• DNA Sequencing Basics and its Applications

    Manu Mitra*

     

    Department of Electrical Engineering, University of Bridgeport, 126 Park Avenue, Bridgeport, CT - 06604, USA

    *Correspondence to: Manu Mitra

    Citation: Mitra M (2018) DNA Sequencing Basics and its Applications. SCIOL Genet Sci 2018;1:80-84.

  • Introduction


    DNA (Deoxyribonucleic Acid) sequencing is to determine the order of four chemical building blocks called "bases" that makes up DNA molecule. DNA sequence is a genetic information that is carried out in specific DNA segment. This DNA sequence information can be used to determine which stretches of DNA that contain genes and which transmit supervisory instructions, turning genes on or off and most importantly, sequence data can highlight variations in a gene that may cause disease.

    In DNA sequence, double helix, the four chemical bases constantly bond with the same paradigm to form base pairs. For instance, adenine (A) always sets with thymine (T); cytosine (C) always sets with guanine (G). This paring is the basis for the mechanism by which DNA molecules imitate when cells divide. Human genome contains about 3 billion base pair sets that have instructions for making and maintaining a human being (Figure 1) [1,2].

    Figure 1

     

    Figure 1: Illustrates DNA Genome Sequence and its fragment Reads [2]. View Figure 1

     

    Single Molecule DNA Sequencing


    Till date, the cost and speed involved in attaining highly accurate DNA sequences has been major challenge. Whereas, various developments have been made over the past decades, high throughout sequencing instruments have widely used; today completely depends on optics for detection of four DNA blocks: A, C, G and T. To discover alternative measurement capabilities, electronic sequencing of an ensemble of DNA templates have been established for genetic analysis. Nanopore component sequencing, at same time; an absolute component of DNA may be circled through the nanoscale apertures under supplied electrical voltage produces electronic signals to arrangement during single elemental level, has recently been discovered. However, because the four nucleotides are very alike in their chemical structures, they cannot be easily recognized using this technique. Experts are therefore actively tracking the research and development of an accurate single molecule electronic DNA sequencing platform as it has the possible potential to generate a miniaturized DNA sequencer was able to perform to decipher the genome to facilitate personalized precision medicine.

    A group of scientists at Columbia Engineering, supervised by Jingyue Ju have discovered a complete system to sequence DNA in nanopores electronically at single molecule level with single base resolution. This work is entitled as "Real Time Single Molecule Electronic DNA Sequencing by Synthesis Using Polymer Tagged Nucleotides on a Nanopore Array" (Figure 2) [3-5].

    Figure 2

     

    Figure 2: Illustrates single molecule nanopore DNA sequencing by synthesis data from a template with homopolymer sequences Image Credit: Jingyue Ju, Columbia Engineering [5]. View Figure 2

     

    Electronic DNA Sequencing: Transformation through Graphene Nanopores


    Expert researchers at University of Pennsylvania have developed a new carbon-based nanoscale platform to electronically detect single DNA molecule. Using electric fields, very minute DNA strands are pushed through nanoscale sized, atomically may be important for quick electronic sequencing of four chemical bases of DNA on their distinctive electrical signature. The pores, scorched into graphene membranes using electron beam technology, providing physicists with electronic measurements of transformation of DNA. The pore distributes into two chambers of electrolyte solution and experts apply voltage, which drives ions through the pores. Ion transportation is determined when current flowing from the voltage source. DNA molecules inserted into the electrolyte that can be driven single file through such nanopores.

    "We need to explore more on the unique properties of graphene; a two-dimensional sheet of carbon atoms. In order to develop a new nanopore electrical platform that could display high resolution" was stated by Marija Drndić, associate professor in the Department of Physics and Astronomy in Penn's School of Arts and Sciences (Figure 3) [6,7].

    Figure 3

     

    Figure 3: Illustrates carbon based, nanoscale platform to electronically detect single DNA molecules. Electric fields push minute DNA strands through atomically thin graphene nanopores that ultimately may sequence DNA bases by their unique electrical signatures. Image Credit: Robert Johnson [7]. View Figure 3

     

    Ancient Eurasian DNA Sequencing Linked with Modern Humans


    Scientists at Chinese Academy of Sciences understood that in Eurasia between 35,000 and 45,000 years ago, at least four distinct populations were present. These were actually early Europeans and Asians, as well as populations with ancestry that is hardly found or not all in modern populations. By 15,000-34,000 a significant time ago, DNA sequencing uncovered that current mankind's for Eurasia are alike to Asians or on Europeans, suggesting that a hereditary Asian- Europeans less averse to happened former on 40,000 prior to 40,000 years ago. By 7,500-14,000 years ago, the inhabitants across Eurasia shared genetic similarities, suggesting greater interactions between geographically distant inhabitants. These investigations also revealed at least two Neanderthal inhabitants mixing events, one approximately 50,000-60,000 years ago and a second more than 37,000 years ago. This Neanderthal ancestry steadily declined in archaic ancestry in Europeans ranging from 14,000-37,000 years ago (approximately).

