scholarly journals Sequence-Specific Detection of DNA Strands Using a Solid-State Nanopore Assisted by Microbeads

Micromachines ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1097
Author(s):  
Yin Zhang ◽  
Zengdao Gu ◽  
Jiabin Zhao ◽  
Liying Shao ◽  
Yajing Kan
Keyword(s):  
Low Cost ◽  
Local Concentration ◽  
Dna Molecules ◽  
Dna Translocation ◽  
Specific Sequence ◽  
Free Dna ◽  
Target Dna ◽  
Dna Strands ◽  
Ionic Pulse ◽  
Biotinylated Probes

Simple, rapid, and low-cost detection of DNA with specific sequence is crucial for molecular diagnosis and therapy applications. In this research, the target DNA molecules are bonded to the streptavidin-coated microbeads, after hybridizing with biotinylated probes. A nanopore with a diameter significantly smaller than the microbeads is used to detect DNA molecules through the ionic pulse signals. Because the DNA molecules attached on the microbead should dissociate from the beads before completely passing through the pore, the signal duration time for the target DNA is two orders of magnitude longer than free DNA. Moreover, the high local concentration of target DNA molecules on the surface of microbeads leads to multiple DNA molecules translocating through the pore simultaneously, which generates pulse signals with amplitude much larger than single free DNA translocation events. Therefore, the DNA molecules with specific sequence can be easily identified by a nanopore sensor assisted by microbeads according to the ionic pulse signals.

PROCEDURES FOR LOGIC AND ARITHMETIC OPERATIONS WITH DNA MOLECULES

2004 ◽  
Vol 15 (03) ◽  
pp. 461-474 ◽  
Author(s):  
AKIHIRO FUJIWARA ◽  
KEN'ICHI MATSUMOTO ◽  
WEI CHEN
Keyword(s):  
Truth Table ◽  
Boolean Operation ◽  
Dna Molecules ◽  
Boolean Operations ◽  
Arithmetic Operations ◽  
Input And Output ◽  
Dna Strands ◽  
Logic Operations ◽  
N Additions

In this paper, we consider procedures for logic and arithmetic operations with DNA molecules. We first show a DNA representation of n binary numbers of m bits, and propose a procedure to assign the same values for the representation. The representation enables addressing feature, and the procedure is applicable to n binary numbers of m bits in O(1) steps in parallel. Next, we propose a procedure for logic operations. The procedure enables any boolean operation whose input and output are defined by a truth table, and executes different kinds of boolean operations simultaneously for any pair of n binary numbers of m bits in O(1) lab steps using O(mn) DNA strands. Finally, we propose a procedure for additions of pairs of two binary numbers. The procedure executes O(n) additions of two m-bit binary numbers in O(1) steps using O(mn) DNA strands.

scholarly journals Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma

2018 ◽  
Vol 115 (46) ◽  
pp. E10925-E10933 ◽  
Author(s):  
Peiyong Jiang ◽  
Kun Sun ◽  
Yu K. Tong ◽  
Suk Hang Cheng ◽  
Timothy H. T. Cheng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Peripheral Circulation ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Plasma Samples ◽  
Dna Molecules ◽  
Plasma Dna ◽  
Cell Free Dna ◽  
Free Dna ◽  
Tumor Dna

