Gracheva, Maria E.

Nikolaev, Alexey

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Simulation of Ionic Current Through the Nanopore in a Double Layered Semiconductor Membrane 

Sunday, March 6, 2011 167a917-Pos Board B717
Transcription Activation via Transcriptional Bursting
Zach Hensel, Haidong Feng, Bo Han, Christine Hatem, Xuefang Liu,
Jin Wang, Jie Xiao.
Transcription factors (TFs) often regulate their own expression; monitoring TF
production in real time will help elucidate autoregulatory mechanisms. How-
ever, many TFs are expressed at low levels and are difficult to detect. Further,
labeling TFs with fluorescent proteins risks disrupting their regulatory func-
tions. Here, we report a novel strategy, Co-Translational Activation by Cleav-
age (CoTrAC), to monitor autoregulation of a transcription factor, l repressor
cI, in live E. coli cells. CI becomes fully functional upon co-translational cleav-
age from a membrane-targeted fluorescent reporter, which can be counted in-
dividually. Using this strategy, we discovered that cI activates its own
expression via transcriptional bursting_the production of multiple mRNA mol-
ecules in brief, well-separated periods of time. CI increases not only the fre-
quency but also the size of transcriptional bursts. Negative autoregulation by
cI decreases the burst frequency, but not the burst size. These results link acti-
vation of gene expression by a TF to burst-like transcription.
Micro and Nanotechnology; Nanopores I
918-Pos Board B718
Single-Molecule Signatures for Characterization and Regulation
of Nucleic Acids Unzipping in a Nanopore
yong wang, Li-qun Gu.
The nanopore has been developed as a molecule force microscope to explore
the unzipping of nucleic acids. The double-stranded DNA (dsDNA) such as
hairpin with an overhang trapped in the nanopore can generate long current
blocks. By measuring the voltage-dependent block duration, the unzipping ki-
netics as well as the force and energy involved in the double strands hybridiza-
tion can be characterized. However, few studies have presented convincing
characteristic current patterns for unzipping occurrence. In this report, we un-
covered such a signature current pattern that can electrically track the entire un-
zipping process, from the time course of unzipping to the motion pathway of
unzipped single-stranded DNA. With the signature signals, the release of
DNA without unzipping as well as DNA trapping directionality can also be dis-
tinguished. Quantitative analysis of signature signals showed that the overhang
of a DNA is more favorable to the nanopore compared to the blunt end. There-
fore the overhang is not only an unzipping driver, but also a controller of DNA
trapping orientation, regulating the unzipping in a programmable manner. Dis-
crimination of unzipping signatures not only gives precise insight into the un-
zipping mechanism, but more importantly in biosensors, the unzipping
signature can act as a single-molecule marker that ensures both selectivity
and sensitivity.
919-Pos Board B719
Electrostatic Trapping of Polymers During Translocation Through a Semi-
conductor Nanopore
George T. Nelson, Maria Gracheva.
The idea that DNA can be sequenced by threading it through a nanopore and
reading the resulting ionic current is a promising one, but one that has not
yet been realized due to some significant roadbloacks. One such issue is the
speed of translocation, where it is difficult to slow the translocation enough
to achieve a meaninful signal to noise ratio. Our proposed solution to this prob-
lem is to create a nanopore in a semiconductor membrane that contains a p-n
junction. In this way, it should be possible to create a voltage difference across
the pore that can momentarily trap DNA base pairs as they move down the elec-
trophoretic gradiant. Presented herein is a computational method for modeling
single-stranded DNA molecules as they undergo translocation through a semi-
conductor nanopore constructed as described above. The results of this Lange-
vin dynamics indicate how effective this type of nanopore is at reducing
translocation times. Furthermore, this simulation provides a better understand-
ing of how to optimize our nanopore for the eventual long term goal of sequenc-
ing DNA base pairs based upon their blocked ionic current signature.
920-Pos Board B720
Unidirectional Translocation of DNA Through the Phi29 Connector
Channel
Peng Jing, Farzin Harque, Dan Shu, Carlo Montemagno, Peixuan Guo.
Nanobiomedical Center, College of Engineering and College of Medicine,
University of Cincinnati, Cincinnati, OH 45267, USA.
When channel diameter is reduced to the nm range (<10 nm), the interaction
between the solution and channel wall starts to dominate ionic flow. An inter-
esting phenomenon, ion current rectification, has thus been well studied, which
has found its application in logic gates and diodes in fluidic circuits.Similar to the ion current rectification, we have found DNA transport through
