Sequencing Deoxyribonucleic Acid Research Articles

High-scale random access on DNA storage systems.

ABSTRACTDue to the rapid cost decline of synthesizing and sequencing deoxyribonucleic acid (DNA), high information density, and its durability of up to centuries, utilizing DNA as an information storage medium has received the attention of many scientists. State-of-the-art DNA storage systems exploit the high capacity of DNA and enable random access (predominantly random reads) by primers, which serve as unique identifiers for directly accessing data. However, primers come with a significant limitation regarding the maximum available number per DNA library. The number of different primers within a library is typically very small (e.g. ≈10). We propose a method to overcome this deficiency and present a general-purpose technique for addressing and directly accessing thousands to potentially millions of different data objects within the same DNA pool. Our approach utilizes a fountain code, sophisticated probe design, and microarray technologies. A key component is locality-sensitive hashing, making checks for dissimilarity among such a large number of probes and data objects feasible.

The Usability Testing of SSAAT, a Bioinformatic Web Application for DNA Analysis at a Nucleotide Level

Sanger sequencing remains the cornerstone method for Deoxyribonucleic Acid (DNA) sequencing due to its high accuracy in targeting smaller genomic regions in a larger number of samples. The analysis of Sanger sequence DNA data requires powerful and intelligent software tools. Most of the preferred tools are proprietary licensed tools that offer a user-friendly interface and have many features, however, their affordability, especially to individual scientists or students, is limited. On the other hand, a few free and open-source licensed tools are available but have limited features. This study focuses on the usability testing of the developed Sanger Sequence Automatic Analysis Tool (SSAAT), a free and open-source web tool for Sanger sequence analysis. Usability tests were conducted with potential users and the results demonstrate that the participants were able to use the tool easily and accomplish the test tasks at the given time. Moreover, the participants were excited with the easy-to-use interface and agreed that most users could use the tool with no need for technical assistance. However, the participants also identified some issues that require more development effort.

Notice of Violation of IEEE Publication Principles: Construction of GC-Balanced DNA With Deletion/Insertion/Mutation Error Correction for DNA Storage System

Synthetic deoxyribonucleic acid (DNA) is a good medium for storing digital data for a long period due to its achievable high data storage density and outstanding longevity. However, synthesizing and sequencing DNA sequences in a DNA storage system are prone to a wide variety of errors, including insertion, deletion and mutation errors. At the same time, it is known that DNA sequences with 50% GC content are less susceptible to errors. This paper presents the construction of a GC-balanced DNA sequence with error correction capability. A systematic single insertion/deletion/substitution error correction code is first proposed and then used to design a GC-balanced scheme for synthesizing DNA sequences. With the proposed method, DNA sequences with exactly 50% GC content are constructed. Such DNA sequences not only have the maximum endurance to errors, but are able to correct both insertion/deletion and mutation of the nucleotide bases. The decoding procedures for the sequences are described and can readily be used in practice. Simulation results show that the proposed GC-balanced DNA sequences can correct base errors adequately.

In Silico Analysis Using Hybrid Support Vector Machine and Second Order of Markov Chain for Multiple Sequence Alignment to Identify the Types of Leukaemia

Cancer is a disease that causes an abnormal growth of cells and can attack every part of the body, which is occurred because of a damage in deoxyribonucleic acid (DNA) that leads to a mutation in a vital gene that controls cell division. The biomarker technology that used in clinical practice still used a high cost and need a long time to detect the cancer signs. As the former studies about cancer, the biomarker has been detected in the microarray data. In this paper, we used a support vector machine (SVM) to classify 4 type of leukaemia. Begin with extracting the data feature of sequence DNA from a string into numeric using Second order of Markov chain, SVM classified DNA using 40 data for the training step and 25 data for testing step. In this paper, SVM used 3 types of the kernel, which are linear, Gaussian radial basis function, and polynomial. The results showed that the Gaussian kernel has the best accuracy then other kernel.