Circulating tumor-derived cell-free DNA (ctDNA) analysis offers an attractive noninvasive means for detection and monitoring of cancers. Evidence for the presence of cancer is dependent on the ability to detect features in the peripheral circulation that are deemed as cancer-associated. We explored approaches to improve the chance of detecting the presence of cancer based on sequence information present on ctDNA molecules. We developed an approach to detect the total pool of somatic mutations. We then investigated if there existed a class of ctDNA signature in the form of preferred plasma DNA end coordinates. Cell-free DNA fragmentation is a nonrandom process. Using plasma samples obtained from liver transplant recipients, we showed that liver contributed cell-free DNA molecules ended more frequently at certain genomic coordinates than the nonliver-derived molecules. The abundance of plasma DNA molecules with these liver-associated ends correlated with the liver DNA fractions in the plasma samples. Studying the DNA end characteristics in plasma of patients with hepatocellular carcinoma and chronic hepatitis B, we showed that there were millions of tumor-associated plasma DNA end coordinates in the genome. Abundance of plasma DNA molecules with tumor-associated DNA ends correlated with the tumor DNA fractions even in plasma samples of hepatocellular carcinoma patients that were subjected to shallow-depth sequencing analysis. Plasma DNA end coordinates may therefore serve as hallmarks of ctDNA that could be sampled readily and, hence, may improve the cost-effectiveness of liquid biopsy assessment.

scholarly journals BEAR reveals that increased fidelity variants can successfully reduce the mismatch tolerance of adenine but not cytosine base editors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
András Tálas ◽  
Dorottya A. Simon ◽  
Péter I. Kulcsár ◽  
Éva Varga ◽  
Sarah L. Krausz ◽  
...  
Keyword(s):  
High Throughput ◽  
Genome Engineering ◽  
Sequence Context ◽  
Base Editing ◽  
Target Dna ◽  
Dna Strands ◽  
Deaminase Domain ◽  
Target Effects ◽  
Target Sets

AbstractAdenine and cytosine base editors (ABE, CBE) allow for precision genome engineering. Here, Base Editor Activity Reporter (BEAR), a plasmid-based fluorescent tool is introduced, which can be applied to report on ABE and CBE editing in a virtually unrestricted sequence context or to label base edited cells for enrichment. Using BEAR-enrichment, we increase the yield of base editing performed by nuclease inactive base editors to the level of the nickase versions while maintaining significantly lower indel background. Furthermore, by exploiting the semi-high-throughput potential of BEAR, we examine whether increased fidelity SpCas9 variants can be used to decrease SpCas9-dependent off-target effects of ABE and CBE. Comparing them on the same target sets reveals that CBE remains active on sequences, where increased fidelity mutations and/or mismatches decrease the activity of ABE. Our results suggest that the deaminase domain of ABE is less effective to act on rather transiently separated target DNA strands, than that of CBE explaining its lower mismatch tolerance.

scholarly journals DISMIR: a deep learning-based cancer-detection method by integrating DNA sequence and methylation information of individual cell-free DNA reads

2021 ◽  
Author(s):  
Jiaqi Li ◽  
Lei Wei ◽  
Xianglin Zhang ◽  
Wei Zhang ◽  
Haochen Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Dna Sequence ◽  
Cancer Detection ◽  
High Throughput Sequencing ◽  
Detection Method ◽  
Low Cost ◽  
Sequencing Data ◽  
Cell Free Dna ◽  
Free Dna ◽  
Novel Approach

ABSTRACTDetecting cancer signals in cell-free DNA (cfDNA) high-throughput sequencing data is emerging as a novel non-invasive cancer detection method. Due to the high cost of sequencing, it is crucial to make robust and precise prediction with low-depth cfDNA sequencing data. Here we propose a novel approach named DISMIR, which can provide ultrasensitive and robust cancer detection by integrating DNA sequence and methylation information in plasma cfDNA whole genome bisulfite sequencing (WGBS) data. DISMIR introduces a new feature termed as “switching region” to define cancer-specific differentially methylated regions, which can enrich the cancer-related signal at read-resolution. DISMIR applies a deep learning model to predict the source of every single read based on its DNA sequence and methylation state, and then predicts the risk that the plasma donor is suffering from cancer. DISMIR exhibited high accuracy and robustness on hepatocellular carcinoma detection by plasma cfDNA WGBS data even at ultra-low sequencing depths. Analysis showed that DISMIR tends to be insensitive to alterations of single CpG sites’ methylation states, which suggests DISMIR could resist to technical noise of WGBS. All these results showed DISMIR with the potential to be a precise and robust method for low-cost early cancer detection.

