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Gene Editing - Part II: The Science of Gene Editing

Gene Editing - Part II: The Science of Gene Editing

Anna Eisenberg
March 22, 2025

Anna's Deep Dives

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DNA 101: The Blueprint of Life

DNA is the instruction manual for life. It tells cells how to grow, function, and reproduce. Every living organism, from bacteria to humans, relies on DNA to carry genetic information.

DNA stands for deoxyribonucleic acid. It has a double-helix shape, resembling a twisted ladder. Each strand consists of repeating units called nucleotides, which include a sugar, a phosphate group, and a nitrogenous base.

There are four DNA bases: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C). They pair specifically—A with T, and G with C—ensuring accurate DNA replication during cell division.

The human genome contains over three billion base pairs. If stretched, the DNA in one cell would be about two meters long. To fit inside the nucleus, DNA is packed into chromosomes. Humans have 46 chromosomes, half from each parent.

Genes are DNA segments that instruct cells to make proteins. Humans have about 23,000 genes. These proteins build and maintain the body, influencing traits like hair color, height, and metabolism.

Genetic information passes from one generation to the next. Studies show genes influence personality, behavior, and health. Specific genes, like MAOA and DRD4, have been linked to aggression and decision-making.

DNA directs protein production through RNA (ribonucleic acid). RNA carries genetic instructions to ribosomes, where proteins are made. This process, known as the central dogma of molecular biology, explains how genetic information flows from DNA to RNA to proteins.

Understanding DNA has led to breakthroughs. In 1966, scientists mapped the genetic code, identifying the 64 codons that direct protein synthesis. The Human Genome Project, completed in 2003, sequenced nearly all three billion DNA bases, helping researchers study diseases and develop treatments.

DNA replication ensures genetic continuity. Before a cell divides, it copies its DNA with high accuracy. Proteins like the Origin Recognition Complex (ORC1-6) help this process. Mutations in these proteins can lead to diseases, including cancer.

How Mutations Shape Evolution & Disease

Mutations are DNA changes that occur naturally during cell division. Some mutations help organisms survive, while others cause disease.

Each person carries mutations in about 50,000 genes. Some mutations are inherited, while others arise from aging, radiation, or chemicals. Some cause no harm, but others lead to diseases like cancer or cystic fibrosis.

Mutations vary. Point mutations change a single DNA letter, while chromosomal mutations involve large DNA segments. Down syndrome results from an extra chromosome 21.

Beneficial mutations spread through populations, helping species adapt. About 80% of loss-of-function mutations improve survival.

Mutations also cause disease. BRCA1 and BRCA2 mutations increase breast and ovarian cancer risk. About 20% of human cancers have mutations in the RAS gene, which drives uncontrolled cell growth.

The environment affects mutation rates. Bacteria under stress mutate up to 158 times faster, aiding antibiotic resistance. Research suggests essential genes mutate less often, reducing harmful effects.

Genetic testing detects harmful mutations. Over 8,000 rare diseases stem from single-gene mutations. Antisense oligonucleotide therapies target these conditions by blocking faulty genes.

Early Gene Editing Techniques: The Precursors to CRISPR

Before CRISPR, scientists used Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs). These tools relied on engineered proteins to cut DNA at specific sites.

ZFNs, developed in the 1990s, used zinc finger proteins to bind DNA and nucleases to cut it. Designing ZFNs for each DNA target was costly and time-consuming, with low efficiency.

TALENs, introduced in the 2000s, worked similarly but used TALE proteins from plant pathogens. They were more precise than ZFNs but required complex engineering.

Restriction enzymes, discovered in the 1970s, acted as molecular scissors, cutting DNA at specific sequences. They allowed DNA manipulation but lacked precision for targeted gene editing.

Homologous recombination enabled gene replacement using matching DNA sequences but had low success rates, often under 10%.

The discovery of CRISPR in 1987 transformed gene editing. Researchers found that bacteria used CRISPR to fight viruses. In 2012, Jennifer Doudna and Emmanuelle Charpentier adapted CRISPR-Cas9 for precise DNA editing, making the process easier, cheaper, and more efficient than older methods.

CRISPR & Beyond: How Gene Editing Works Today

CRISPR is the leading gene editing tool. It stands for Clustered Regularly Interspaced Short Palindromic Repeats. Scientists discovered CRISPR in bacteria, where it defends against viruses.

CRISPR works with Cas9, a protein that cuts DNA at specific sites. Scientists design a guide RNA to direct Cas9 to a target sequence. After the cut, cells repair the DNA, allowing scientists to remove, add, or modify genes.

CRISPR is faster and cheaper than earlier methods. Gene editing once took weeks or months; now, it can be done in 24 to 48 hours. The cost of sequencing a human genome has dropped from $2.7 billion in 2003 to under $600 in 2025.

CRISPR is revolutionizing medicine. In December 2023, the FDA approved Casgevy, the first CRISPR-based therapy for sickle cell disease and beta thalassemia. Clinical trials show that 93.5% of treated patients no longer experience severe pain.

Scientists are improving CRISPR with base editing and prime editing. Base editing changes a single DNA letter without cutting the strand. Prime editing allows precise insertions and deletions.

Beyond medicine, CRISPR is transforming agriculture. It has been used to enhance over 41 crops, improving yield, disease resistance, and nutrition. Scientists are also developing gene-edited animals, such as pigs resistant to swine fever.

CRISPR has challenges. Off-target effects can cause unintended DNA changes. Scientists use tools like Digenome-seq to improve precision. Researchers are also exploring enzymes like Cas12 and Cas13 for better accuracy.

New gene editing tools are emerging. SeekRNA and bridge RNA systems enhance targeting. Recombinase enzymes allow precise DNA modifications. AI-driven models now assist in designing better guide RNAs.

CRISPR is shaping the future of genetic engineering. It has led to FDA-approved treatments, improved crops, and more efficient gene therapies. As new tools emerge, gene editing will continue advancing medicine, agriculture, and synthetic biology.

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