What is DNA?
DNA (deoxyribonucleic acid) is a material that contains an encoded version of all the information necessary to build and maintain an organism. DNA is a nucleic acid - a large biological molecule composed of building units called nucleotides (guanine, adenine, thymine and cytosine). Most DNA molecules consist of two biopolymer strands, coiled around each other to form a double helix.
When organisms reproduce, biological information in replicated as the two strands separate and a portion of their DNA is passed along to their offspring, helping to ensure continuity between generations (while allowing changes that create diversity). A gene is a segment of DNA that is passed down from parents to children and confers a trait to the offspring. Genes are organized in units named chromosomes - humans have 23 pairs of them, one from the mother and one from the father. An entire set of genes, 46 chromosomes in total, is a genome.
All living organisms have DNA within their cells, and nearly every cell in a human being contains a full set of DNA. DNA can replicate, and each strand of the double helix can serve as a pattern for duplicating the sequence of bases from the other strand, because bases pair together in a certain way - A with T, C with G. The order of these bases determines the information for building the organism, similar to how letters of the alphabet appear in a certain order to form words.
What is DNA sequencing?
DNA sequencing is the process of determining the order of nucleotide bases in a DNA molecule. It may be used for determining sequences of specific genes, clusters of genes, full chromosomes or even entire genomes. Knowing the sequence of bases helps understand the nature of genetic information in a particular segment of DNA, which can have diverse applications like identifying gene associations with diseases, understanding developmental processes in humans, studying evolution of different species, manipulating plants and agriculture for various ends, acquiring a deeper understanding of microbes and viruses and more.
How is DNA sequencing done?
Basic DNA sequencing methods include the Maxam-Gilbert method, also known as chemical sequencing, which was developed in 1977 and is based on chemical modification of DNA and cleavage at specific bases. The method’s use of radioactive labelling and its technical complexity hindered its extensive use. Another method invented in 1977 is the Sanger method, or chain-termination, which is relatively easy, reliable and uses fewer toxic chemicals and radioactivity. It was quickly adopted into use and further along became automated, and was even used in the first generation of DNA sequencers. Technological advances of the following decades enabled it to become more efficient and less expensive, resulting in its use in the first human genome project in 2001.
A large number of different methods and approaches reached the market following drastic technological changes, with different applications ranging from mapping an entire genome to a targeted search of specific genomic region. Some approaches are used to determine the sequence of DNA with no previously known sequence (“de novo” methods), some are “shotgun” sequencing, which means sequencing long strands of DNA by breaking the target DNA into random fragments and later reassembling them, and next generation methods are constantly researched, opting to lower costs, improve efficiency and cater to various sequencing needs.
Graphene and DNA sequencing
Graphene is a material made from honeycomb sheets of carbon just one atom thick. Science journals and researchers are exhausted from trying to find new superlatives for this wondrous material: it's the lightest, strongest, thinnest, best heat and electricity conducting material ever discovered. It holds promise to revolutionize everything from computing to tennis rackets.
In the fields of biotechnology and medicine, it seems graphene’s thin form and malleable nature make it well suited for many possible applications such as disease and tumor detection, drug delivery, DNA sequencing and more. In DNA sequencing, a main concept is creating a graphene membrane, immerse it in conductive fluid and apply a voltage to one end so DNA can be drawn through the graphene’s miniscule pores. This method is called nanopore sequencing and it would allow DNA to be analyzed one nucleotide at a time (each nucleotide effecting the membrane differently due to its unique dimensions and electrical properties). Additional concepts involve graphene-based DNA sensors, and alternative ways of making DNA sequencing faster and more efficient.
The latest graphene DNA sequencing news:
Researchers at the Institute for Basic Science (IBS) managed to observe the movement of molecules stored inside a graphene pocket without the need to stain them. This study opens the door to using graphene for observing the dynamics of life building blocks like proteins, DNA and more.
Due to its operating mechanism, electron microscopy is known to be suitable for visualizing inert, dead samples, while living material needs to be chemically locked in place. IBS scientists broke this rule and visualized non-fixed chains of atoms, called polymers, swimming in a liquid inside graphene pockets. These consist of 3-5 graphene layers on the bottom and two on top. The sheets are impermeable to small molecules, and also prevent the electron beam from instantly harming the sample: the scientists had an average of 100 seconds to admire the dynamic movement of individual polymer molecules, before these were destroyed by the electron beam. During these valuable seconds, molecules change position, rearrange or "jump around".
Researchers in India and Japan have developed an improved method for using graphene-based transistors to detect disease-causing genes.
The team improved sensors that can detect genes through DNA hybridization, which occurs when a 'probe DNA' combines with its complementary 'target DNA.' Electrical conduction changes in the transistor when hybridization occurs. The improvement was done by attaching the probe DNA to the transistor through a drying process. This eliminated the need for a costly and time-consuming addition of 'linker' nucleotide sequences, which have been commonly used to attach probes to transistors.
A team of researchers at the University of California, San Diego, is developing a chip that has a graphene field effect transistor which contains a DNA probe. The double-stranded DNA has a sequence coding engineered to detect DNA or RNA with a specific single nucleotide mutation. An electrical signal is produced by the chip whenever this targeted type of DNA or RNA binds to the probe.
Attached to the probe is a regular strand of DNA, and bonded to this strand is a “weak” strand. The weak strand has four G’s in its sequence replaced with inosines, effectively weakening its bond. Together, the two strands create a double helix which operates DNA strand displacement. Any DNA strands which perfectly complement the normal strand will bind to the normal strand, and the weak strand will be knocked off. Because the DNA probe is connected to the graphene transistor, the chip is able to operate electronically. Eventually, this information could then be wirelessly transmitted to a mobile device.
Researchers at the National Institute of Standards and Technology (NIST) have simulated a new concept for rapid, accurate gene sequencing by pulling a DNA molecule through a tiny hole in graphene and detecting changes in electrical current. This new method might ultimately be faster and cheaper than conventional DNA sequencing.
The study suggests that the method could identify about 66 billion bases (the smallest units of genetic information) per second with 90% accuracy and no false positives. Conventional sequencing involves separating, copying, labeling and reassembling pieces of DNA to read the genetic information. The new NIST way offers a twist on the more recent "nanopore sequencing" idea of pulling DNA through a hole in specific materials, originally a protein. This concept is based on the passage of electrically charged particles (ions) through the pore and poses challenges such as unwanted electrical noise and inadequate selectivity.
Researchers from the University of Illinois at Urbana-Champaign (UIUC) have developed a new nanopore sequencing method based on graphene nanoribbons that detects double and single stranded DNA in different configurations. This graphene-based detector shows great sensitivity and holds promise for developing a portable, high-throughput sequencer that can also detect DNA morphological transformations.
In a nanopore sequencing reaction, DNA passes through a nanopore drilled in a membrane to which an electrical voltage is applied. When DNA goes through the pore, it causes dips in the electrical current. Reading the magnitude and duration of the electrical changes allows to identify the bases that go through.