scholarly journals Nanobody Detection of Standard Fluorescent Proteins Enables Multi-Target DNA-PAINT with High Resolution and Minimal Displacement Errors

2018 ◽  
Author(s):  
Shama Sograte-Idrissi ◽  
Nazar Oleksiievets ◽  
Sebastian Isbaner ◽  
Mariana Eggert-Martinez ◽  
Jörg Enderlein ◽  
...  
Keyword(s):  
Fluorescent Proteins ◽  
Super Resolution ◽  
Resolving Power ◽  
Acquisition Time ◽  
Efficient Manner ◽  
Target Dna ◽  
Multiplexed Imaging ◽  
Dna Strands ◽  
Linkage Error ◽  
20 Nm

AbstractDNA-PAINT is a rapidly developing fluorescence super-resolution technique which allows for reaching spatial resolutions below 10 nm. It also enables the imaging of multiple targets in the same sample. However, using DNA-PAINT to observe cellular structures at such resolution remains challenging. Antibodies, which are commonly used for this purpose, lead to a displacement between the target protein and the reporting fluorophore of 20-25 nm, thus limiting the resolving power. Here, we used nanobodies to minimize this linkage error to ~4 nm. We demonstrate multiplexed imaging by using 3 nanobodies, each able to bind to a different family of fluorescent proteins. We couple the nanobodies with single DNA strands via a straight forward and stoichiometric chemical conjugation. Additionally, we built a versatile computer-controlled microfluidic setup to enable multiplexed DNA-PAINT in an efficient manner. As a proof of principle, we labeled and imaged proteins on mitochondria, the Golgi apparatus, and chromatin. We obtained super-resolved images of the 3 targets with 20 nm resolution, and within only 35 minutes acquisition time.

scholarly journals Nanopore design for exceptional rectification of DNA translocation

2021 ◽  
Author(s):  
Ngan Pham ◽  
Yao Yao ◽  
Chenyu Wen ◽  
Shiyu Li ◽  
Shuangshuang Zeng ◽  
...  
Keyword(s):  
Numerical Simulation ◽  
Solid State ◽  
Surface Charge ◽  
Dna Translocation ◽  
Sensor Applications ◽  
Sensor Performance ◽  
On Demand ◽  
Dna Strands ◽  
Large Opening ◽  
Shape And Size

Abstract Solid-state nanopores (SSNPs) of on-demand shape and size can facilitate desired sensor performance. However, reproducible production of arrayed nanopores of predefined geometry is yet to demonstrate despite of numerous methods explored. Here, bowl-shape SSNPs combining unique properties of ultrathin membrane and tapering geometry are demonstrated. The bowl-SSNP upper opening is 100-120 nm in diameter, with the bottom opening reaching sub-5 nm. Numerical simulation reveals the formation of multiple electroosmotic vortexes (EOVs) originating from distributed surface charge around the pore-bowl. The EOVs determine, collaboratively with electrophoretic force, how nanoscale objects translocate the bowl-SSNPs. Exceptional rectification with higher frequencies, longer duration and larger amplitude is found when DNA strands translocate downwards from the upper large opening than upwards from the bottom smallest restriction. The rectification is a manifestation of the interplay between electrophoresis and electroosmosis. The resourceful silicon nanofabrication technology is ingeniously shown to enable innovative nanopore designs targeting unprecedented sensor applications.

scholarly journals Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients

2015 ◽  
Vol 112 (11) ◽  
pp. E1317-E1325 ◽  
Author(s):  
Peiyong Jiang ◽  
Carol W. M. Chan ◽  
K. C. Allen Chan ◽  
Suk Hang Cheng ◽  
John Wong ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatitis B ◽  
Molecular Diagnostic ◽  
Dna Molecules ◽  
Plasma Dna ◽  
Cell Free Dna ◽  
Free Dna ◽  
Size Profile ◽  
A Genome ◽  
Circulating Cell Free Dna

