For a non-technical introduction to the topic, see Introduction to genetics.

The structure of part of a DNA double helix

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.

Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, and fungi) store their DNA inside the cell nucleus, while in prokaryotes (bacteria and archae) it is found in the cell’s cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

Share This

Colloquially, the term gene is often used to refer to an inheritable trait which is usually accompanied by a phenotype as in (”tall genes” or “bad genes”) — the proper scientific term for this is allele.

In cells, genes consist of a long strand of DNA that contains a promoter, which controls the activity of a gene, and coding and non-coding sequence. Coding sequence determines what the gene produces, while non-coding sequence can regulate the conditions of gene expression. When a gene is active, the coding and non-coding sequence is copied in a process called transcription, producing an RNA copy of the gene’s information. This RNA can then direct the synthesis of proteins via the genetic code. But some RNAs are used directly, for example as part of the ribosome. These molecules resulting from gene expression, whether RNA or protein, are known as gene products.

Genes often contain regions that do not encode products, but regulate gene expression. The genes of eukaryotic organisms can contain regions called introns that are removed from the messenger RNA in a process called splicing. The regions encoding gene products are called exons. In eukaryotes, a single gene can encode multiple proteins, which are produced through the creation of different arrangements of exons through alternative splicing. In prokaryotes (bacteria and archaea), introns are less common and genes often contain a single uninterrupted stretch of DNA, called a cistron, that codes for a product. Prokaryotic genes are often arranged in groups called operons with promoter and operator sequences that regulate transcription of a single long RNA. This RNA contains multiple coding sequences. Each coding sequence is preceded by a Shine-Dalgarno sequence that ribosomes recognize.

The total set of genes in an organism is known as its genome. An organism’s genome size is generally lower in prokaryotes, both in number of base pairs and number of genes, than even single-celled eukaryotes. However, there is no clear relationship between genome sizes and complexity in eukaryotic organisms. One of the largest known genomes belongs to the single-celled amoeba Amoeba dubia, with over 670 billion base pairs, some 200 times larger than the human genome. The estimated number of genes in the human genome has been repeatedly revised downward since the completion of the Human Genome Project; current estimates place the human genome at just under 3 billion base pairs and about 20,000–25,000 protein-coding genes, with a article from 2007 giving a number of 20,488 plus perhaps 100 more yet to be discovered. The gene density of a genome is a measure of the number of genes per million base pairs (called a megabase, Mb); prokaryotic genomes have much higher gene densities than eukaryotes. The gene density of the human genome is roughly 12–15 genes per megabase pair

Share This

RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. Some of these RNA-processing enzymes contain RNA as part of their structures. RNA is also central to the translation of some RNAs into proteins. In this process, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can and read messenger RNAs and translate the information they carry into proteins. It has also been known since the 1990s that several types of RNA regulate which genes are active.

A hairpin loop from a pre-mRNA. Notice its nitrogen-rich (blue) bases and oxygen-rich (red) backbone.

Share This

Other than another young company - an upstart called Promega - and a few more, the producer of DNA analysis software was in need of companionship. The early 1980s was an era where it was considered bad form - even a social stigma - for an academician like Blattner to start a business. The dominant perception was that research and development was a “big company” function.

“We were among the first five or 10 [technology] companies getting off the ground at that time,” said Blattner, a genetics professor at the University of Wisconsin-Madison and CEO of DNASTAR. “We were pretty lonely.”

Amid the solitude, Blattner wanted to take advantage of the expanding knowledge of DNA. He launched DNASTAR in his basement with the help of an SBIR grant and then UW-Madison undergrad John Schroeder, now the company’s vice president of R&D.

Blattner was among the first professors on the UW campus to conduct DNA sequencing. Even nationally, he was part of a small universe, but since it was impossible for anyone to scan volumes of genomic data with the naked eye, there was strong demand for analysis software.

Unfortunately for DNASTAR, the weak link in the sales process was the fact that Apple was still largely a gleam in someone’s eye. Since it was developing software before there were computers that could run it, the company had to build the computers and sell the software and computer in a bundle, but that didn’t stop Blattner from mowing a different landscape. Little by little, the personal computer would begin to proliferate in research labs and businesses, and he would be joined by other university professors who discovered a market for their research tools.

And now, with a revolution underway in structural biology and its 25th anniversary approaching, DNASTAR still offers DNA sequencing, which permits a more in-depth analysis of genes, and has moved into database searching and micro arrays.

