molecule (in cis), all previous studies that directly assessed RSS synapsis were performed with the two DNA substrates in trans. To overcome this limitation,

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24

Hogrefe, H. H., R. I. Hogrefe, R. Y. Walder, and J. A. Walder. "Kinetic analysis of Escherichia coli RNase H using DNA-RNA-DNA/DNA substrates." Journal of Biological Chemistry 265, no. 10 (1990): 5561–66. http://dx.doi.org/10.1016/s0021-9258(19)39397-4.

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25

Csitkovits, Vanessa C., Damir Ðermić, and Ellen L. Zechner. "Concomitant Reconstitution of TraI-catalyzed DNA Transesterase and DNA Helicase Activityin Vitro." Journal of Biological Chemistry 279, no. 44 (2004): 45477–84. http://dx.doi.org/10.1074/jbc.m407970200.

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TraI protein of plasmid R1 possesses two activities, a DNA transesterase and a highly processive 5′-3′ DNA helicase, which are essential for bacterial conjugation. Regulation of the functional domains of the enzyme is poorly understood. TraI cleaves supercoiledoriTDNA with site and strand specificityin vitrobut fails to initiate unwinding from this site (nic). The helicase requires an extended region of adjacent single-stranded DNA to enter the duplex, yet interaction of purified TraI withoriTDNA alone or as an integral part of the IncF relaxosome does not melt sufficient duplex to load the he

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26

Wang, Yaqing, Zhiqiang Sun, Piero R. Bianco, and Yuri L. Lyubchenko. "Atomic force microscopy–based characterization of the interaction of PriA helicase with stalled DNA replication forks." Journal of Biological Chemistry 295, no. 18 (2020): 6043–52. http://dx.doi.org/10.1074/jbc.ra120.013013.

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In bacteria, the restart of stalled DNA replication forks requires the DNA helicase PriA. PriA can recognize and remodel abandoned DNA replication forks, unwind DNA in the 3′-to-5′ direction, and facilitate the loading of the helicase DnaB onto the DNA to restart replication. Single-stranded DNA–binding protein (SSB) is typically present at the abandoned forks, but it is unclear how SSB and PriA interact, although it has been shown that the two proteins interact both physically and functionally. Here, we used atomic force microscopy to visualize the interaction of PriA with DNA substrates with

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27

Girotti, S., M. Musiani, P. Pasini, et al. "Application of a low-light imaging device and chemiluminescent substrates for quantitative detection of viral DNA in hybridization reactions." Clinical Chemistry 41, no. 12 (1995): 1693–97. http://dx.doi.org/10.1093/clinchem/41.12.1693.

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Abstract In this quantitative dot-blot hybridization assay for detecting B19 parvovirus DNA, we used three different chemiluminescent substrates [adamantyl-1,2-dioxetane phenyl phosphates (PPD and the new PPD-Plus) and the chloro-5-substituted adamantyl-1,2-dioxetane phosphate (CSPD) plus Emerald enhancer] and a high-performance, low-intensity-light imaging luminograph apparatus. The hybridization test uses digoxigenin-labeled DNA probes, which are immunoenzymatically revealed by anti-digoxigenin Fab fragments conjugated with alkaline phosphatase. All the detection systems with the various che

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28

Sidorova, Julia M., and Linda L. Breeden. "Rad53 Checkpoint Kinase Phosphorylation Site Preference Identified in the Swi6 Protein of Saccharomyces cerevisiae." Molecular and Cellular Biology 23, no. 10 (2003): 3405–16. http://dx.doi.org/10.1128/mcb.23.10.3405-3416.2003.

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ABSTRACT Rad53 of Saccharomyces cerevisiae is a checkpoint kinase whose structure and function are conserved among eukaryotes. When a cell detects damaged DNA, Rad53 activity is dramatically increased, which ultimately leads to changes in DNA replication, repair, and cell division. Despite its central role in checkpoint signaling, little is known about Rad53 substrates or substrate specificity. A number of proteins are implicated as Rad53 substrates; however, the evidence remains indirect. Previously, we have provided evidence that Swi6, a subunit of the Swi4/Swi6 late-G1-specific transcriptio

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29

Rosa, Marta, Wenming Sun, and Rosa Di Felice. "Interaction of DNA Bases with Gold Substrates." Journal of Self-Assembly and Molecular Electronics 1, no. 1 (2013): 41–68. http://dx.doi.org/10.13052/same2245-4551.112.

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30

Painter, Robert B., and Leon N. Kapp. "Replication intermediates as substrates for DNA rearrangements." Mutation Research Letters 262, no. 1 (1991): 21–23. http://dx.doi.org/10.1016/0165-7992(91)90100-i.

