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DNA well suited as blueprint for life

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DNA double helix contorts/ Huiqing Zhou, Duke U

A new study could explain why DNA and not RNA, its older chemical cousin, is the main repository of genetic information. The DNA double helix is a more forgiving molecule that can contort itself into different shapes to absorb chemical damage to the basic building blocks — A, G, C and T — of genetic code. In contrast, when RNA is in the form of a double helix it is so rigid and unyielding that rather than accommodating damaged bases, it falls apart completely.

“For something as fundamental as the double helix, it is amazing that we are discovering these basic properties so late in the game,” said Al-Hashimi. “We need to continue to zoom in to obtain a deeper understanding regarding these basic molecules of life.” More. Paper. (paywall) – Huiqing Zhou, Isaac J Kimsey, Evgenia N Nikolova, Bharathwaj Sathyamoorthy, Gianmarc Grazioli, James McSally, Tianyu Bai, Christoph H Wunderlich, Christoph Kreutz, Ioan Andricioaei, Hashim M Al-Hashimi. m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nature Structural & Molecular Biology, 2016; DOI: 10.1038/nsmb.3270

Jussanotheraccident, right?

It’s getting to the point where useful science knowledge will cease unless the role of information as a real feature of the universe is acknowledged. It’ll all just be Perceptronium Man and New Scientist astounding us with nonsense like: Information is physical. That sells and what else matters.

See also: Data basic

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One Reply to “DNA well suited as blueprint for life

  1. 1
    bornagain77 says:

    semi related:

    Scientists discover light could exist in a previously unknown form – August 5, 2016
    Excerpt: In normal materials, light interacts with a whole host of electrons present on the surface and within the material. But by using theoretical physics to model the behaviour of light and a recently-discovered class of materials known as topological insulators, Imperial researchers have found that it could interact with just one electron on the surface.
    This would create a coupling that merges some of the properties of the light and the electron. Normally, light travels in a straight line, but when bound to the electron it would instead follow its path, tracing the surface of the material.
    Their models showed that as well as the light taking the property of the electron and circulating the particle, the electron would also take on some of the properties of the light.
    Normally, as electrons are travelling along materials, such as electrical circuits, they will stop when faced with a defect. However, Dr Giannini’s team discovered that even if there were imperfections in the surface of the nanoparticle, the electron would still be able to travel onwards with the aid of the light.
    If this could be adapted into photonic circuits, they would be more robust and less vulnerable to disruption and physical imperfections.
    Dr Giannini said: “The results of this research will have a huge impact on the way we conceive light. Topological insulators were only discovered in the last decade, but are already providing us with new phenomena to study and new ways to explore important concepts in physics.”

    It appears that molecular biology has already beat human engineers, once again, to the punch in utilizing the advantages of Topological insulators

    Polymer models of topological insulators
    Boryana Doyle 1*, Maxim Imakaev 2, Geoffrey Fudenberg 3, Leonid Mirny 2,3,4
    From Epigenetics & Chromatin: Interactions and processes Boston, MA, USA. – 11-13 March 2013
    Excerpt: Our simulations show that the polymeric nature of chromatin is essential for modulating the action of topological insulators that modulate contact frequency between promoters and enhancers.


    A topological insulator is a material with non-trivial topological order that behaves as an insulator in its interior but whose surface contains conducting states, meaning that electrons can only move along the surface of the material

    adjective, Chemistry.
    of or relating to a polymer.
    (of compounds) having the same elements combined in the same proportion but different molecular weights.

    A polymer (/?p?l?m?r/;[2][3] Greek poly-, “many” + -mer, “parts”) is a large molecule, or macromolecule, composed of many repeated subunits. Because of their broad range of properties,[4] both synthetic and natural polymers play an essential and ubiquitous role in everyday life.[5] Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function

    Chromatin is a complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells. Nuclear DNA does not appear in free linear strands; it is highly condensed and wrapped around nuclear proteins in order to fit inside the nucleus.

    Of related note:

    Into the Quantum Internet at the Speed of Light – Feb. 4, 2013
    Excerpt: Northup report how they have directly transferred the quantum information stored in an atom onto a particle of light. Such information could then be sent over optical fiber to a distant atom.