    Genetic studies of ancient individuals have become more common in recent years because of technology. As an outcome, we can now see the presence of multiple distinct subpopulations in Asia and Europe and these in turn subsidize different amounts of ancestry to more subpopulations was said by Fu (Figure 4) [8,9].

    Figure 4

     

    Figure 4: Illustrates schematic of inhabitants in Eurasia and the Americas from 45,000 to 7,500 years ago. A brief of major events in each of the time periods is on the left. Image Credit: Melinda A Yang and Qiaomei Fu [9]. View Figure 4

     

    First DNA Sequence from Mitochondria


    Mitochondria is a component of cells that have their own DNA (mtDNA), generates energy for the body, among other functions. One mitochondrion can contain 10 or more divergent genomes with hundreds to thousands of individual mitochondria residing in each cell. A large quantity of mitochondrial diseases arises from mutations adding in mtDNA. For instance, these mutations have been found in colorectal, ovarian, breast, bladder, kidney, lung and pancreatic tumors. Utilizing various methods James Eberwine and their team extracted single mitochondrion and then extracted its mtDNA. They separated mutations that would introduce over single mitochondrion in unique mouse human neurons and found that mouse cells required a greater amount amassed mutation contrasted with human units. Because of their findings that mutations accumulate at a dissimilar rate in mice versus human, Eberwine records that one vital information to take from the study is to ensure that mitochondrial diseases or potential therapeutics in cells are investigated in models where the mutations parallel those that occur in humans.

    "This roadmap of the location and number of mutations within the DNA of a mitochondrion and across all of a cell's mitochondria is where we have to start" was confirmed by Eberwine (Figure 5) [10,11].

    Figure 5

     

    Figure 5: Illustrates Manual isolation of a single live mitochondria. The mitochondria can be seen under a microscope where a thin glass tube can be used to isolate mitochondria from the dendrite region of a mouse neuron. Image Credit: Jacqueline Morris and Jaehee Lee, Perelman School of Medicine, University of Pennsylvania [11]. View Figure 5

     

    DNA Sequencing Through Nanopore of Graphene


    Traditional sequencing was developed in the year 1970's that involves separating, copying, labeling and reassembling pieces of DNA to read the genetic information. The new model of National Institute of Standards and Technology (NIST) proposal is a new turn on the more recent "nanopore sequencing" of pulling DNA through a hole in specific materials, initially a protein. This concept was initiated 20 years ago at NIST; it is based on the passage of electrically charged particles (ions) through pore. The concept remains popular but poses challenges such as unwanted electrical noise, interference and inadequate selectivity. Graphene is more popular in nanopore sequencing applications due to its electrical properties and miniaturized thin film structure. In this new method, a graphene nanoribbon (4.5 by 15.5 nm) has multiple copies of a base involved to the nanopore (2.5 nm wide). DNA's genetic code is built from four kinds of bases which bond pairs as cytosine-guanine and thymine-adenine.

    The authors decided that those anticipated technique reveals to "significant guarantee for reasonable DNA sensing devices" without those advanced reason for propelled microscopes, propelled information transforming alternately profoundly confined working states. Theoretical analysis suggests that simple electronic filtering methods can isolate useful electrical signals. The suggested method can also be used with other strain sensitive membranes, for instance molybdenum disulfide (Figure 6) [12,13].

    Figure 6

     

    Figure 6: Illustrates National Institute of Standards and Technology (NIST) idea for DNA sequencing through a graphene nanopore. Image Credit: Smolyanitsky/NIST [13]. View Figure 6

     

    Acknowledgment


    Author would like to thank Prof. Navarun Gupta, Prof. Hassan Bajwa, Prof. Linfeng Zhang and Prof. Hmurcik for their academic support. Author also thanks anonymous reviewers for their comments.

    Conflicts of Interest


    There is no conflict of interest as per Author's point of view.

    References


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