CRISPR-Cas9

Human body has been under constant surveillance since the existence of humanity, and even now, after all this time, there are a lot of mysteries buried in it. For example, nobody knows what causes headaches.

Our bodies can safely be assumed to be the most sophisticated and complex bit of engineering. The DNA(Deoxyribonucleic acid) inside our cells, is a double-stranded helical structure that carries the genetic information for the development, functioning, growth, and reproduction of all known organisms and many viruses. All this info is encoded in little things called genes.

Genes decide almost everything about a living being. One or more genes can affect a specific trait. Genes may interact with an individual’s environment too and change what the gene makes. Genes affect hundreds of internal and external factors, such as whether a person will get a particular color of eyes or what diseases they may develop. Some diseases, such as sickle-cell anemia and Huntington’s disease, are inherited, and these are also affected by genes.

If only we could alter our genes, right? As mentioned earlier certain DNA encodings(genes) are responsible for certain functions. Diseases like diabetes, cardiac-diseases, Alzheimer's, and many more are termed as genetic. So if the genes responsible for these diseases are modified using the CRISPR technique then it would be a cure for otherwise incurable diseases.

Imagine how good it would be, you could decide practically everything about your offspring while it's in the embryonic stage. But is it possible? If yes, then, to what extent? Let’s find it out.

The answer to the former half of the question is YES, it has been made possible by the combined efforts of Nobel Laureates Emmanuelle Charpentier and Jennifer A. Doudna. Compared to previous techniques for modifying DNA, this new approach is much faster and easier. This technology is referred to as “CRISPR/Cas9” and it has changed not only the way basic research is conducted but also the way we can now think about treating diseases.

What is CRISPR?

CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeat. This name refers to the unique organization of short, partially palindromic repeated DNA sequences found in the genomes of bacteria and other microorganisms. While seemingly harmless, CRISPR sequences are a crucial component of the immune systems of these simple life forms. 

Just like us, bacterial cells can be invaded by viruses, which are small infectious agents. If a viral infection threatens a bacterial cell, the CRISPR immune system can thwart the attack by destroying the genome of the invading virus. The genome of the virus includes genetic material that is necessary for the virus to continue replicating. Thus, by destroying the viral genome, the CRISPR immune system protects bacteria from ongoing viral infection.

In short, Using CRISPR the bacteria snip out parts of the virus DNA and keep a bit of it behind to help them recognize and defend against the virus next time it attacks.

How does CRISPR-Cas9 work? Let’s find out.

The CRISPR-Cas9 system consists of two key molecules that introduce a change into the DNA. These are (a) a protein-based enzyme called cas9 and (b)a guide RNA.

Cas9 acts as a pair of ‘molecular scissors’ that can cut the two strands of DNA at a specific location in the genome so that bits of DNA can then be added or removed. While the guide RNA consists of a small piece of pre-designed RNA sequence (about 20 bases long) located within a longer RNA scaffold. The scaffold part binds to DNA and the pre-designed sequence ‘guides’ Cas9 to the right part of the genome. This makes sure that the Cas9 enzyme cuts at the right point in the genome.

The guide RNA is designed to find and bind to a specific sequence in the DNA. The guide RNA has RNA bases that are complementary to those of the target DNA sequence in the genome. This means that, at least in theory, the guide RNA will only bind to the target sequence and no other regions of the genome.

The Cas9 follows the guide RNA to the same location in the DNA sequence and cuts across both strands of the DNA.

At this stage, the cell recognizes that the DNA is damaged and tries to repair it. Scientists can use the DNA repair machinery to introduce changes to one or more genes in the genome of a cell of interest.

What are some applications of the CRISPR system?

Beyond applications encompassing bacterial immune defenses, scientists have learned how to harness CRISPR technology in the lab to make precise changes in the genes of organisms as diverse as fruit flies, fish, mice, plants, and even human cells. Genes are defined by their specific sequences, which provide instructions on how to build and maintain an organism’s cells. 