    (“Delocalized” Quantum) Sound-like bubbles whizzing around in DNA essential to life – Jun 1, 2016
    Excerpt: new research in the UK has detected sound-like bubbles in DNA that is essential to life and which will change the fundamental understanding of biochemical reactions inside a cell.
    The research,,, describes how double-stranded DNA splits using delocalized sound waves that are the hallmark of quantum effects.,,,
    Dedicated enzymes responsible for making new proteins read the code by splitting the double strand in order to access the information.
    One of the big outstanding questions of biology has been how these enzymes find the initial hole or “bubble” in the double strand to start reading the code.,,,
    researcher Gopakumar Ramakrishnan said: “It had been proposed by theoreticians that such DNA bubbles might behave like sound waves, bouncing around in DNA like echoes in a cathedral. However, the current paradigm in biology is that such sound-like dynamics are irrelevant to biological function, as interaction of a biomolecule with the surrounding water will almost certainly destroy any of these effects.”,,,
    Researchers in the Ultrafast Chemical Physics group carried out experiments with a laser that produces femtosecond laser pulses about a trillion times shorter than a camera flash.
    This allowed them to succeed in the detection of sound-like bubbles in DNA. They could show that these bubbles whiz around like bullets in a shooting gallery even in an environment very similar to that which can be found in a living cell.
    Thomas Harwood said, a researcher said: “The sound waves in DNA are not your ordinary sound waves. They have a frequency of a few terahertz or a billion times higher than a human or a dog can hear!”
    Professor Klaas Wynne, leader of the research team and Chair in Chemical Physics at the University of Glasgow, said, “The terahertz sound-like bubbles we have seen alter our fundamental understanding of biochemical reactions. There were earlier suggestions for a role of delocalized quantum phenomena in light harvesting, magneto reception, and olfaction.”
    The new results now imply a much more general role for sound-like delocalized phenomena in biomolecular processes.

    The Real Bioinformatics Revolution – Proteins and Nucleic Acids ‘Singing’ to One Another?
    Excerpt: the molecules send out specific frequencies of electromagnetic waves which not only enable them to ‘see’ and ‘hear’ each other, as both photon and phonon modes exist for electromagnetic waves, but also to influence each other at a distance and become ineluctably drawn to each other if vibrating out of phase (in a complementary way).,,, More than 1,000 proteins from over 30 functional groups have been analysed. Remarkably, the results showed that proteins with the same biological function share a single frequency peak while there is no significant peak in common for proteins with different functions; furthermore the characteristic peak frequency differs for different biological functions.,,, The same results were obtained when regulatory DNA sequences were analysed.

    Quantum criticality in a wide range of important biomolecules
    Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say.
    That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.”
    The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
    “what exactly is the advantage that criticality confers?”

    Proteins ‘ring like bells’ – June 2014
    As far back as 1948, Erwin Schrödinger—the inventor of modern quantum mechanics—published the book “What is life?”
    In it, he suggested that quantum mechanics and coherent ringing might be at the basis of all biochemical reactions. At the time, this idea never found wide acceptance because it was generally assumed that vibrations in protein molecules would be too rapidly damped.
    Now, scientists at the University of Glasgow have proven he was on the right track after all.
    Using modern laser spectroscopy, the scientists have been able to measure the vibrational spectrum of the enzyme lysozyme, a protein that fights off bacteria. They discovered that this enzyme rings like a bell with a frequency of a few terahertz or a million-million hertz. Most remarkably, the ringing involves the entire protein, meaning the ringing motion could be responsible for the transfer of energy across proteins.
    The experiments show that the ringing motion lasts for only a picosecond or one millionth of a millionth of a second. Biochemical reactions take place on a picosecond timescale and,,, (are) optimised enzymes to ring for just the right amount of time. Any shorter, and biochemical reactions would become inefficient as energy is drained from the system too quickly. Any longer and the enzyme would simple oscillate forever: react, unreact, react, unreact, etc. The picosecond ringing time is just perfect for the most efficient reaction.
    These tiny motions enable proteins to morph quickly so they can readily bind with other molecules, a process that is necessary for life to perform critical biological functions like absorbing oxygen and repairing cells.
    The findings have been published in Nature Communications.
    Klaas Wynne, Chair in Chemical Physics at the University of Glasgow said: “This research shows us that proteins have mechanical properties that are highly unexpected and geared towards maximising efficiency. Future work will show whether these mechanical properties can be used to understand the function of complex living systems.”

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