Related Experiment Video
Updated: Jul 13, 2026
09:43
Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores
Published on: October 31, 2013
Ionic current blockades from DNA and RNA molecules in the alpha-hemolysin nanopore
Tom Z Butler1, Jens H Gundlach, Mark Troll
1Department of Physics, University of Washington, Seattle, Washington, USA. twb2@u.wasington.edu
Biophysical Journal
|August 7, 2007
Summary
Single-stranded polynucleotides form current blockades in alpha-hemolysin pores, showing distinct substates. Polymer orientation and voltage influence translocation dynamics and escape from the pore vestibule.
Area of Science:
- Biophysics
- Nanotechnology
- Molecular Biology
Background:
- The alpha-hemolysin (α-HL) protein pore is a well-established model system for single-molecule studies.
- Understanding ion current blockades is crucial for nanopore sensing applications.
Purpose of the Study:
- To characterize the substate structure of ionic current blockades induced by single-stranded polynucleotides in the α-HL pore.
- To investigate the influence of polymer orientation and applied voltage on translocation dynamics.
Main Methods:
- Electrophoretic manipulation of single-stranded polynucleotides into the α-HL pore.
- Analysis of ionic current blockades and substates.
- Development of a semiquantitative model to explain observed trends.
Main Results:
- Frequent observation of current blockades reduced by ~50%, associated with polymer occupying vestibule or beta-barrel regions.
- Polymer escape from the vestibule is favored at low voltages (<140 mV), while threading and translocation dominate at higher voltages.
- Applied voltage increases vestibule configuration duration; escape is voltage-dependent and orientation-independent, while threading is orientation-dependent.
Conclusions:
- The α-HL pore system effectively reveals single-molecule physical and chemical processes.
- Polymer-pore interactions are complex, influenced by voltage, polymer orientation, and pore geometry.
- These findings advance the understanding of nanopore translocation mechanisms for potential biosensing applications.
Related Concept Videos
01:52Eukaryotic Transcription Inhibitors
Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a DNA...
Eukaryotic transcription inhibitors usually contain two distinct domains, a DNA...
01:25Inhibitors of Bacterial Protein Synthesis
Aminoglycosides constitute a highly potent class of bactericidal antibiotics that exert their antimicrobial effects by targeting the bacterial ribosome, specifically disrupting protein synthesis. These polycationic molecules consist of amino-modified sugars linked via glycosidic bonds to an aminocyclitol core such as 2-deoxystreptamine or streptamine. Their strong positive charges facilitate tight binding to the negatively charged phosphate backbone of ribosomal RNA (rRNA), primarily at the 16S...
01:28Inhibitors of Bacterial DNA Synthesis
Bacterial pathogens depend on precise and efficient DNA replication to sustain infection. Two type II topoisomerases—DNA gyrase and topoisomerase IV—are critical to this process, as they resolve DNA supercoiling and unlink chromosomes during replication. Fluoroquinolones, synthetic derivatives of quinolones, exploit this mechanism by stabilizing the transient DNA–enzyme cleavage complex, preventing strand religation, and causing lethal double-strand breaks. These antibiotics are selectively...
02:02DNA Topoisomerases
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...
01:03Single-Strand DNA Binding Proteins
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
00:55DNA Helicases
DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...