A sequential strand-displacement strategy enables efficient six-step DNA-templated synthesis.
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ABSTRACT:
SUBMITTER: He Y
PROVIDER: S-EPMC3125949 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:DNA polymerase ? (Pol ?) is a replicative DNA polymerase with an associated 3'-5' exonuclease activity. Here, we explored the capacity of Pol ? to perform strand displacement synthesis, a process that influences many DNA transactions in vivo We found that Pol ? is unable to carry out extended strand displacement synthesis unless its 3'-5' exonuclease activity is removed. However, the wild-type Pol ? holoenzyme efficiently displaced one nucleotide when encountering double-stranded DNA after filling a gap or nicked DNA. A flap, mimicking a D-loop or a hairpin structure, on the 5' end of the blocking primer inhibited Pol ? from synthesizing DNA up to the fork junction. This inhibition was observed for Pol ? but not with Pol ?, RB69 gp43 or Pol ?. Neither was Pol ? able to extend a D-loop in reconstitution experiments. Finally, we show that the observed strand displacement synthesis by exonuclease-deficient Pol ? is distributive. Our results suggest that Pol ? is unable to extend the invading strand in D-loops during homologous recombination or to add more than two nucleotides during long-patch base excision repair. Our results support the hypothesis that Pol ? participates in short-patch base excision repair and ribonucleotide excision repair.
| S-EPMC5041465 | biostudies-literature
Project description:Quenched autoligation probes have been employed previously in a target-templated nonenzymatic ligation strategy for detecting nucleic acids in cells by fluorescence. A common source of background signal in such probes is the undesired reaction with water and other cellular nucleophiles. Here, we describe a new class of self-ligating probes, double displacement (DD) probes, that rely on two displacement reactions to fully unquench a nearby fluorophore. Three potential double displacement architectures, all possessing two fluorescence quencher/leaving groups (dabsylate groups), were synthesized and evaluated for templated reaction with nucleophile (phosphorothioate) probes both in vitro and in intact bacterial cells. All three DD probe designs provided substantially better initial quenching than a single-Dabsyl control. In isothermal templated reactions in vitro, double displacement probes yielded considerably lower background signal than previous single displacement probes; investigation into the mechanism revealed that one dabsylate acts as a sacrificial leaving group, reacting nonspecifically with water, but yielding little signal because another quencher group remains. Templated reaction with the specific nucleophile probe is required to activate a signal. The double displacement probes provided a ca. 80-fold turn-on signal and yielded a 2-4-fold improvement in signal/background over single Dabsyl probes. The best-performing probe architecture was demonstrated in a two-color, FRET-based two-allele discrimination system in vitro and was shown to be capable of discriminating between two closely related species of bacteria differing by a single nucleotide at an rRNA target site.
| S-EPMC2891565 | biostudies-literature
Project description:BackgroundThe general approach to the synthesis of metal complexes begins with ligand synthesis, followed by ligand reaction with metal salts to afford organometallic complexes. Our research group first reported a one-pot multicomponent synthesis of chiral oxazolinyl-zinc complexes, in the presence of a large amount of ZnCl2 (0.4-2.6 equiv.), with the yields of some products reaching 90%.ResultsOur prior strategy was extended to use copper, cobalt, nickel, manganese, palladium or platinum salts as the third component. The one-step method used 1.0 equivalent of a metal salt, such as M(OAc)2·nH2O or MCl2·nH2O (M: Cu, Co, Ni, Pd or Pt, n = 1, 2 or 4), as a reagent to generate chiral salicyloxazoline complexes 1-8 in the reaction of 2-cyanophenol with different d- and l-amino alcohols.ConclusionComplexes 1-8 were obtained using a one-pot method with a sequential strategy. The reaction outcome was demonstrated for three-component reactions between metal salts, amino alcohols and 2-hydroxybenzonitrile to afford organometallic complexes in good yields (65-95%).