A change in the sequence of even one gene can significantly affect the biology of the cell and in turn, may affect the health of an organism. CRISPR techniques allow scientists to modify specific genes while sparing all others, thus clarifying the association between a given gene and its consequence to the organism.

Rather than relying on bacteria to generate CRISPR RNAs, scientists first design and synthesize short RNA molecules that match a specific DNA sequence—for example, in a human cell. Then, as in the targeting step of the bacterial system, this ‘guide RNA’ shuttles molecular machinery to the intended DNA target. 

Once localized to the DNA region of interest, the molecular machinery can silence a gene or even change the sequence of a gene. This type of gene editing can be likened to editing a sentence with a word processor to delete words or correct spelling mistakes. One important application of such technology is to facilitate making animal models with precise genetic changes to study the progress and treatment of human diseases.

Future?

It is likely to be many years before CRISPR-Cas9 is used routinely in humans. Much research is still focusing on its use in animal models or isolated human cells, to eventually use the technology to routinely treat diseases in humans.

Certain issues must be resolved before its application to the human genome. In most cases, the guide RNA consists of a specific sequence of 20 bases. These are complementary to the target sequence in the gene to be edited. However, not all 20 bases need to match for the guide RNA to be able to bind. The problem with this is that a sequence with, for example, 19 of the 20 complimentary bases may exist somewhere completely different in the genome. 

This means there is potential for the guide RNA to bind there instead of or as well as at the target sequence. The Cas9 enzyme will then cut at the wrong site and end up introducing a mutation in the wrong location. While this mutation may not matter at all to the individual, it could affect a crucial gene or another important part of the genome.

If all these complications are resolved, which is just a matter of time, this technique may prove to be a boon for millions of people, suffering from genetic diseases, who have lost hopes of living a perfectly normal life.

All this said, I now leave you with high hopes and a burning question.

What would be the ethical implications of genome editing? Would deciding the physiological properties of a human being as per one’s will be immoral?

Present your views in the comment section. Thank you for your time.

Qubits : Heart of a Quantum Computer

Quantum Computing has been creating a lot of buzz for the past few years. Since it was first conceived it has captivated intelligent minds all over the world. Due to its ability to solve problems in minutes, which the current supercomputers will take millennia, these computers promise to solve problems that have haunted researchers and scientists for years.

The last decade has been exceptional for Quantum Computing. Years of research started showing its results and a big breakthrough came last October when Google claimed to achieve Quantum Supremacy.    

But what makes it stand apart from classical computers? It’s the Quantum Bits or Qubits that gives them this incredible processing power. Unlike a classical bit, which can be either 0 or 1 at a time, qubits can also be any combination of 1 and 0 simultaneously. These qubits exploit quantum phenomena like Superposition and Entanglement to provide you the results as fast as possible while you anxiously stare at the computer.       

Qubits are fascinating but their implementation is an arduous task. The information in the qubits is easily destroyed by thermal heats and other disturbances from the environment. This is known as Decoherence.

The colder and more isolated the qubit is, the less likely it is to flip to a different quantum state when it’s not supposed to. But it’s really difficult to keep the qubits cold and isolated.

So with all these challenges, how scientists and researchers are making these bizarre bits possible? Let’s find out.

Superconducting Circuits

This is the most widely used method for making qubits. Companies like IBM and Google rely on this method for their quantum computers. Superconductor materials that have zero resistance when cooled below a certain temperature, like Aluminium and Niobium, are used.

When the temperature drops below a critical value, two electrons form a weak bond and become a Cooper pair that experiences no resistance when traveling through the metal. The pairing opens a gap in the energy state, which any excitation requires some minimum energy. This gap leads to superconductivity since not any random increase in energy is allowed.  

Each qubit is actually an LC circuit, an inductor, and a capacitor. We manipulate its energy state to represent a superposition of |0⟩ and|1⟩.

Now the challenge is to make the energy levels uneven such that the superposition is confined to |0⟩ and |1⟩. To overcome that, the superconducting circuit includes a Josephson Junction.

