Linking RNA structure to function

By: James V. Kohl | Published on: September 9, 2016

(click to enlarge)

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage was reported on September 8, 2016 as:

Linking RNA structure and function

Excerpt 1)

Learning more about how lncRNAs control cell differentiation could offer a new approach to developing drugs for patients whose hearts have been damaged by cardiovascular disease, aging, or cancer.

The insult to the intelligence of all serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction is carefully packaged in claims like this:
Excerpt 2)

“We’re taking this motif and we’re using it to build a fingerprint so we can potentially find motifs that resemble that lncRNA across species,” Boyer says. “We also hope to extend this work to identify the modes of action of a catalog of motifs so that we can better predict lncRNAs with important functions.”

Energy-dependent changes in the microRNA/messenger RNA balance link hydrogen-atom transfer in DNA base pairs in solution to RNA methylation and RNA-directed DNA methylation, which links more than 53,000 published works on microRNAs to biophysically constrained cell type differentiation via the physiology of nutrient energy-dependent reproduction. It should already be perfectly clear that the motifs that resemble that lncRNA across species must be linked from microRNAs to energy-dependent biodiversity, or be linked from virus-driven energy theft to all pathology.
MicroRNA Search results Items: 1 to 20 of 53493
See also: Single-molecule dissection of stacking forces in DNA
Structured Abstract
INTRODUCTION

In DNA double helices, hydrogen bonds connect the base pairs across the two strands, and stacking bonds act along the helical axis between neighboring base pairs. Our understanding of DNA and the way it is processed in biology would profit from improved knowledge about the elementary bonds in DNA.

Reported on September 8, 2016 as Measuring forces in the DNA molecule

…the scientists also observed that the bonds spontaneously broke up and formed again within just a few milliseconds. The strength and the lifetime of the interactions depends to a great extent on which base pairs are stacked on each other.

The spontaneity, strength, and lifetime of the interactions is energy-dependent and it is controlled by the physiology of reproduction in species from microbes to humans. See “What is Life?” (1944)

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

with forward by Roger Penrose:
Excerpt:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”

See also: Unraveling the physics of DNA’s double helix July 12, 2007

Excerpt:

“The stability of DNA is so fundamental to life that it’s important to understand all factors,” said Piotr Marszalek, a professor of mechanical engineering and materials sciences at Duke. “If you want to create accurate models of DNA to study its interaction with proteins or drugs, for example, you need to understand the basic physics of the molecule. For that, you need solid measurements of the forces that stabilize DNA.”

The stability of DNA is RNA-mediated.

The leftmost picture shows the protein reference structure. Three disulfide bridges establishing a highly structured part of the protein are shown in sticks, and the cysteine being mutated is labeled (Cys409).

The rightmost picture shows the mutated amino acid (Tyr409) in space-filling, to illustrate how the increased size of the side chain will not fit inside the rigid structure. The amino acid is colored to show clashing atoms in red.

The functional connectivity linked to behavior during development is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).

The catechol-o-methyltransferase Val158Met polymorphism modulates the intrinsic functional network centrality of the parahippocampal cortex in healthy subjects

COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia

the COMT val158met polymorphism is not found in species other than humans (Palmatier et al., 1999)

The fact that an energy-dependent species-specific RNA-mediated amino acid substitution was linked to pathological human behavior in 1999 attests to the amount of ignorance touted by theorists who claim that beneficial mutations can be linked to biodiversity.

Linking RNA structure to function

Linking RNA structure and function

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