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:
Scientists at the University of Melbourne, the Australian Synchrotron and La Trobe University discovered that graphene can distinguish the four nucleobases that make up DNA and potentially be used to sequence DNA without the need for labels.
The researchers found that each nucleobase influenced the electronic structure of graphene in a measurably different way. When used together with a nanopore, a single DNA molecule would pass through the graphene-based electrical sensor enabling real-time, high-throughput sequencing of a single DNA molecule. The use of graphene to electrically sequence DNA promises to improve the speed, throughput, reliability and accuracy whilst reducing the price compared to current techniques.
Researchers from the Amrita Centre for Nanoscience and molecular Medicine in India developed a simple graphene-based method of thermally ablating highly resistant cancer cells. The method involves biodegradable graphene nanoparticles, which were found to be able to convert non-ionizing radio waves into heat energy at microscopic levels.
This heat may be enough to eliminate proteins and DNA insode cancer cells, bypassing even the most resistant cancer-cell mechanisms. The method itself is minimally invasive and can be executed on any part of the body. Once the graphene platelets get to the target tumor cells, the radio waves sent from outside the body can supply a large amount of heat at highly localized levels and destroy all cellular proteins, which should lead to cell death.
Researchers at MIT and Harvard University found a way to use folded DNA to control the nanostructure of inorganic materials. DNA structures are built in a certain shape, then used as templates to create nanoscale patterns on sheets of graphene. This technique can further large-scale production of graphene electronic chips.
This technique forms DNA nanostructures with precisely planned shapes using short synthetic DNA strands called single-stranded tiles. Each of these tiles acts as an interlocking brick and binds with four designated neighbors. The researchers transferred the structural information encoded in DNA to graphene, using a relatively simple process that includes anchoring the DNA onto a graphene surface using a molecule called aminopyrine, which is similar in structure to graphene. The DNA is then coated with small clusters of silver along the surface, which allows a subsequent layer of gold to be deposited on top of the silver.
Researchers from Berkeley Lab and the University of California (UC) Berkeley have come up with a simple process for producing nanopores (about 2 nanometers in diameter) in a graphene membrane using the photothermal properties of gold nanorods.
The researchers aim to use this discovery to construct a direct DNA sequencing process, which will be simultaneously electrical and optical. This should facilitate a faster sequencing procedure, as traditional methods in which DNA components are sorted by an electrical current passing through nanopores on a silicon chip tend to get congested and slow, as information flowing through thousands of nanopores needs to be handled. Adding an optical component should, according to the researchers, help eliminate bottlenecks and speed up the sequencing process.
The National Institutes of Health (NIH) awarded a $880,000 grant for a University of Pennsylvania 2-year project that aims to develop fast and cost-effective genome sequencing. The project uses the DNA translocation process which threads DNA through nanopoers in a thin membrane - in this case a graphene nanoribbon (GNR) membrane.
A GNR is very useful for sequencing because it's thin and strong, and also its electrical properties enable to read the bases signals directly from the membrane as the DNA passes through the pore. We posted about this project last year, and it's great to see them receive more funding.