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31

Pasquardini, L., L. Lunelli, C. Potrich, et al. "Organo-silane coated substrates for DNA purification." Applied Surface Science 257, no. 24 (2011): 10821–27. http://dx.doi.org/10.1016/j.apsusc.2011.07.112.

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32

Wang, Zhenguang, Qingwang Xue, Wenzhi Tian, Lei Wang, and Wei Jiang. "Quantitative detection of single DNA molecules on DNA tetrahedron decorated substrates." Chemical Communications 48, no. 77 (2012): 9661. http://dx.doi.org/10.1039/c2cc35208g.

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Shiels, Jerome C., Bozidar Jerkovic, Anne M. Baranger, and Philip H. Bolton. "RNA–DNA Hybrids Containing Damaged DNA are Substrates for RNase H." Bioorganic & Medicinal Chemistry Letters 11, no. 19 (2001): 2623–26. http://dx.doi.org/10.1016/s0960-894x(01)00527-3.

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Countryman, Preston J., Jiangguo Lin, Parminder Kaur, et al. "Determining the DNA Diffusion Behavior of SA2 on Various DNA Substrates." Biophysical Journal 108, no. 2 (2015): 397a. http://dx.doi.org/10.1016/j.bpj.2014.11.2177.

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Schwartz, Rachel A., Seema S. Lakdawala, Heather D. Eshleman, Matthew R. Russell, Christian T. Carson, and Matthew D. Weitzman. "Distinct Requirements of Adenovirus E1b55K Protein for Degradation of Cellular Substrates." Journal of Virology 82, no. 18 (2008): 9043–55. http://dx.doi.org/10.1128/jvi.00925-08.

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ABSTRACT The E1b55K and E4orf6 proteins of adenovirus type 5 (Ad5) assemble into a complex together with cellular proteins including cullin 5, elongins B and C, and Rbx1. This complex possesses E3 ubiquitin ligase activity and targets cellular proteins for proteasome-mediated degradation. The ligase activity has been suggested to be responsible for all functions of E1b55K/E4orf6, including promoting efficient viral DNA replication, preventing a cellular DNA damage response, and stimulating late viral mRNA nuclear export and late protein synthesis. The known cellular substrates for degradation

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36

Interthal, Heidrun, and James J. Champoux. "Effects of DNA and protein size on substrate cleavage by human tyrosyl-DNA phosphodiesterase 1." Biochemical Journal 436, no. 3 (2011): 559–66. http://dx.doi.org/10.1042/bj20101841.

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TDP (tyrosyl-DNA phosphodiesterase) 1 catalyses the hydrolysis of phosphodiester linkages between a DNA 3′ phosphate and a tyrosine residue as well as a variety of other DNA 3′ substituents, and has been implicated in the repair of covalent complexes involving eukaryotic type IB topoisomerases. To better understand the substrate features that are recognized by TDP1, the size of either the DNA or protein component of the substrate was varied. Competition experiments and gel-shift analyses comparing a series of substrates with DNA lengths increasing from 6 to 28 nt indicated that, contrary to pr

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37

LEPSE, CAROL L., RAMESH KUMAR, and DOINA GANEA. "Extrachromosomal Eukaryotic DNA Substrates for Switch Recombination: Analysis of Isotype and Cell Specificity." DNA and Cell Biology 13, no. 12 (1994): 1151–61. http://dx.doi.org/10.1089/dna.1994.13.1151.

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Montgomery, G. P., and B. C. Lu. "Involvement of Coprinus endonuclease in preparing substrate for in vitro recombination." Genome 33, no. 1 (1990): 101–8. http://dx.doi.org/10.1139/g90-016.

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A functional recombination assay involving the tetracycline mutant plasmids, pUW1 and pUW4, was used to assess (i) the nature of the DNA substrates needed and (ii) the involvement of Coprinus endonuclease in preparing substrate, for the RecA-directed recombination process. A gapped circular plasmid and a linear or a nicked circular plasmid are efficient substrate combinations in this system to achieve a 160-fold increase in the in vitro recombination frequency over the control levels. The Coprinus endonuclease obtained from early meiotic prophase can produce such substrates. The recombination

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Yakovlev, D. A., A. A. Kuznetsova, O. S. Fedorova, and N. A. Kuznetsov. "Search for Modified DNA Sites with the Human Methyl-CpG-Binding Enzyme MBD4." Acta Naturae 9, no. 1 (2017): 88–98. http://dx.doi.org/10.32607/20758251-2017-9-1-88-98.