The junction behaves as a non-linear non-dissipating inductor. It contains two Aluminum superconducting electrodes that are weakly coupled and are separated by a thin insulator about a thousandth of a hair thick. It is non-linear such that the energy level is unevenly separated so we can use two lower states as the bases for our superpositions.

This inductor is combined with a linear capacitor using a Niobium superconductor to create an LC resonator. With correct tuning, the circuit behaves like an atom with two quantum energy levels, i.e. our qubit.

Quantum operations are performed by sending electromagnetic impulses at microwave frequencies (around 4–6 kHz) to the resonator coupled to the qubit. This frequency resonates with the energy separation between the energy levels for |0⟩ and |1⟩. And the duration of the pulse controls the angle of rotation of the qubit state around a particular axis of the Bloch sphere.

To make a measurement, it sends a microwave tone to the resonator and analyzes the signal it reflects back. The amplitude and phase of the reflected signal depend on the qubit state. Once it is amplified, we know the energy level and therefore we can determine the state of the qubit.

To isolate the qubits, the computer contains a dilution refrigerator to cool down the quantum processor to as near as 0 Kelvin.

Silicon Spin Qubits aka “Hot Qubits”

This is a method that many think is the future of quantum computing. Two separate teams of researchers from Australia and Netherlands published a paper in April this year stating that they had performed the 2-qubit operation at 1.5 Kelvin, which is 15 times hotter than rival technologies can withstand.

Each silicon spin qubit consists of a few electrons held within a quantum dot. These quantum dots are tiny wells or divots in silicon that lay just beneath the gate electrode of a conventional transistor. As charge flows through the transistor, electrons drop into the well, and electrostatic forces hold them in place.

To compute with them, the Australian team applied an AC electric field, while the Netherlands team used an AC magnetic field to manipulate the electron spins, causing the spins to point up (1), down (0), or in both directions at once.

With this technique, electrons can be forced to occupy the same quantum dot only if their spins are opposite. If their spins match, the electrons stay put in their respective wells.

After this successful demonstration, Intel has also shifted its focus to hot qubits as these qubits can be made using transistors and Intel ships 400 quadrillion transistors a year.

Trapped Ion Pair

 Another approach to make qubits is through trapping ions and then precisely controlling them using lasers. To trap ions, scientists start with a steel vacuum chamber, housing electrodes on a chip that is chilled to nearly 450 degrees below zero Fahrenheit. 

Ca and Sr atoms stream into the chamber. Multiple lasers knock electrons from the atoms, turning the Ca and Sr atoms into ions. The electrodes generate electric fields that catch the ions and hold them 50 micrometers above the surface of the chip. Other lasers cool the ions, maintaining them in the trap. 

Then, the ions are brought together to form a Ca+/Sr+ crystal. Each type of ion plays a unique role in this partnership. The Sr ion houses the qubit for computation. The Ca ion, which has a similar mass to the Sr ion, takes away extra energy from the Sr ion to keep it cool and help it maintain its quantum properties. Laser pulses then nudge the two ions into entanglement, forming a gate through which the Sr ion can transfer its quantum information to the Ca ion.

To read out this state, the scientists interrogate the Ca ion with a laser at a wavelength that only the Ca ion's electron will interact with, leaving the Sr ion unaffected. 

What's nice about using this helper ion for reading out is that we can use wavelengths that don't impact the computational ions around it; the quantum information stays healthy. So, the helper ion does dual-duty; it removes thermal energy from the Sr ion and has low crosstalk when we want to read out just that one qubit.

Now answer this: Can we manipulate the Nucleus of an atom as a Qubit?? If yes then how?

The race to make a commercial quantum computer continues as researchers and tech giants keep finding ideas to make qubits that can work at an optimal temperature. Until then we will keep tabs on all the quantum computing breakthroughs until one of them finally establishes the quantum age.

References-

1. https://www.qutisgroup.com/wp-content/uploads/2014/10/Amaia_TFG.pdf

2. https://analyticsindiamag.com/how-this-breakthrough-makes-silicon-based-qubit-chips-future-quantum-computing/

3. https://news.mit.edu/2020/trapped-ion-pair-may-help-scale-quantum-computers-0128