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Topoisomerase II enzymes, amazing evidence of design

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Topoisomerase II enzymes, amazing evidence of design

http://reasonandscience.heavenforum.org/t2111-topoisomerase-ii-enzymes-amazing-evidence-of-design

Complete and equal transmission of DNA to daughter cells is  crucial during mitosis. During cell division, each daughter cell inherits one copy of every chromosome. The metaphase-to-anaphase transition is the critical point in the cell cycle where the cell commits to separation of sister chromatids . Once spindle attachment is complete, cohesion must be eliminated to enable the physical separation of sister chromatids. This requires cleavage of the protein complex cohesin by separase and, in some instances, completion of chromosome decatenation. Catenation is the process by which two circular DNA strands are linked together like chain links. This occurs after DNA replication, where two single strands are catenated and can still replicate but cannot separate into the two daughter cells. 


II Topoisomerase enzymes  is a ubiquitous enzyme that is essential for the survival of all eukaryotic organisms and plays critical roles in virtually every aspect of DNA metabolism. It performs the amazing feat of breaking a DNA double helix, passing another helix through the gap, and resealing the double helix behind it.  They are essential in the separation of entangled daughter strands during replication. This function is believed to be performed by topoisomerase II in eukaryotes and by topoisomerase IV in prokaryotes. Failure to separate these strands leads to cell death. As genetic material DNA is wonderful, but as a macromolecule it is unruly, voluminous and fragile. Without the action of DNA replicases, topoisomerases, helicases, translocases and recombinases, the genome would collapse into a topologically entangled random coil that would be useless to the cell.  The topoisomerase is thought to be a highly dynamic structure, with several gates for entry of DNA into the two DNA-sized holes. Loss of topoisomerase activity in metaphase leads to delayed exit and extensive anaphase chromosome bridging, often resulting in cytokinesis failure, although maintenance of limited catenation until anaphase may be important for sister chromatid structural organization 9 Accurate transmission of chromosomes requires that the sister DNA molecules created during DNA replication are disentangled and then pulled to opposite poles of the cell before division. Defects in chromosome segregation produce cells that are aneuploid (containing an abnormal number of chromosomes)-a situation that can have dire consequences. 

Like many other enzymes, topoisomerase II are essential for cell function, and had to be present in the first living cell to exercise their function right in the beginning, when life began.

Within each chromosome, two dimensions of organization are at play: condensation along the axes ensures the entire chromatid, end-to-end, is kept together 8 , while the tight association of sister chromatids until anaphase, termed sister chromatid cohesion (SCC), ensures that each daughter cell receives only one copy . Two mechanisms are known to play a role in SCC: DNA catenation, which physically interlocks (catenates) DNA across the sister chromatids ; and protein linkages through the cohesin complex, which physically tether the sister chromatids to one another.

Topoisomerase II forms a covalent linkage to both strands of the DNA helix at the same time, making a transient double-strand break in the helix. These enzymes are activated by sites on chromosomes where two double helices cross over each other such as those generated by supercoiling in front of a replication fork 

Once a topoisomerase II molecule binds to such a crossing site, the protein uses ATP hydrolysis to perform the following set of reactions efficiently:

(1) it breaks one double helix reversibly to create a DNA “gate”;
(2) it causes the second, nearby double helix to pass through this opening; and
(3) it then reseals the break and dissociates from the DNA. At crossover points generated by supercoiling, passage of the double helix through the gate occurs in the direction that will reduce supercoiling. In this way, type II topoisomerases can relieve the overwinding tension generated in front of a replication fork. Their reaction mechanism also allows type II DNA topoisomerases to efficiently separate two interlocked DNA circles. Topoisomerase II also prevents the severe DNA tangling problems that would otherwise arise during DNA replication. The enormous usefulness of topoisomerase II for untangling chromosomes can readily be appreciated by anyone who has struggled to remove a tangle from a fishing line without the aid of scissors.


These molecular machines are far beyond what unguided processes involving chance and necessity can produce. Indeed, machinery of the complexity and sophistication of Topoisomerase enzymes are, based on our experience, usually atributed to intelligent agents. 

Type IIA topoisomerases consist of several key motifs: an

N-terminal GHKL ATPase domain 

Toprim domain
 
central DNA-binding core 

C-terminal domain

Each of these key motifs are essential for the proper function of the enzyme. No part can be reduced, and neither is it possible any of the subparts to emerge by natural means. Not only had the enzyme to emerge prior to the first cell being formed, and so could not be the result of evolution, but the sub parts by themself, and the enzyme by itself even fully formed,  would have no use, unless the DNA double helix molecules were already existing as well, and so the whole process of cell division, mitosis, and catenation, which happens through DNA replication. The enzyme is however essential for life, so if Topo II is removed, life could not exist. So we have here one of inumerous essential seemingly tiny and aparently unimportant parts, which by closer looking reveal to be life essential. This provides another big question mark in regard of naturalistic explanations, provides on the other part ones more a powerful argument for design. 

http://reasonandscience.heavenforum.org/t2111-topoisomerase-ii-enzymes-amazing-evidence-of-design#3754


Introduction:

The eukaryotic cell is a prime example of a functioning nano machinery. 9



Complete and equal transmission of DNA to daughter cells is  crucial during mitosis. During cell division, each daughter cell inherits one copy of every chromosome. The metaphase-to-anaphase transition ( see picture above ) is the critical point in the cell cycle where the cell commits to separation of sister chromatids 2. Once spindle attachment is complete, cohesion must be eliminated to enable the physical separation of sister chromatids. This requires cleavage of the protein complex cohesin by separase and, in some instances, completion of chromosome decatenation. Catenation is the process by which two circular DNA strands are linked together like chain links. This occurs after DNA replication, where two single strands are catenated and can still replicate but cannot separate into the two daughter cells. ( see picture below) 