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The MBD4 enzyme initiates the process of DNA demethylation by the excision of modified DNA bases, resulting in the formation of apurinic/apyrimidinic sites. MBD4 contains a methyl-CpG-binding domain which provides the localization of the enzyme at the CpG sites, and a DNA glycosylase domain that is responsible for the catalytic activity. The aim of this work was to clarify the mechanisms of specific site recognition and formation of catalytically active complexes between model DNA substrates and the catalytic N-glycosylase domain MBD4cat. The conformational changes in MBD4cat and DNA substrate

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40

Jakubowski, Simon J., Eric Cascales, Vidhya Krishnamoorthy, and Peter J. Christie. "Agrobacterium tumefaciens VirB9, an Outer-Membrane-Associated Component of a Type IV Secretion System, Regulates Substrate Selection and T-Pilus Biogenesis." Journal of Bacteriology 187, no. 10 (2005): 3486–95. http://dx.doi.org/10.1128/jb.187.10.3486-3495.2005.

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ABSTRACT Agrobacterium tumefaciens translocates DNA and protein substrates between cells via a type IV secretion system (T4SS) whose channel subunits include the VirD4 coupling protein, VirB11 ATPase, VirB6, VirB8, VirB2, and VirB9. In this study, we used linker insertion mutagenesis to characterize the contribution of the outer-membrane-associated VirB9 to assembly and function of the VirB/D4 T4SS. Twenty-five dipeptide insertion mutations were classified as permissive for intercellular substrate transfer (Tra+), completely transfer defective (Tra−), or substrate discriminating, e.g., selecti

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Ross, Jason P., Isao Suetake, Shoji Tajima, and Peter L. Molloy. "Recombinant mammalian DNA methyltransferase activity on model transcriptional gene silencing short RNA–DNA heteroduplex substrates." Biochemical Journal 432, no. 2 (2010): 323–32. http://dx.doi.org/10.1042/bj20100579.

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The biochemical mechanism of short RNA-induced TGS (transcriptional gene silencing) in mammals is unknown. Two competing models exist; one suggesting that the short RNA interacts with a nascent transcribed RNA strand (RNA–RNA model) and the other implying that short RNA forms a heteroduplex with DNA from the unwound double helix, an R-loop structure (RNA–DNA model). Likewise, the requirement for DNA methylation to enact TGS is still controversial. In vitro assays using purified recombinant murine Dnmt (DNA methyltransferase) 1-dN (where dN indicates an N-terminal truncation), 3a and 3b enzymes

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Wahls, W. P., L. J. Wallace, and P. D. Moore. "The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture." Molecular and Cellular Biology 10, no. 2 (1990): 785–93. http://dx.doi.org/10.1128/mcb.10.2.785-793.1990.

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Tracts of the alternating dinucleotide polydeoxythymidylic-guanylic [d(TG)].polydeoxyadenylic-cytidylic acid [d(AC)], present throughout the human genome, are capable of readily forming left-handed Z-DNA in vitro. We have analyzed the effects of the Z-DNA motif d(TG)30 upon homologous recombination between two nonreplicating plasmid substrates cotransfected into human cells in culture. In this study, the sequence d(TG)30 is shown to stimulate homologous recombination up to 20-fold. Enhancement is specific to the Z-DNA motif; a control DNA fragment of similar size does not alter the recombinati

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43

Wahls, W. P., L. J. Wallace, and P. D. Moore. "The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture." Molecular and Cellular Biology 10, no. 2 (1990): 785–93. http://dx.doi.org/10.1128/mcb.10.2.785.

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Abstract:

Tracts of the alternating dinucleotide polydeoxythymidylic-guanylic [d(TG)].polydeoxyadenylic-cytidylic acid [d(AC)], present throughout the human genome, are capable of readily forming left-handed Z-DNA in vitro. We have analyzed the effects of the Z-DNA motif d(TG)30 upon homologous recombination between two nonreplicating plasmid substrates cotransfected into human cells in culture. In this study, the sequence d(TG)30 is shown to stimulate homologous recombination up to 20-fold. Enhancement is specific to the Z-DNA motif; a control DNA fragment of similar size does not alter the recombinati

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Eoff, Robert L., Travis L. Spurling, and Kevin D. Raney. "Chemically Modified DNA Substrates Implicate the Importance of Electrostatic Interactions for DNA Unwinding by Dda Helicase†." Biochemistry 44, no. 2 (2005): 666–74. http://dx.doi.org/10.1021/bi0484926.