| S-EPMC6661745 | biostudies-literature
Project description:Replicative holoenzymes exhibit rapid and processive primer extension DNA synthesis, but inefficient strand displacement DNA synthesis. We investigated the bacteriophage T4 and T7 holoenzymes primer extension activity and strand displacement activity on a DNA hairpin substrate manipulated by a magnetic trap. Holoenzyme primer extension activity is moderately hindered by the applied force. In contrast, the strand displacement activity is strongly stimulated by the applied force; DNA polymerization is favoured at high force, while a processive exonuclease activity is triggered at low force. We propose that the DNA fork upstream of the holoenzyme generates a regression pressure which inhibits the polymerization-driven forward motion of the holoenzyme. The inhibition is generated by the distortion of the template strand within the polymerization active site thereby shifting the equilibrium to a DNA-protein exonuclease conformation. We conclude that stalling of the holoenzyme induced by the fork regression pressure is the basis for the inefficient strand displacement synthesis characteristic of replicative polymerases. The resulting processive exonuclease activity may be relevant in replisome disassembly to reset a stalled replication fork to a symmetrical situation. Our findings offer interesting applications for single-molecule DNA sequencing.
| S-EPMC3401438 | biostudies-literature
Project description:Okazaki fragment maturation to produce continuous lagging strands in eukaryotic cells requires precise coordination of strand displacement synthesis by DNA polymerase delta (Pol delta) with 5.-flap cutting by FEN1(RAD27) endonuclease. Excessive strand displacement is normally prevented by the 3.-exonuclease activity of Pol delta. This core maturation machinery can be assisted by Dna2 nuclease/helicase that processes long flaps. Our genetic studies show that deletion of the POL32 (third subunit of Pol delta) or PIF1 helicase genes can suppress lethality or growth defects of rad27Delta pol3-D520V mutants (defective for FEN1(RAD27) and the 3.-exonuclease of Pol delta) that produce long flaps and of dna2Delta mutants that are defective in cutting long flaps. On the contrary, pol32Delta or pif1Delta caused lethality of rad27Delta exo1Delta double mutants, suggesting that Pol32 and Pif1 are required to generate longer flaps that can be processed by Dna2 in the absence of the short flap processing activities of FEN1(RAD27) and Exo1. The genetic analysis reveals a remarkable flexibility of the Okazaki maturation machinery and is in accord with our biochemical analysis. In vitro, the generation of short flaps by Pol delta is not affected by the presence of Pol32; however, longer flaps only accumulate when Pol32 is present. The presence of FEN1(RAD27) during strand displacement synthesis curtails displacement in favor of flap cutting, thus suggesting an active hand-off mechanism from Pol delta to FEN1(RAD27). Finally, RNA-DNA hybrids are more readily displaced by Pol delta than DNA hybrids, thereby favoring degradation of initiator RNA during Okazaki maturation.
| S-EPMC2590699 | biostudies-literature
Project description:Macrocycles provide an attractive modality for drug development, but generating ligands for new targets is hampered by the limited availability of large macrocycle libraries. We have established a solution-phase macrocycle synthesis strategy in which three building blocks are coupled sequentially in efficient alkylation reactions that eliminate the need for product purification. We demonstrate the power of the approach by combinatorially reacting 15 bromoacetamide-activated tripeptides, 42 amines, and 6 bis-electrophile cyclization linkers to generate a 3780-compound library with minimal effort. Screening against thrombin yielded a potent and selective inhibitor (K i = 4.2 ± 0.8 nM) that efficiently blocked blood coagulation in human plasma. Structure-activity relationship and X-ray crystallography analysis revealed that two of the three building blocks acted synergistically and underscored the importance of combinatorial screening in macrocycle development. The three-component library synthesis approach is general and offers a promising avenue to generate macrocycle ligands to other targets.
