scholarly journals Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit

2019 ◽  
Vol 10 (7) ◽  
pp. 1953-1961 ◽  
Author(s):  
Zhentong Zhu ◽  
Ruiping Wu ◽  
Bingling Li
Keyword(s):  
Solid State ◽  
Nucleic Acid ◽  
Base Pair ◽  
Quantitative Method ◽  
Dna Assembly ◽  
Characterization Methods ◽  
Catalytic Dna ◽  
Acid Amplifier

We adapt a solid-state nanopore for analyzing DNA assembly mixtures, which is usually a tougher task for either traditional characterization methods or nanopores themselves. A trigger induced nucleic acid amplifier, SP-CHA, is designed as a model. We propose an electrophoresis-gel like, but homogeneous, quantitative method that can comprehensively profile the “base-pair distribution” of SP-CHA concatemer mixtures.

scholarly journals Direct Detection of Conserved Viral Sequences and Other Nucleic Acid Motifs with Solid-State Nanopores

ACS Nano ◽  
2021 ◽  
Author(s):  
Komal Sethi ◽  
Gabrielle P. Dailey ◽  
Osama K. Zahid ◽  
Ethan W. Taylor ◽  
Jan A. Ruzicka ◽  
...  
Keyword(s):  
Solid State ◽  
Nucleic Acid ◽  
Direct Detection ◽  
Viral Sequences

scholarly journals Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores

ACS Nano ◽  
2017 ◽  
Vol 11 (10) ◽  
pp. 9701-9710 ◽  
Author(s):  
Mohammad Amin Alibakhshi ◽  
Justin R. Halman ◽  
James Wilson ◽  
Aleksei Aksimentiev ◽  
Kirill A. Afonin ◽  
...  
Keyword(s):  
Solid State ◽  
Nucleic Acid

scholarly journals Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 532
Author(s):  
Jonathan H. Sheehan ◽  
Jarrod A. Smith ◽  
Pradeep S. Pallan ◽  
Terry P. Lybrand ◽  
Martin Egli
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Base Pair ◽  
Crystal Packing ◽  
Md Simulations ◽  
Conformational Flexibility ◽  
Dynamics Simulation ◽  
Dna Duplex ◽  
Solution Studies

The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking.

Helicase mechanisms and the coupling of helicases within macromolecular machines Part I: Structures and properties of isolated helicases

2002 ◽  
Vol 35 (4) ◽  
pp. 431-478 ◽  
Author(s):  
Emmanuelle Delagoutte ◽  
Peter H. von Hippel
Keyword(s):  
Crystal Structure ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Site ◽  
Crystal Structures ◽  
Base Pair ◽  
Biochemical Properties ◽  
Functional Coupling ◽  
Hexameric Helicases ◽  
Base Pair Opening

1. Mechanisms of nucleic acid (NA) unwinding by helicases 4322. Helicases may take advantage of ‘breathing’ fluctuations in dsNAs 4342.1 Stability and dynamics of dsNAs 4342.2 dsNAs ‘breathe’ in isolation 4352.3 Thermodynamics of terminal base pairs of dsNA 4382.4 Thermal fluctuations may be responsible for sequential base-pair opening at replication forks 4392.5 Helicases may capture single base-pair opening events sequentially 4403. Biochemical properties of helicases 4433.1 Binding of NAs 4433.2 Binding and hydrolysis of NTP 4453.3 Coordination between NA binding and NTP binding and hydrolysis activities 4464. Helicase structures and mechanistic consequences 4474.1 Amino-acid sequence analysis reveals conserved motifs that constitute the NTP-binding pocket and a portion of the NA-binding site 4474.2 Organization of hepatitis virus C NS3 RNA helicase 4494.2.1 Biochemical properties of HCV NS3 4494.2.2 Crystal structures of HCV NS3 helicase 4504.2.2.1 The apoprotein 4504.2.2.2 The protein–dU8 complex 4504.2.3 A possible unwinding mechanism 4524.2.4 What is the functional oligomeric state of HCV NS3? 4524.3 Organization of the PcrA helicase 4534.3.1 The apoenzyme and ADP–PcrA complex 4544.3.2 The protein–DNA–sulfate complex 4564.3.3 The PcrA–DNA–ADPNP complex 4564.3.4 A closer look at the NTP-binding site in the crystal structure of PcrA–ADPNP–DNA 4574.3.5 Communication between domains A and B 4574.3.6 How might ssDNA stimulate the ATPase activity of PcrA? 4574.3.7 A possible helicase translocation mechanism 4584.3.8 A possible unwinding mechanism 4584.4 Organization of the Rep helicase 4594.4.1 Biochemical properties 4594.4.2 Crystal structure of Rep bound to ssDNA 4624.5 Organization of the RecG helicase 4624.6 Hexameric helicases 4664.6.1 Insights from crystal structures of hexameric helicases 4674.6.2 Possible translocation and unwinding mechanisms 4685. Conclusions 4696. Acknowledgments 4727. References 472Helicases are proteins that harness the chemical free energy of ATP hydrolysis to catalyze the unwinding of double-stranded nucleic acids. These enzymes have been much studied in isolation, and here we review what is known about the mechanisms of the unwinding process. We begin by considering the thermally driven ‘breathing’ of double-stranded nucleic acids by themselves, in order to ask whether helicases might take advantage of some of these breathing modes. We next provide a brief summary of helicase mechanisms that have been elucidated by biochemical, thermodynamic, and kinetic studies, and then review in detail recent structural studies of helicases in isolation, in order to correlate structural findings with biophysical and biochemical results. We conclude that there are certainly common mechanistic themes for helicase function, but that different helicases have devised solutions to the nucleic acid unwinding problem that differ in structural detail. In Part II of this review (to be published in the next issue of this journal) we consider how these mechanisms are further modified to reflect the functional coupling of these proteins into macromolecular machines, and discuss the role of helicases in several central biological processes to illustrate how this coupling actually works in the various processes of gene expression.

scholarly journals Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Shu-ichi Nakano ◽  
Masayuki Fujii ◽  
Naoki Sugimoto
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Double Helix ◽  
Nucleoside Analogs ◽  
Structural Analog ◽  
Base Pairs ◽  
Nucleic Acid Analogs ◽  
Dna Double Helix ◽  
Nucleic Acid Interactions ◽  
Site Selective

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

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