Information usually takes a form of sequences of something such as letters, numbers and DNA nucleic acids. A sequence can create an information. There are two types of sequences. Always becoming the same order because there is a reason to form the certain order. For example, the shape of snowflakes. It is the consequence of a self-assemble mechanism of crystallization based on physics. Therefore, snowflakes at the north pole can be same to the one at the south pole. On the other hand, the other type of sequences has no reason to form a specific order, thus it looks random. However, with a rule for coding and decoding, an apparently random sequence would carry a meaningful information. For example, think about alphabets and words. No physical reason to form the specific order. Not self-assemble. With a rule, a specific order carries an information, and the encoded information can be decoded from the sequence.
Amino acids are the units composing of a protein. The sequence of amino acids defines the protein and its 3D structure. This 3D structure creates multiple 3D interphases (not one!!) allowing to interact to other proteins and small molecules. In this sense, the 1D amino acids sequence carries the 3D interface information. No biochemical reason to take specific orders of amino acids. No preference in their order. Theoretically, amino acids can create thousands of random peptides. However, when a peptide forms a specific 3D interface to interact with others or to catalyze something, the peptide with the specific sequence becomes enable to ‘work’. Then, the ‘work’ is called as ‘function’ of the peptide or protein from us.
DNA, deoxy-ribonucleic acid has an amazing molecular property. DNA is a double strand polymers consisting of four deoxy-ribonucleotides, A,T,C and G. Through hydrogen bonds of A/T, and C/G, two complementary sequences of double strands are held together to form a double helix structure. The structure was discovered by Watson and Crick in 1959 based on Franklin’s DNA X-ray tomograph. The property to form the double helix with a complementary sequence strand is essential for the inheritance of genetic information in living-organisms. When DNA duplicates, a paired double strand unfold to permit each strand work as a template for making the other strand. New two paired double strands will be generated from each single original strand.
This means that DNA is a machinery permitting the inheritance of unique DNA sequence information to next generations. Great! By the way, how does DNA carry the information? The 1D DNA sequence can be translated into the 1D amino acids sequence. This means that the 3D interphase information of proteins is encoded in the DNA 1D sequence. Some proteins can bind DNA like histones, and others recognize specific 1D DNA sequences like transcriptional factors. In a combination of the DNA 1D sequence and a repertoire of DNA binding proteins, genes to be expressed in a cell are controlled. The regulation of gene expression dictates the cellular identity. Is this all information that DNA carries? I do not think so. DNA should carry the information of our organism identity like humans, dogs, snakes and dragon flies. We look different from other species because of our human DNA. How is our ‘looking’ (anatomical) information carried?
I think our body is primarily built by 2D information. I consider our body is a sac like a plastic bag. All positional information is set in two dimensions. Then, by blowing an air in it, 2D information becomes three dimensions. Our body, organs and tissues are primarily patterned in two dimensions and then forming a hallow based on the 2D information during development. The repertoire of DNA binding proteins and DNA 1D sequence define the X, Y positions in the flat 2D space. The concept of morphogens in development is one mechanism for cells to sense their position and to control their gene expression. Now, the cellular identity is controlled in the 2D space.
Then, where are 3D information of our body, organs and tissues encoded? What is equivalent to an air for a plastic bag? I think that is self-assemble properties of proteins. Interestingly, the self-assemble properties of proteins also control the self-organizing properties of cells. Once a cell learns how to be cohesive (this is the beginning of metazoans), multiple adhesive cells always self-organize to form cell aggregates. This means that the 3D interphases of proteins dictate our 3D body, organ, and tissue structures. Therefore, the 1D DNA sequence can carry the 3D structural information.
So far, I navigate you how the 1D DNA sequence can carry the 3D information of our body. Is this sufficient to form ourselves from the 1D DNA sequence? I do not think so. Because our body is not punched out from a pre-made mold like plastic figures. We all need to develop from a single fertilized egg. Development is a series of sequential events. Each species has a unique developmental series leading to their unique morphology. On the other hand, the last decades of studies in development, genetics and evolution revealed that each individual event is often common across different species, even classes and phyla.
What information is required for the successful completion of development? I think that ‘timing’ is essential. A proper time sequence of multiple events. Where is ‘timing’ encoded? I think the ‘timing’ information is encoded in the 3D structure of DNA. Not within the hydrogen-bonds linked double strands but in the 3D structure of the double helix that can create the 3D nested structure. Twisting! Please imagine a rubber band (I recommend trying this yourself). If grab both ends with your fingers and twist it. Keep twisting it to one direction. Then, pull both ends or relax its tension without losing the twist. What do you see? I believe that you observe the nested structure when relaxing the rubber band. This is the unique property of DNA. RNA and proteins can form weak nests but do not have the replicable property. DNA has the replicable property and the property to form the nested structure.
Why is the structural nest important and interesting? Because it creates ‘time’ through ‘a sequence of events’. To access the inside of the nest, always the outside structure of the nest needs to be removed in advance. The strict order of accessibility emerges! Impossible to flip the order without destroying the original 3D structure. DNA, as a polymer has the property to form the nested structure. Then, the next question is if the pattern of the nests can be controlled? My answer is YES! With the help of those sequence specific and non-specific DNA binding proteins, the 1D DNA sequence dictates the 3D nested structure of DNA!! Incredible! This means that the 1D DNA sequence carries the information of ‘time’. DNA is a unique molecule that can carry the 4D information in the 1D sequence with the replicable property. Evolution is the changes in the 1D DNA sequence that carries the 4D information within the nested structure.
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