| S-EPMC8163216 | biostudies-literature
Project description:The cost-efficient large-scale production of novel carbon nanostructure with high performance is still a challenge, restricting their applications in catalysis. Herein, we present a low-cost one-pot and one-step approach for the synthesis of both N-doped graphene (NG) and N-doped carbon nanotubes (NCNTs) from self-templated organic nanoplates. By varying the FeCl3 concentration in the precursor, we can control the formation of graphene or CNTs. To the best of our knowledge, this is the first example for the controllable synthesis of graphene or CNTs by varying the precursors' compositions. This provides a simple and cost-effective route for the large-scale production of both NG and NCNTs for applications in catalysis. By example, we show how these unique structured nanocarbons can be applied in electrocatalysis for oxygen reduction reaction (ORR). The obtained NG and NCNTs show excellent ORR activities with long-term stability under alkaline conditions. The unique porous nanostructure, abundant defects, homogeneous N-doping and high N-content in the NG and NCNTs can provide abundant active sites, leading to the excellent ORR performance. This research not only displayed a simple and cost-effective approach for the large-scale production of novel carbon nanoarchitectures, but also revealed the exceptional application potential of these nanocarbons for electrocatalysis.
| S-EPMC4908410 | biostudies-other
Project description:Organohydrogels with distinct antifreezing and antidehydration properties have aroused great interest among researchers, and various organohydrogels and organohydrogel-based applications have emerged recently. There are two popular synthesis strategies to prepare these antifreezing and antidehydration organohydrogels: the in-situ gelling and the solvent displacement strategies. Although both strategies have been widely applied, there is a lack of comparative study of these two strategies. In this work, to elucidate the comparative advantages of the two synthesis strategies, we studied and compared the mechanical and environmental tolerant properties of the organohydrogels synthesized from both strategies. The glycerol-based and ethylene glycol-based chemical polyacrylamide (PAAm) organohydrogel and the glycerol-based physical gelatin organohydrogel were synthesized and studied. Through the comparative study, we have found that the organohydrogels from different strategies with the same dispersion medium showed similar antifreezing and antidehydration properties but different mechanical properties. The mechanical properties of these organohydrogels are influenced by two opposite factors for each strategy: the enhanced physical interactions induced strengthening and solvent effect or swelling induced weakening. We hope this study may provide a better understanding of the synthesis strategies of organohydrogels and provide a valuable guide to choose the suitable synthesis strategy for each application.
| S-EPMC7696091 | biostudies-literature
Project description:The Werner syndrome protein (WRN) suppresses the loss of telomeres replicated by lagging-strand synthesis by a yet to be defined mechanism. Here, we show that whereas either WRN or the Bloom syndrome helicase (BLM) stimulates DNA polymerase ? progression across telomeric G-rich repeats, only WRN promotes sequential strand displacement synthesis and FEN1 cleavage, a critical step in Okazaki fragment maturation, at these sequences. Helicase activity, as well as the conserved winged-helix (WH) motif and the helicase and RNase D C-terminal (HRDC) domain play important but distinct roles in this process. Remarkably, WRN also influences the formation of FEN1 cleavage products during strand displacement on a nontelomeric substrate, suggesting that WRN recruitment and cooperative interaction with FEN1 during lagging-strand synthesis may serve to regulate sequential strand displacement and flap cleavage at other genomic sites. These findings define a biochemical context for the physiological role of WRN in maintaining genetic stability.
| S-EPMC5247617 | biostudies-literature
Project description:DNA tandem lesions are comprised of two contiguously damaged nucleotides. This subset of clustered lesions is produced by a variety of oxidizing agents, including ionizing radiation. Clustered lesions can inhibit base excision repair (BER). We report the effects of tandem lesions composed of a thymine glycol and a 5'-adjacent 2-deoxyribonolactone (LTg) or tetrahydrofuran abasic site (FTg). Some BER enzymes that act on the respective isolated lesions do not accept the tandem lesion as a substrate. For instance, endonuclease III (Nth) does not excise thymine glycol (Tg) when it is part of either tandem lesion. Similarly, endonuclease IV (Nfo) does not incise L or F when they are in tandem with Tg. Long-patch BER overcomes inhibition by the tandem lesion. DNA polymerase beta (Pol beta) carries out strand displacement synthesis, following APE1 incision of the abasic site. Pol beta activity is enhanced by flap endonuclease (FEN1), which cleaves the resulting flap. The tandem lesion is also incised by the bacterial nucleotide excision repair system UvrABC with almost the same efficiency as an isolated Tg. These data reveal two solutions that DNA repair systems can use to counteract the formation of tandem lesions.
| S-EPMC2432464 | biostudies-literature