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Leite, Barbara R., Sofia Duarte, Jesús S. Troncoso, and Filipe O. Costa. "Artificial Seaweed Substrates Complement ARMS in DNA Metabarcoding-Based Monitoring of Temperate Coastal Macrozoobenthos." Diversity 15, no. 5 (2023): 657. http://dx.doi.org/10.3390/d15050657.

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We used DNA metabarcoding to compare macrozoobenthic species colonization between autonomous reef monitoring structures (ARMS) and artificial seaweed monitoring systems (ASMS). We deployed both substrates in two different locations (Ría de Vigo and Ría de Ferrol, NW Iberian coast) and collected them after 6, 9, and 12 months to assess species composition of the colonizing communities through high-throughput sequencing of amplicons within the barcode region of the mitochondrial cytochrome c oxidase I (COI-5P) and the V4 domain of the 18S rRNA genes. We observed a consistently low similarity in

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Vatta, Maritza, Bronwyn Lyons, Kayla A. Heney, Taylor Lidster, and A. Rod Merrill. "Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies." Toxins 13, no. 1 (2021): 55. http://dx.doi.org/10.3390/toxins13010055.

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Scabin is a mono-ADP-ribosyltransferase toxin/enzyme and possible virulence factor produced by the agriculture pathogen, Streptomyces scabies. Recently, molecular dynamic approaches and MD simulations revealed its interaction with both NAD+ and DNA substrates. An Essential Dynamics Analysis identified a crab-claw-like mechanism, including coupled changes in the exposed motifs, and the Rβ1-RLa-NLc-STTβ2-WPN-WARTT-(QxE)ARTT sequence motif was proposed as a catalytic signature of the Pierisin family of DNA-acting toxins. A new fluorescence assay was devised to measure the kinetics for both RNA an

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Symington, L. S., P. Morrison, and R. Kolodner. "Plasmid recombination intermediates generated in a Saccharomyces cerevisiae cell-free recombination system." Molecular and Cellular Biology 5, no. 9 (1985): 2361–68. http://dx.doi.org/10.1128/mcb.5.9.2361-2368.1985.

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We have developed an assay utilizing Saccharomyces cerevisiae cell extracts to catalyze recombination in vitro between homologous plasmids containing different mutant alleles of the tet gene. Electrophoretic analysis of product DNA indicated that a number of novel DNA species were formed during the reaction. These species migrated through agarose gels as distinct bands with decreased electrophoretic mobility compared with the substrate DNA. The DNA from each individual band was purified and shown to be enriched 5- to 100-fold for tetracycline-resistant recombinants by using a transformation as

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Symington, L. S., P. Morrison, and R. Kolodner. "Plasmid recombination intermediates generated in a Saccharomyces cerevisiae cell-free recombination system." Molecular and Cellular Biology 5, no. 9 (1985): 2361–68. http://dx.doi.org/10.1128/mcb.5.9.2361.

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Abstract:

We have developed an assay utilizing Saccharomyces cerevisiae cell extracts to catalyze recombination in vitro between homologous plasmids containing different mutant alleles of the tet gene. Electrophoretic analysis of product DNA indicated that a number of novel DNA species were formed during the reaction. These species migrated through agarose gels as distinct bands with decreased electrophoretic mobility compared with the substrate DNA. The DNA from each individual band was purified and shown to be enriched 5- to 100-fold for tetracycline-resistant recombinants by using a transformation as

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Tsujita, Saori, Mikimasa Tanada, Tomonobu Kataoka, and Shigeki Sasaki. "Equilibrium shift by target DNA substrates for determination of DNA binding ligands." Bioorganic & Medicinal Chemistry Letters 17, no. 1 (2007): 68–72. http://dx.doi.org/10.1016/j.bmcl.2006.09.089.

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Interthal, Heidrun, Hong Jing Chen, and James J. Champoux. "Human Tdp1 Cleaves a Broad Spectrum of Substrates, Including Phosphoamide Linkages." Journal of Biological Chemistry 280, no. 43 (2005): 36518–28. http://dx.doi.org/10.1074/jbc.m508898200.

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Human tyrosyl-DNA phosphodiesterase (Tdp1) hydrolyzes the phosphodiester bond between a DNA 3′ end and a tyrosyl moiety. In eukaryotic cells, this type of linkage is found in stalled topoisomerase I-DNA covalent complexes, and Tdp1 has been implicated in the repair of such complexes in vivo. We confirm here that the Tdp1 catalytic cycle involves a covalent reaction intermediate in which a histidine residue is connected to a DNA 3′-phosphate through a phosphoamide linkage. Most surprisingly, this linkage can be hydrolyzed by Tdp1, and unlike a topoisomerase I-DNA complex, which requires modific

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