Was four-stranded, ‘quadruple helix’ DNA designed or mutated?

_{David L. Hagen

January 21, 2013

Biophysics, Cell biology, Genetics, Human evolution, Intelligent Design}

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‘Quadruple helix’ DNA seen in human cells

Balasubramanian’s group has been pursuing a four-stranded version of the molecule (DNA) that scientists have produced in the test tube now for a number of years.

It is called the G-quadruplex. The “G” refers to guanine, one of the four chemical groups, or “bases”, that hold DNA together and which encode our genetic information (the others being adenine, cytosine, and thymine).

The G-quadruplex seems to form in DNA where guanine exists in substantial quantities. . . .
This revealed the four-stranded DNA arose most frequently during the so-called “s-phase” when a cell copies its DNA just prior to dividing. . . .
If the G-quadruplex could be implicated in the development of some cancers, it might be possible, he said, to make synthetic molecules that contained the structure and blocked the runaway cell proliferation at the root of tumours.

See article:
Quantitative visualization of DNA G-quadruplex structures in human cells Giulia Biffi, David Tannahill, John McCafferty & Shankar Balasubramanian, Nature Chemistry (2013) doi:10.1038/nchem.1548

If the quadruple helix is from mutated or erroneous copying, that could be a cause of cancer. From an ID perspective, if double helix DNA was designed and the quadruple helix DNA was not, then I hypothesize that there may be detection and repair mechanisms designed to prevent the quadruple helix DNA from being formed. The underlying cause for the quadruple helix DNA may thus be failure of the detection and repair mechanisms. John C. Sanford’s studies suggest there is an accumulation of mutations in the genome over time. See Mendel’s Accountant, and Genetic Entropy and the Mystery of the Genome.

Consequently this suggests an increase in the relative frequency quadruple helix DNA to population over time. This raises the potential to identify historic mutations causing this aberration with consequent potential to detect it.

Comments

If this is true, it sounds like information has a way of defying entropy ;)Aspire to Solomon_{June 27, 2014
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Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role - September 2012 Excerpt: There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect. http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=1&pagewanted=allbornagain77_{January 23, 2013
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One of the primary reasons to presuppose that the quadruplex DNA is designed and in not the result of mutations, or erroneous copying, besides the fact that 'it looks designed', is that it is now known that the genome will take on different 3-Dimensional configurations in different situations: Multidimensional Genome – Dr. Robert Carter – video (Notes in video description) http://www.metacafe.com/w/8905048 “Three-Dimensional Connections Across the Genome“ Keith Dunaway - 2012 http://www.nature.com/encode/#/threads/three-dimensional-connections-across-the-genome Safeguarding genome integrity through extraordinary DNA repair - April, 2011 Excerpt: Unlike euchromatin, where most of an organism’s genes reside and where most DNA consists of long, unrepetitive sequences of base pairs, DNA in heterochromatin consists mostly of short repeated sequences that don’t code for proteins; indeed, heterochromatin was long regarded as containing mostly “junk” DNA. Heterochromatin is now known to be anything but junk, playing a crucial role in organizing chromosomes and maintaining their integrity during cell division. It is concentrated near centromeres, where chromatids are in closest contact, which are required to transmit chromosomes from one generation to the next. Maintaining heterochromatin structure is necessary to the normal growth and functions of cells and organisms. http://phys.org/news/2011-04-safeguarding-genome-extraordinary-dna.html Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks - 25 October 2012 Excerpt Introduction: Long-range chromatin interactions are pervasive in the human genome and serve to regulate gene expression.,, Proximity ligation in combination with next-generation sequencing has recently enabled us to explore genome-wide spatial crosstalk in the chromatin.,,, The observation of most interest was that interacting promoters not only correlate with gene coexpression, but can also regulate each other’s transcriptional states, which blurs the traditional definitions of gene-regulatory elements in the genome. These observations support the notion of a chromatin interactome encompassing a dense repertoire of regulatory elements for transcriptional regulation. http://www.cell.com/cell-reports/abstract/S2211-1247%2812%2900326-9?switch=standard Comment from crev.info on the preceding article: News from Epigenetics - Dec. 21, 2012 Excerpt: They are organized into “nonrandom spatial clustering” the authors dub“rich clubs,” communities and spokes. This large-scale organization helps repress mutations among vital genes, and “shapes functionally compartmentalized and error-tolerant transcriptional regulation of human genome in three dimensions.” http://crev.info/2012/12/news-from-epigenetics/ Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. 2009 Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. http://www.sciencemag.org/cgi/content/abstract/326/5950/289 Shoddy Engineering or Intelligent Design? Case of the Mouse's Eye - April 2009 Excerpt: -- The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. -- So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell - remind them of the rod cell nuclei of the humble mouse. http://www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig.html Tissue-specific spatial organization of genomes - 2004 Excerpt: Using two-dimensional and three-dimensional fluorescence in situ hybridization we have carried out a systematic analysis of the spatial positioning of a subset of mouse chromosomes in several tissues. We show that chromosomes exhibit tissue-specific organization. Chromosomes are distributed tissue-specifically with respect to their position relative to the center of the nucleus and also relative to each other. Subsets of chromosomes form distinct types of spatial clusters in different tissues and the relative distance between chromosome pairs varies among tissues. Consistent with the notion that nonrandom spatial proximity is functionally relevant in determining the outcome of chromosome translocation events, we find a correlation between tissue-specific spatial proximity and tissue-specific translocation prevalence. Conclusion: Our results demonstrate that the spatial organization of genomes is tissue-specific and point to a role for tissue-specific spatial genome organization in the formation of recurrent chromosome arrangements among tissues. http://genomebiology.com/content/5/7/R44 Not in the Genes: Embryonic Electric Fields - Jonathan Wells - December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels -- which determines the form of the endogenous electric field -- constitutes an independent source of information in the developing embryo.bornagain77_{January 23, 2013
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Actually,,, there is reason to believe that the Quadruple helix is designed and is not a 'degenerate' state 'Quadruple helix' DNA discovered in human cells - January 20, 2013 Excerpt: While quadruplex DNA is found fairly consistently throughout the genome of human cells and their division cycles, a marked increase was shown when the fluorescent staining grew more intense during the 's-phase' - the point in a cell cycle where DNA replicates before the cell divides.,,, It's a philosophical question as to whether they are there by design or not - but they exist and nature has to deal with them.,,, "The 'quadruple helix' DNA structure may well be the key to new ways of selectively inhibiting the proliferation of cancer cells. The confirmation of its existence in human cells is a real landmark." http://phys.org/news/2013-01-quadruple-helix-dna-human-cells.html And I disagree that it is a purely 'philosophical question' if they are there by design or not, if the Quadruple helix is necessary, i.e. 'Designed', for cell division then there should be various 'knock out' approaches that could be used to establish that fact. ,,, The 'philosophy' that would be supported by that scientific fact is obvious.bornagain77_{January 22, 2013
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