“They were one of the early leaders in bioinformatics and in assisting researchers with tools,” said Jim Leonhart, executive vice president of the Wisconsin Biotechnology and Medical Device Association. “They are now quite a major player around the world.”

Share This

Share This

Share This

Non-coding RNA genes include transfer RNA (tRNA) and ribosomal RNA (rRNA), small RNAs such as snoRNAs, microRNAs, siRNAs and piRNAs and lastly long ncRNAs that include examples such as Xist, Evf, Air, CTN and PINK. The number of ncRNAs encoded within the genome is unknown, however recent transcriptomic and microarray studies suggest the existence of over 30,000 long ncRNAs and at least as many small regulatory RNAs within the mouse genome alone. Since most of the newly identified ncRNAs have not been validated for their function, it is possible that the majority of them are meaningless (e.g. non-functional or truncated transcript).

One of the major findings of the 2007 ENCODE Pilot Project was that “nearly the entire genome may be represented in primary transcripts that extensively overlap and include many non-protein-coding regions

Share This

• Single locus DNA fingerprinting: Polymorphism at a single locus is characterized, usually through use of a specific probe or specific PCR primers. Because the single loci detected by this method are characterized, one obtains a DNA genotype from single locus methods.
• Multilocus DNA fingerprinting: Polymorphism at multiple loci is simultaneously identified. This can be performed by application of a mixture of single locus probes or application of a single probe that identifies multiple similar sequence polymorphisms. In the latter case, one is detecting unidentified fragments of DNA and the result is therefore a DNA phenotype rather than a genotype.

Each of these methods has advantages over the other in specific situations. For example, single locus but not multilocus methods are useful when the DNA is degraded and for mixed (i.e. victim and pertetrator) samples. On the other hand, multilocus fingerprinting typically provides more information per sample than single locus fingerprints. Examples of both types of fingerprinting follow.

Example 1: Single Locus Fingerprinting Minisatellite fingerprinting to demonstrate kinship using mixtures of two or three single locus probes (probe sets 1 and 2). The loci detected in the child (C) are clearly a composite of those present in the mother (M) and father (F).
Example 2: Multilocus Fingerprinting Microsatellite fingerprinting to establish parentage. The probe, (CAG)5, recognizes a large number of loci. Examine the bands detected in DNA from the child that are not detected with DNA from the mother. Which male is the biologic father of the child?
Example 3: Multilocus Fingerprinting Multilocus fingerprinting to match trace evidence from a crime with suspects. Which suspect matches the specimen?

Share This

A distinct group of DNA-binding proteins are the single-stranded-DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-characterised member of this family and is essential for most processes where the double helix is separated, including DNA replication, recombination and DNA repair. These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases.

The lambda repressor helix-turn-helix transcription factor bound to its DNA target

In contrast, other proteins have evolved to specifically bind particular DNA sequences. The most intensively studied of these are the various classes of transcription factors, which are proteins that regulate transcription. Each one of these proteins bind to one particular set of DNA sequences and thereby activates or inhibits the transcription of genes with these sequences close to their promoters. The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.^[Alternatively, transcription factors can bind enzymes that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase.

As these DNA targets can occur throughout an organism’s genome, changes in the activity of one type of transcription factor can affect thousands of genes. Consequently, these proteins are often the targets of the signal transduction processes that mediate responses to environmental changes or cellular differentiation and development. The specificity of these transcription factors’ interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to “read” the DNA sequence. Most of these base-interactions are made in the major groove, where the bases are most accessible.

Share This

The energy for the process of DNA polymerization comes from the two additional phosphates attached to each of the unincorporated nucleotides — these free nucleotides, also known as nucleoside triphosphates, contain a total of three phosphates. When a nucleotide is being added to a growing DNA strand, two of the phosphates are removed and the energy produced is used to attach the remaining phosphate to the growing chain. The energetics of this process may also explain the directionality of synthesis - if DNA were synthesized in the 3′ to 5′ direction, the energy for the process would come from the 5′ end of the growing strand rather than from free nucleotides. During proofreading, if the 5′ nucleotide needed to be removed this triphosphate end would be lost, losing the energy source required to add a new nucleotide to the end.

DNA polymerase can only extend an existing DNA strand paired with a template strand, it cannot begin the synthesis of a new strand. To do this a short fragment of DNA or RNA, called a primer, must be created and paired with the template strand before DNA polymerase can synthesize new DNA.

Share This