the connector channel experienced a one-way traffic mechanism. Using NTA-
Ni Nanogold, we characterized the DNA transport directionality by means of
single channel recording, i.e., DNA can only go through the Phi29 connector
channel from the N-terminal narrow end to the C-terminal wide end. The
uni-directional control in dsDNA transportation would potentially provide
a novel system with a natural gate to control dsDNA loading and gene delivery
in bioreactors, liposomes, and other nano-machines. The findings also forecast
a ratchet or valvular mechanism of the viral DNA packaging motor.
921-Pos Board B721
Mapping the Sensing Zone of Alpha-Hemolysin Using Immobilized DNA
Containing a Single Abasic Residue
Eric N. Ervin, John J. Watkins, Geoffrey A. Barrall, Prithwish Pal,
Michael G. Keehan, Andrew D. Hibbs.
As efforts to sequence individual strands of DNA using biological nanopores
continue to evolve, it has become increasingly important to understand the na-
ture of the DNA-nanopore interaction. More specifically, characterizing the
‘‘sensing’’ zone inside the nanopore is an important part of understanding
how nucleotide differentiation occurs. In order to characterize the sensing
zone of the biological nanopore alpha-Hemolysin (aHL), we have examined
how an adenine homopolymer containing a single abasic site blocks current
flow through an aHL pore as the position of the abasic site is moved sequen-
tially through the pore. In these experiments, single stranded DNA (ssDNA) ol-
igonucleotides with a biotin (BTN) group at the 3’ terminus were allowed to
complex with streptavidin. Due to the inability of the large streptavidin to trans-
locate through the aHL, the attached oligonucleotide could be electrophoreti-
cally immobilized inside the pore. Creating and capturing numerous
oligonucleotides in which the single abasic site was positioned progressively
farther from the BTN termination (e. g. 7 adenines from the BTN end, 8 ade-
nines from the BTN end, etc.) allowed a blocking current map of the aHL lu-
men to be developed. This blocking current map of aHL yielded a single peak,
which is approximately two nucleotides in width, centered midway through the
aHL pore where the beta-barrel meets the vestibule. This single peak corre-
sponds to the primary sensing zone of aHL. Further experiments have demon-
strated that both the width and location of the primary sensing zone can be
altered by creating mutant aHL proteins in which the residues inside the
aHL pore have been changed. These studies should prove integral in creating
a class of mutant aHL pores capable of discriminating between single nucleo-
tides in ssDNA.
922-Pos Board B722
Simulation of Ionic Current Through the Nanopore in a Double Layered
Semiconductor Membrane
Alexey Nikolaev, Maria E. Gracheva.
Starting with a description of an electrostatic model of a double-layered semi-
conductor membrane immersed in an electrolyte solution, we provide a compar-
ison of the electric potential and ionic concentrations in a nanopore for different
nanopore geometries (double-conical, single-conical, cylindrical) and for vari-
ous voltages applied to the membrane. Voltage-current characteristics for ionic
currents, as well as their rectification ratios are calculated using a simple ion
transport model. The rectification ratio is found to be a linear function of poten-
tial variation in the pore. Based on our calculations, we find that the double lay-
ered semiconductor membrane with a single-conical nanopore with a narrow
opening in the n-Si layer exhibits the largest range of available potential vari-
ations in the pore, and thus, may be better suited for control of polymer trans-
location through the nanopore.
923-Pos Board B723
Determining the Resolution of Biological Porin Mspa for Nanopore
Sequencing
Elizabeth A. Manrao, Ian M. Derrington, Mikhail Pavlenok,
Michael Niederweis, Jens H. Gundlach.
Nanopore sequencing has the potential to become a fast and low-cost DNA se-
quencing platform. The ion current passing through a small pore identifies the
sequence of single stranded DNA (ssDNA) electrophorically driven through the
constriction. A mutant pore protein, MspA, derived from Mycobacterium
smegmatis forms a short and narrow channel ideal for resolving single nucle-
otides. To study the resolution, we immobilize ssDNA within the pore using
a biotin-NeutrAvidin complex. Each base, adenine, cytosine, thymine, and gua-
nine, produces a distinct current signature and methylated cytosine is distin-
guishable from unmethylated cytosine. Single heteronucleotide substitutions
within homopolymer ssDNA are used to characterize the resolution of the
pore. Using single nucleotide polymorphisms, we show that single nucleotides
within heteromeric ssDNA can be identified when the substitution is held in


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Simulation of Ionic Current Through the Nanopore in a Double Layered Semiconductor Membrane

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