The Relationship and Differences in Genomic DNA and Complimentary DNA

DNA: the Building Block of Life

Deoxyribonucleic acid, (DNA) is the molecule that carries the instructions for all aspects of an organism’s functions, from growth, to metabolism, to reproduction. In living organisms, most of the DNA resides in tightly coiled structures called chromosomes, located inside the nucleus in each cell. DNA is made up of four different building blocks, called nucleotides, which are each made up of one of four nitrogenous bases demonstrated in Figure 1. These are the purines: guanine (G) and adenine (A), and the pyrimidines: thymine (T) and cytosine (C). These nucleotides are coupled to a deoxyribose sugar and are able to bind to other deoxyribose sugars via phosphate linkages to form long chains, some of which can be well over 100,000,000 molecules long. Since each deoxyribose in a DNA chain is coupled to one of the four nitrogenous bases (G, A, T, or C), these long chains can carry information.

Groups of three nucleotides form the smallest, but most well-defined “words” in the DNA language. These “words” are called codons.  Codons are used to call for specific amino acids to be bonded together to form proteins. For instance the codon adenosine-adenosine-guanosine (AAG) calls for the amino acid lysine (lys) to be incorporated into a protein molecule.  The codon AGG calls for the amino acid arginine (arg). So the AAG-AGG would call for one lys to be coupled to one arg in a growing protein chain. There are also codons that, under the right circumstances, call for a protein to begin to be formed (start codons), or for a protein chain to be finished (stop codons). As you can see from this simple example, DNA can carry a massive amount of information.

cdna vs genomic dna

Figure 1: Adenine binds to thymine; guanine binds to cytosine.
This creates the double helix strands of DNA (Nature Education).

What are Genomic and Complimentary DNA?

The DNA residing in chromosomes inside the nucleus, with all the biological information to be transferred to the next generation, is called genomic DNA (gDNA). The words “genome” and “genomic” come from the word “gene”. A gene is a set of codons that specify a specific protein chain, along with the associated start and stop codons. The word genome is an extension of this concept and means the collection of all genes and other information contained inside the nuclei of an organism’s cells. Often, when the word “DNA” is used without further clarification, it refers to gDNA.

In nature, the process for information to be passed on from DNA can occur through either replication or gene expression. There are some important factors to note:

  • DNA can copy itself in a process known as replication, using DNA polymerase.
  • Information from DNA is passed through messenger RNA (mRNA), which contains sets of four nucleotides (uracil, adenine, guanine, and cytosine).
  • mRNA is produced when enzymes, such as RNA polymerase, bind to specific genes and copy their information into RNA using a ribose sugar (not deoxyribose as in DNA). This process is called transcription.
  • Ribosomes assemble around mRNA, creating an amino acid chain to create specific proteins. This is called translation.
  • Due to the ribose sugar chains, mRNA is short lived. It is designed to convey information from the chromosomes in the nucleus to the machinery that makes proteins.
  • mRNA degrades rapidly after it has completed it’s purpose.

Initially, it was observed that gDNA was always read and transcribed into mRNA, which guided protein formation and then was disposed. The notion that information might always flow from DNA to RNA to protein was somewhat jokingly referred to as the Central Dogma of molecular biology. Calling it that challenged scientists to find exceptions to this rule.

Virologists eventually did find one such exception. Retroviruses were discovered to have mechanisms for “reverse transcription.” This means that they can take RNA chains and produce DNA chains from them. In this way, during reverse transcription, information flowed backwards from RNA back to DNA. DNA that arises from this process is called complementary DNA (cDNA). cDNA is either produced by some viruses or synthesized in laboratories. The various processes involved in creating DNA and RNA are demonstrated in Figure 2.

Central dogma of biology

Figure 2: the “Central Dogma” of biology fails to take reverse transcription into account (Research Gate).

The Functions of gDNA and cDNA

cDNA can be described as gDNA without all the necessary noncoding regions, which is how it gets its name as complimentary DNA.

