Encapsulating a Single G-Quadruplex Aptamer in a Protein Nanocavity

Shim, Jiwook; Gu, Li-Qun

doi:10.1021/jp0775911

Cited by 53 publications

(82 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Type 1 and type 2 events both ended with an intermediate current level, which is an indication that they did not translocate through the narrow constriction zone (~1.4 nm) of the β-barrel to the trans side of the channel. This observation is in stark contrast to that observed for the thrombin binding aptamer in KCl solution 40,41 and DNA hairpins 49,50 that were all capable of unraveling and traversing through the ion channel. Type 3 (Figure 2) events contributed 21 ± 2% of the total recordings, and they typically showed simple deep blockage current levels.…”

Section: Resultscontrasting

confidence: 88%

Interactions of the Human Telomere Sequence with the Nanocavity of the α-Hemolysin Ion Channel Reveal Structure-Dependent Electrical Signatures for Hybrid Folds

Fleming

Burrows

2013

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Human telomeric DNA consists of tandem repeats of the sequence 5′-TTAGGG-3′, including a 3′ terminal single-stranded overhang of 100–200 nucleotides that can fold into quadruplex structures in the presence of suitable metal ions. In the presence of an applied voltage, the α-hemolysin (α-HL) protein ion channel can produce unique current patterns that are found to be characteristic for various interactions between G-quadruplexes and the protein nanocavity. In this study, the human telomere in a complete sequence context, 5′-TAGGG(TTAGGG)3TT-3′ was evaluated with respect to its multiple folding topologies. Notably, the coexistence of two interchangeable conformations of the K+-induced folds, hybrid-1 and hybrid-2, were readily resolved at a single-molecule level along with triplex folding intermediates, whose characterization has been challenging in experiments that measure the bulk solution. These results enabled us to profile the thermal denaturation process of these structures to elucidate the relative distributions of hybrid-1, hybrid-2 and folding intermediates such as triplexes. For example, at 37 °C, pH 7.9 in 50 mM aqueous KCl, the ratio of hybrid-1:hybrid-2:triplex is approximately 11:5:1 in dilute solution. The results obtained lay the foundation for utilizing the α-HL ion channel as a simple tool for monitoring how small molecules and physical context shift the equilibrium between the many G-quadruplex folds of the human telomere sequence.

show abstract

Section: Resultscontrasting

confidence: 88%

Interactions of the Human Telomere Sequence with the Nanocavity of the α-Hemolysin Ion Channel Reveal Structure-Dependent Electrical Signatures for Hybrid Folds

Fleming

Burrows

2013

J. Am. Chem. Soc.

View full text Add to dashboard Cite

show abstract

“…This is in contrast to the DNA G-quadruplex, which can be trapped in the nanocavity and partially reduce the pore current ( I/I 0 ~ 50%). 54 Therefore, it was expected that when 5′- or 3′-PK is captured by the nanopore, its pseudoknot domain should be anchored at the cis entrance; and the chimera cannot be trapped in the opposite orientation with pseudoknot heading into the pore. By analyzing the block frequency, we estimated that 40% of T2-PK molecules fold into pseudoknot (Figure S6).…”

Section: Resultsmentioning

confidence: 99%

Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel

Zhang

Yang

et al. 2015

J. Am. Chem. Soc.

Self Cite

View full text Add to dashboard Cite

Pseudoknots are a fundamental RNA tertiary structure with important roles in regulation of mRNA translation. Molecular force spectroscopic approaches such as optical tweezers can track the pseudoknot’s unfolding intermediate states by pulling the RNA chain from both ends, but the kinetic unfolding pathway induced by this method may be different from that in vivo, which occurs during translation and proceeds from the 5′ to 3′ end. Here we developed a ribosome-mimicking, nanopore pulling assay for dissecting the vectorial unfolding mechanism of pseudoknots. The pseudoknot unfolding pathway in the nanopore, either from the 5′ to 3′ end or in the reverse direction, can be controlled by a DNA leader that is attached to the pseudoknot at the 5′ or 3′ ends. The different nanopore conductance between DNA and RNA translocation serves as a marker for the position and structure of the unfolding RNA in the pore. With this design, we provided evidence that the pseudoknot unfolding is a two-step, multistate, metal ion-regulated process depending on the pulling direction. Most notably, unfolding in both directions is rate-limited by the unzipping of the first helix domain (first step), which is Helix-1 in the 5′ → 3′ direction and Helix-2 in the 3′ → 5′ direction, suggesting that the initial unfolding step in either pulling direction needs to overcome an energy barrier contributed by the noncanonical triplex base-pairs and coaxial stacking interactions for the tertiary structure stabilization. These findings provide new insights into RNA vectorial unfolding mechanisms, which play an important role in biological functions including frameshifting.

show abstract

“…[32] In einer anderen Studie wurde aHL genutzt, um die gefalteten und entfalteten Zustände eines Aptamers zu unterscheiden; die Konformation des Aptamers ist der Schlüssel für die spezifische Bindung eines Zielmoleküls. [33] Die G-QuadruplexStruktur des Aptamers unterliegt einem Entfaltungsprozess im Vorhof des aHL, woraufhin ein veränderter Blockadestrom resultiert.…”

Section: Konformationsabhängige Detektion Von Nukleinsäuren Mittels Aunclassified

Nanoporentechniken zur Sequenzierung und Detektion von Nukleinsäuren

et al. 2013

View full text Add to dashboard Cite

Nanoporentechniken, die die Funktionen natürlicher Ionenkanäle nachahmen, sind nützliche Methoden für den Einzelmolekülnachweis. Das Verfahren erlaubt die selektive Analyse von Nukleinsäuren in Echtzeit und im Hochdurchsatz. Zwei Arten von Nanoporen finden Anwendung: biologische Nanoporen und Festkörpernanoporen. Dieser Kurzaufsatz beleuchtet die Grundlagen und jüngsten Fortschritte bei der nanoporenbasierten Sequenzierung und Detektion von Nukleinsäuren. Außerdem wird eine neuartige, erst kürzlich eingeführte Nanoporentechnik für die Analyse von Biomolekülen vorgestellt.

show abstract

Encapsulating a Single G-Quadruplex Aptamer in a Protein Nanocavity

Cited by 53 publications

References 68 publications

Interactions of the Human Telomere Sequence with the Nanocavity of the α-Hemolysin Ion Channel Reveal Structure-Dependent Electrical Signatures for Hybrid Folds

Interactions of the Human Telomere Sequence with the Nanocavity of the α-Hemolysin Ion Channel Reveal Structure-Dependent Electrical Signatures for Hybrid Folds

Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel

Nanoporentechniken zur Sequenzierung und Detektion von Nukleinsäuren

Contact Info

Product

Resources

About