The analysis of tumor-derived circulating cell-free DNA opens up new possibilities for performing liquid biopsies for the assessment of solid tumors. Although its clinical potential has been increasingly recognized, many aspects of the biological characteristics of tumor-derived cell-free DNA remain unclear. With respect to the size profile of such plasma DNA molecules, a number of studies reported the finding of increased integrity of tumor-derived plasma DNA, whereas others found evidence to suggest that plasma DNA molecules released by tumors might be shorter. Here, we performed a detailed analysis of the size profiles of plasma DNA in 90 patients with hepatocellular carcinoma, 67 with chronic hepatitis B, 36 with hepatitis B-associated cirrhosis, and 32 healthy controls. We used massively parallel sequencing to achieve plasma DNA size measurement at single-base resolution and in a genome-wide manner. Tumor-derived plasma DNA molecules were further identified with the use of chromosome arm-levelz-score analysis (CAZA), which facilitated the studying of their specific size profiles. We showed that populations of aberrantly short and long DNA molecules existed in the plasma of patients with hepatocellular carcinoma. The short ones preferentially carried the tumor-associated copy number aberrations. We further showed that there were elevated amounts of plasma mitochondrial DNA in the plasma of hepatocellular carcinoma patients. Such molecules were much shorter than the nuclear DNA in plasma. These results have improved our understanding of the size profile of tumor-derived circulating cell-free DNA and might further enhance our ability to use plasma DNA as a molecular diagnostic tool.

PCR-BASED SYNTHESIS OF REPETITIVE SINGLE-STRANDED DNA FOR APPLICATIONS TO NANOBIOTECHNOLOGY

2005 ◽  
Vol 04 (03) ◽  
pp. 287-294
Author(s):  
SIMA S. ZEIN ◽  
ALEXANDRE A. VETCHER ◽  
STEPHEN D. LEVENE
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Repetitive Sequences ◽  
Practical Interest ◽  
Telomeric Sequence ◽  
Automated Synthesis ◽  
Dna Molecules ◽  
Specific Sequence ◽  
Single Stranded Dna ◽  
Pcr Method

Recent data show that assembly of repetitive-sequence, single-stranded DNA molecules (ssDNA) and carbon nanotubes (CNTs) depend on the specific sequence repeat. Therefore, it is of practical interest to assess various methods for generating single-stranded DNA molecules that contain repetitive sequences. Existing automated synthesis procedures for generating long (> 100 nt) ssDNA molecules generate ssDNA products of variable purity and yield. An alternative to automated synthesis is the polymerase chain reaction (PCR), which provides a powerful tool for the amplification of minute amounts of specific DNA sequences. Here we show that a modified asymmetric PCR method allows synthesis of long ssDNAs comprised of tandem repeats of the repetitive vertebrate telomeric sequence (TTAGGG)n, and is also applicable to arbitrary (repetitive or nonrepetitive) DNA. Long, repetitive deoxynucleotides produced by automated synthesis are surprisingly heterogeneous with respect to both length and sequence. Benefits of the method described here are that long, repetitive ssDNA sequences are generated with high sequence fidelity and yield.

A low-cost, label-free DNA detection method in lab-on-chip format based on electrohydrodynamic instabilities, with application to long-range PCR

Lab on a Chip ◽  
2012 ◽  
Vol 12 (22) ◽  
pp. 4738 ◽  
Author(s):  
Mohamed Lemine Youba Diakité ◽  
Jerôme Champ ◽  
Stephanie Descroix ◽  
Laurent Malaquin ◽  
François Amblard ◽  
...  
Keyword(s):  
Long Range ◽  
Detection Method ◽  
Dna Detection ◽  
Low Cost ◽  
Label Free ◽  
Lab On Chip ◽  
Free Dna ◽  
Chip Format ◽  
Long Range Pcr ◽  
On Chip
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