A primary distinction to be made between cDNA and gDNA is in the existence of introns and exons. Introns are nucleotides in genes that don’t have any coding sequences. Generally, introns are spliced out, or “edited out” of RNA in the transcription process before proteins are created. It should be noted that prokaryotes are not capable of splicing out introns. Exons are a necessary part of the coding system, being retained after introns are spliced out. This is displayed in Figure 3. Exitrons are introns that are not spliced out, despite containing no coding sequences.

Gene structure

Figure 3: Introns (blue) are spliced out from RNA to create mRNA for protein synthesis (Daycd)

When scientists use viral enzymes to make cDNA from RNA isolated from the cells and tissues that they are studying, it does not contain introns due to being spliced out in mRNA. cDNA also does not contain any other gDNA that does not directly code for a protein (referred to as non coding DNA). Lastly, not all genes in the gDNA are being transcribed into mRNA at any given time. As a result, cDNA will only contain genes that are actively being used by a specific cell or tissue at a point in time. There is much less total information in cDNA than gDNA, but what information remains can be a lot more relevant to what a researcher is looking at since it doesn’t contain sequences that are unnecessary to the functioning and replication of the DNA.

Once isolated, gDNA can be used to make genomic libraries for DNA sequencing, fingerprinting, differentiation and other applications with both clinical and research fields.

cDNA can also be used also be used to make cDNA libraries, permanent collections of cDNA that can be copied and/or stored long term, and it is commonly used to clone eukaryotic genes in a prokaryote. This way a protein expressed in a eukaryotic organism can be introduced into a prokaryote. For this process cDNA is used over gDNA, since prokaryotes cannot spice out introns contained in gDNA.

In order to isolate cDNA, first the RNA of an organism must be isolated. Then, using a reverse transcriptase enzyme, cDNA can be made. This is the process retroviruses use to incorporate into their host’s cells. Retroviruses, such as Simian Immunodeficiency Virus (SIV) and Avian Myeloblastosis Virus (AMV), use their cDNA to produce mRNA in the host, leading to the production of viral proteins. This is possible because retroviruses use RNA as their genomic material instead of DNA, and it is reverse transcribed into the cDNA, which then undergoes normal transcription and leads to the viral protein in the host. The life cycle of a retrovirus is shown in Figure 4.

retrovirus

Figure 4: A retrovirus uses reverse transcription to integrate into the host genome (Essential Cell Biology).

Custom and Premade gDNA and cDNA Available at BioChain

BioChain provides access to a comprehensive, well-documented tissue bank containing isolated samples that have been tested for contaminants. As part of rigorous quality control, gDNA samples are tested by spectrophotometer and electrophoresis, with concentration determined by UV260 measure and plant concentration determined by pico green measurement. All gDNA is treated with RNase to eliminate all RNA.

Genomic DNA comes from unique sources, including hundreds of healthy/diseased organ tissue from humans, animals, and plants. The gDNA has applications ranging from SNP analysis, methylation studies, copy number variation (CNV) analysis, comparative genomic hybridation (CGH), Southern Blotting, Next Generation Sequencing, and PCR.

Shop the Largest Tissue cDNA Selection in the Market

 BioChain’s cDNA samples are synthesized using total RNA isolation at the facility with modified techniques to ensure consistency. cDNA undergoes both visual inspection detecting intact bands of ribosomal DNA, and tested by purity with a spectrophotometer. The first strand is synthesized using MMLV reverse transcriptase with low RNase H activity, with an oligo dT primer to ensure presence of the entire cDNA.

Sources originate from a variety of animal, plant matter, and human/fetal tissue (including healthy and diseased organs). Documentation on clinical history of tissues is available. The cDNA can be used for PCR, gene discovery, analysis or mRNA, and cloning among others.

Medicinal Chemistry PhD candidate from The University of Toledo.

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