Cells use RNA strings to store information that is then translated into function in the form of proteins. Like DNA, RNA consists of a long string of only four different molecules, called bases. But RNA is more than just an information carrier — it can fold up into complex structures that then participate in chemical reactions themselves. However, unlike proteins, which are mostly static, the chaotic nature of RNA makes it difficult to handle or predict its shape. Now, Zhaoming Su and colleagues have developed a new method that tackles this problem by characterizing these RNAs at sub-nanometer resolution.
To do so, they combined existing methods of electron microscopy, chemical probing, and computer modelling. This allowed them to figure out the structure of the so-called Tetrahymena RNA, the first RNA ever discovered to participate in chemical reactions. In particular, this RNA glues two separate strings of other RNA together, resulting in a longer RNA string. Their method resolved how every single base on the RNA string is placed. Importantly, they could even see the bases that stretch out and reach across the whole structure, providing the bridges that define its overall shape. The speed of their method also enables them to look at the RNA at various stages in time, stacking these static images to make a movie that shows the whole mechanism.
Initially, this discovery means researchers can design artificial versions of Tetrahymena RNA to glue strings of RNA together more efficiently in a lab setting. Ultimately, beyond this specific RNA, this method can provide detailed enough models of other RNAs of interest to identify the position of every single base. With this information, scientists can make guided changes to the design and function of these RNAs, just as they have already been doing with proteins for decades.
The three lead authors are Zhaoming Su, now a PI at Sichuan University; Kaiming Zhang now at the University of Science and Technology of China in Hefei and both at the Department of Bioengineering and James H. Clark Center, Stanford University at the during the time of this work; and Kalli Kappel, now a postdoc at the Broad Institute of MIT and Harvard and a former graduate student in the Biophysics Program, Stanford University. Last authors are Rhiju Das, a PI in the Department of Biochemistry and Department of Physics at Stanford University and Wah Chiu, a professor in the Department of Bioengineering and James H. Clark Center at Stanford University
Managing Correspondent: Raphael Haslecker
Original Journal Article: https://doi.org/10.1038/s41586-021-03803-w
Image Credit: Pexels Free Photos
2 thoughts on “The (Very) Little Molecule that could: an HD Image Opens a New Chapter in RNA Science”
Molecular gene (DNA) concept is wrong
Phenomena of life and death
The genome (DNA structure) is supposed to encode the genetic program of an organism. This is the biggest mistake ever happened in science. DNA is supposed to determine the amino acid and hence protein. How can just the DNA coded information for amino acid / protein create a living organism and make it function?
Further, how can the organism die or stop functioning when the genome is intact?
Genome is a static chemical structure. How can it code for continuously changing instructions (for example, development of foetus from zygote)?
The Scriptures reveal that the soul is responsible for life. Phenomena of life and death can be understood based on the soul and computer model of organism.
The living and nonliving components of the universe God created are fully automated systems like computer systems. The universe is divine expert system in which divine instructions (programs) are immanent. There are two kinds of components in the universe namely one, the so-called living and the other nonliving. Therefore, two kinds of programs can be thought of in operation. One is the chemical information encoded by the chemical structure of nonliving system that is responsible for its properties and behaviour. The other is nonphysical biological information stored on the chromosomes of the body cells of living system that is responsible for its biological functioning.
A living organism is comparable with a computer or robot. A computer has hardware and software. Similarly a living organism has hardware and biosofware. The phenotype is the hardware and the genetic program is the biosoftware. The soul mentioned in the Scriptures is the biosoftware of an organism. The soul (biosoftware) mentioned in the Scriptures is nonphysical. This agrees well with the nonphysical gene originally proposed by Wilhelm Johannsen in1909. It is like the software of a computer and is stored on the chromosomes like the software is stored on the memory device of a computer. It is not coded by a chemical structure (eg. DNA). The sofftware of the computer is its soul. It is according to the software the hardware components of a computer operate. Similarly, it is according to the divine soul (biosoftware) the cells and organs (hardware components) of an organism are formed and function.
The Quran reveals that the soul (Arabic word ‘rooh’ is used to mean soul and in certain contexts, the word ‘nafs’ is also used) is responsible for life. The Quran further reveals that the removal (deletion) of soul from the body causes death. Therefore, the phenomenon of life can be defined and understood as the manifestation of operation of body structures according to the biosotware. Death can be defined as the result of deletion of biosoftware from the body cells. In other words, a dead body is like a computer or robot without software. This indicates that life cannot be restored to a dead body or created from nonliving matter. The computer, robot or anything that operates on man-made software can be considered as form of ‘artificial life’.
The molecular gene (DNA) concept is wrong. The genetic program or the biosoftware (soul) is nonphysical like the software of a computer. That is why in biology, the science of life, it has not been possible to define the phenomena of life and death.
For more information please see my book ‘The Quran: Scientific Exegesis’
Prof. P.A. Wahid.
Publisher: Adam Publishers, New Delhi, India, pages 525.
The soft copy of the book can be downloaded free from ResearchGate. The link is:
“Genome is a static chemical structure. How can it code for continuously changing instructions (for example, development of foetus from zygote)?”
DNA does not directly encode instructions; instead, different genes from DNA are transcribed into mRNA first, which is more dynamic and expressed at variable levels. This is why different types of cells can have the same static DNA, but function differently.
“The other is nonphysical biological information stored on the chromosomes of the body cells of living system that is responsible for its biological functioning.”
If it’s nonphysical, this would mean that it’s not stored in the form of molecular structures that can participate in chemical reactions, right? In which case, how would it be that it’s stored on chromosomes, which are a physical component?
“Death can be defined as the result of deletion of biosoftware from the body cells. In other words, a dead body is like a computer or robot without software. This indicates that life cannot be restored to a dead body or created from nonliving matter.”
A computer or robot without software could have new software installed to restore normal functioning, so this analogy isn’t completely applicable. Like, for example if Windows was uninstalled from a system, a different operating system could then be installed next.