Detecting translocation of individual single stranded DNA homopolymers through a fabricated nanopore chip

Kim, Young-Rok; Li, Chang Ming; Wang, Qiao; Chen, Peng

doi:10.2741/2287

Cited by 10 publications

(6 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There is potential to optimize both the speed and sensitivity of DI sequencing by altering operating parameters such as pH and ionic strength of the buffer, using duplex-binding reagents, improving oligo annealing, and using more sophisticated data analysis techniques (28). In comparison to previously proposed sequencing methods involving converted DNA (19,29), DI sequencing does not require additional hardware such as fluorescence detection or conversion to binary codes. While DI sequencing is a promising step forward, the realization of MspA-based nanopore sequencing using unmodified DNA remains the primary goal of our research.…”

Section: Sequencing Proof Of Principle Experimentsmentioning

confidence: 99%

Nanopore DNA sequencing with MspA

Derrington

Butler

Collins

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

483

473

View full text Add to dashboard Cite

Nanopore sequencing has the potential to become a direct, fast, and inexpensive DNA sequencing technology. The simplest form of nanopore DNA sequencing utilizes the hypothesis that individual nucleotides of single-stranded DNA passing through a nanopore will uniquely modulate an ionic current flowing through the pore, allowing the record of the current to yield the DNA sequence. We demonstrate that the ionic current through the engineered Mycobacterium smegmatis porin A, MspA, has the ability to distinguish all four DNA nucleotides and resolve single-nucleotides in single-stranded DNA when double-stranded DNA temporarily holds the nucleotides in the pore constriction. Passing DNA with a series of double-stranded sections through MspA provides proof of principle of a simple DNA sequencing method using a nanopore. These findings highlight the importance of MspA in the future of nanopore sequencing.bionanotechnology | next generation sequencing | single-molecule | stochastic sensing | protein pore T he information encoded in DNA is of paramount importance to medicine and to the life sciences. The mapping of the human genome is revolutionizing the understanding of genetic disorders and the prediction of disease and will aid in developing therapies as in refs. 1-3. The ability to sequence DNA quickly and inexpensively is essential to individualized medicine and to scientific research and has prompted the development of new sequencing techniques beyond the original Sanger sequencing (4-7). Nanopore DNA sequencing represents one of the approaches being developed to rapidly sequence a human genome for under $1,000 (www.genome.gov/12513210).In the most elementary form of nanopore DNA sequencing, a nanometer-scale pore provides the sole pathway for an ionic current. Single-stranded DNA (ssDNA) is electrophoretically driven through the pore, and as the ssDNA passes through, it reduces the ionic current through the pore. If each passing nucleotide yields a characteristic residual ionic current then the record of the current will correspond to the DNA sequence. This simple and reagent-free sequencing technique holds the promise to inexpensively read long lengths of DNA molecules at intrinsically fast rates (8). Due to its inherently small size, this system is amenable to parallelization (9).Lately, nanopore sequencing techniques have progressed substantially. This progress and the remaining challenges in nanopore DNA sequencing are summarized in a review article by Branton et al. (8). While nanotechnology usually involves materials such as Si and SiN, nanopore DNA sequencing first evolved using the well-studied protein porin α-hemolysin (10). In contrast to pores made from inorganic materials (11, 12), protein pores can be easily modified and produced with repeatable subnanometer accuracy. Stoddart (13) and Purnell (14) demonstrated that several locations within the beta barrel of α-hemolysin exhibit nucleotide-specific sensitivity with immobilized ssDNA (13). However, α-hemolysin's 5 nm-long cylindrical beta barrel presents...

show abstract

Section: Sequencing Proof Of Principle Experimentsmentioning

confidence: 99%

Nanopore DNA sequencing with MspA

Derrington

Butler

Collins

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

483

473

View full text Add to dashboard Cite

show abstract

“…In summary, nanotechnology is bringing tremendous new opportunities to biology Kim et al, 2007). As another example, herein, we show that SWNT-net can be used as growth substrate for astrocytes and label-freely detects local ATP release from these cells.…”

Section: Discussionmentioning

confidence: 95%

Label-free detection of ATP release from living astrocytes with high temporal resolution using carbon nanotube network

Huang

Sudibya

et al. 2009

Biosensors and Bioelectronics

View full text Add to dashboard Cite

“…Although nanopores were primarily developed for nucleic acid sequencing, due to their effectiveness and versatility, nanopores are employed in a variety of applications, especially for probing single molecules. A number of applications of nanopores are already reported to detect and probe a variety of biomolecules such as single-stranded (ss) DNA [394][395][396][397][398][399][400], double-stranded (ds) DNA [400][401][402][403][404][405][406], RNA [407][408][409][410], proteins [275,[411][412][413][414], ribosomes [275,415] etc. Another remarkable feature of nanopores is their integration capabilities.…”

Section: Electrical Methods For Single-molecule Experimentsmentioning

confidence: 99%

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Rahman

Islam

et al. 2022

Micromachines

View full text Add to dashboard Cite

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

show abstract

Detecting translocation of individual single stranded DNA homopolymers through a fabricated nanopore chip

Cited by 10 publications

References 21 publications

Nanopore DNA sequencing with MspA

Nanopore DNA sequencing with MspA

Label-free detection of ATP release from living astrocytes with high temporal resolution using carbon nanotube network

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Contact Info

Product

Resources

About