Transcriptional repressor CopR: Structure model-based localization of the deoxyribonucleic acid binding motif

The plasmid pIP501 encoded transcriptional repressor CopR is one of the two regulators of plasmid copy number. CopR binds as a dimer to a nearly palindromic operator with the consensus sequence 5'-CGTG. Intermediate sequence searches revealed a significant structural relationship between CopR and the bacteriophage P22 c2 and the 434 c1 repressors. In this report we describe the experimental verification of a CopR homology model, which is based on a fairly low-sequence identity of 13.8% to P22 c2 repressor. A model for the complex of CopR with the deoxyribonucleic acid (DNA) target was built on the basis of experimental footprinting data, the above-mentioned CopR homology model, and the crystal structure of the 434 c1 repressor-DNA complex. Site-directed mutagenesis was used to test the function of amino acids involved in sequence and nonsequence-specific DNA recognition and amino acids important for correct protein folding. CD measurements were performed to detect structural changes caused by the mutations. Exchanges of residues responsible for sequence-specific DNA recognition reduced binding to a nonspecific level. Mutations of amino acids involved in nonspecific DNA binding lead to decreased binding affinity while maintaining selectivity. Substitution of amino acids necessary for proper folding caused dramatic structural changes. The experimental data support the model of CopR as a helix-turn-helix protein belonging to the lambda repressor superfamily.

Progress in sequencing deoxyribonucleic acid with an atomic force microscope

Atomic force microscope (AFM) images of single-stranded deoxyribonucleic acid (DNA) showing nucleotide resolution have been obtained using two sample preparation methods: DNA covalently attached to a polymerized lipid monolayer and then imaged under water and DNA on mica rinsed with a Ba(NO3)2 solution and then imaged under ethanol. Some of the bases were identified in the AFM image of DNA on polymerized lipid. Current problems in sequencing DNA with the AFM include movement of the DNA during imaging and the difficulty of reproducing experiments.

18] Direct transfer electrophoresis used for DNA sequencing

This chapter discusses the utilization of direct transfer electrophoresis for deoxyribonucleic acid (DNA) sequencing. As the maximal number of nucleotides that can be read correctly in a single electrophoresis run is of importance for the economy of sequencing projects, considerable efforts have also been devoted for improving electrophoretic methods. Very thin and temperature-controlled gels improve the resolution. The methodology developed for genomic sequencing with the use of specific hybridization reactions offers a new approach for the sequencing of nucleic acids. For this approach, the mixture of DNA molecules has to be blotted and covalently fixed to a membrane after separation by electrophoresis. Direct transfer electrophoresis can simplify this process. The chapter describes the authors' experience of using the electrophoresis method for sequencing DNA. The direct transfer method can or has been used also for other blotting procedures, such as Southern, Northern, or Western blotting. The chapter discusses materials and methods, including design of the apparatus for DNA sequencing, setting up of an experiment, comparison between standard and direct transfer electrophoresis for DNA sequencing, and so on.

9] pEMBL: A new family of single-stranded plasmids for sequencing DNA

This chapter describes a series of plasmids, the “pEMBL family,” that have the property of being encapsidated as single-stranded deoxyribonucleic acid (DNA) upon superinfection with phage F1. The plasmids can be used for DNA sequencing and for all the other uses that require single-stranded DNA, but, in the absence of F1 helper phage, they replicate as any other doubles-stranded plasmid. This is very useful for the preparation of a large quantity of plasmid and for the stability of longer inserts. The class of M13 derivative vectors, largely used for DNA sequencing with the dideoxy method, has, in fact, the limitation that large inserts tend to be unstable. The chapter discusses the principle of the method and characteristics of pEMBL vectors along with the construction of pEMBL plasmids. The chapter discusses the property of a short segment of F1 genome containing all the cis-acting elements for DNA replication and morphogenesis. To have a series of polylinkers containing a large number of unique sites for restriction endonucleases, in different reciprocal orientation is very useful, because it allows the insertion of DNA fragments in a preselected orientation or in a preselected frame inside the sequence encoding the a-fragment of th/3-galactosidase. The DNA, which is prepared through the procedures described in the chapter, is suitable for DNA sequencing experiments with the dideoxy method.

16] A new and simple rapid method for sequencing DNA

Publisher Summary This chapter describes a current and simple rapid method for sequencing long fragments of deoxyribonucleic acid (DNA) by combining the advantages of the two systems: (1) a systematic shortening of double-stranded DNA and (2) subcloning. In this method, a fragment of DNA carrying the origin of replication from a single-stranded phage, F1 or M13, is inserted into a plasmid to make a single-stranded:double-stranded bifunctional plasmid of the shortened fragments into sequencing vectors. The new family of bifunctional plasmid constructed is of pAA-PZ1, pAA-PZ2, pAA-PZ3, and pAA-PZ4. The chapter presents the methods in a simplified way for selecting the transposon-generated deletion plasmids of different sizes and for isolating the single-stranded plasmid DNA for DNA sequence analysis. The chapter discusses solutions, buffers, media, and sources of enzymes for the method. The chapter also discusses construction and properties of pAA-PZ plasmids, construction and property of E. coli strain AA102F', cloning of foreign DNA into pAA-PZ plasmids, and several related concepts and procedures.