II Topoisomerase enzymes  is a ubiquitous enzyme that is essential for the survival of all eukaryotic organisms and plays critical roles in virtually every aspect of DNA metabolism 5 It performs the amazing feat of breaking a DNA double helix, passing another helix through the gap, and resealing the double helix behind it.  They are essential in the separation of entangled daughter strands during replication. This function is believed to be performed by topoisomerase II in eukaryotes and by topoisomerase IV in prokaryotes. Failure to separate these strands leads to cell death. As genetic material DNA is wonderful, but as a macromolecule it is unruly, voluminous and fragile. Without the action of DNA replicases, topoisomerases, helicases, translocases and recombinases, the genome would collapse into a topologically entangled random coil that would be useless to the cell. 3 The topoisomerase is thought to be a highly dynamic structure, with several gates for entry of DNA into the two DNA-sized holes. Loss of topoisomerase activity in metaphase leads to delayed exit and extensive anaphase chromosome bridging, often resulting in cytokinesis failure, although maintenance of limited catenation until anaphase may be important for sister chromatid structural organization 9 Accurate transmission of chromosomes requires that the sister DNA molecules created during DNA replication are disentangled and then pulled to opposite poles of the cell before division. Defects in chromosome segregation produce cells that are aneuploid (containing an abnormal number of chromosomes)-a situation that can have dire consequences. 7

Like many other enzymes, topoisomerase II are essential for cell function, and had to be present in the first living cell to exercise their function right in the beginning, when life began.



Within each chromosome, two dimensions of organization are at play: condensation along the axes ensures the entire chromatid, end-to-end, is kept together 8 , while the tight association of sister chromatids until anaphase, termed sister chromatid cohesion (SCC), ensures that each daughter cell receives only one copy . Two mechanisms are known to play a role in SCC: DNA catenation, which physically interlocks (catenates) DNA across the sister chromatids ; and protein linkages through the cohesin complex, which physically tether the sister chromatids to one another.

The link below shows a  animated model of the DNA transport mechanism employed by a type II DNA topoisomerases.  N-terminal domain of ParC is shown in blue, C-terminal domain of ParC in cyan, N-terminal domain of ParE in purple, C-terminal domain of ParE in yellow, G-segment in green and the DNA strand in red.

https://upload.wikimedia.org/wikipedia/commons/8/8b/Structural-Basis-of-Gate-DNA-Breakage-and-Resealing-by-Type-II-Topoisomerases-pone.0011338.s005.ogv



https://bioslawek.files.wordpress.com/2011/09/numern-5.gif?w=450&h=450







Type II topoisomerases cut both strands of the DNA helix simultaneously in order to manage DNA tangles and supercoils. They use the hydrolysis of ATP 1

Sister-chromatid cohesion also results, at least in part, from DNA catenation, the intertwining of sister DNA molecules that occurs when two replication forks meet during DNA synthesis.



The enzyme topoisomerase II gradually disentangles the catenated sister DNAs between
S phase and early mitosis by cutting one DNA molecule, passing the other through the break,
and then resealing the cut DNA

Picture below: The DNA-helix-passing reaction catalyzed by DNA topoisomerase II. type II enzymes hydrolyze ATP (red), which is needed to release and reset the enzyme after each cycle. Type II topoisomerases are largely confined to proliferating cells in eukaryotes; partly for that reason, they have been effective targets for anticancer drugs. Some of these drugs inhibit topoisomerase II at the third step in the figure and thereby produce high levels of double-strand breaks that kill rapidly dividing cells. The small yellow circles represent the phosphates in the DNA backbone that become covalently bonded to the topoisomerase



Topoisomerase II forms a covalent linkage to both strands of the DNA helix at the same time, making a transient double-strand break in the helix. These enzymes are activated by sites on chromosomes where two double helices cross over each other such as those generated by supercoiling in front of a replication fork

Once a topoisomerase II molecule binds to such a crossing site, the protein uses ATP hydrolysis to perform the following set of reactions efficiently:

(1) it breaks one double helix reversibly to create a DNA “gate”;
(2) it causes the second, nearby double helix to pass through this opening; and
(3) it then reseals the break and dissociates from the DNA. At crossover points generated by supercoiling, passage of the double helix through the gate occurs in the direction that will reduce supercoiling. In this way, type II topoisomerases can relieve the overwinding tension generated in front of a replication fork. Their reaction mechanism also allows type II DNA topoisomerases to efficiently separate two interlocked DNA circles. Topoisomerase II also prevents the severe DNA tangling problems that would otherwise arise during DNA replication. The enormous usefulness of topoisomerase II for untangling chromosomes can readily be appreciated by anyone who has struggled to remove a tangle from a fishing line without the aid of scissors.


These molecular machines are far beyond what unguided processes involving chance and necessity can produce. Indeed, machinery of the complexity and sophistication of Topoisomerase enzymes are, based on our experience, usually atributed to intelligent agents. 

1) https://en.wikipedia.org/wiki/Type_II_topoisomerase
2) http://www.rcsb.org/pdb/101/motm.do?momID=73
3) http://www.nature.com/nrm/journal/v7/n8/full/nrm1982.html
4) http://www.ncbi.nlm.nih.gov/books/NBK21703/
5) http://www.sciencedirect.com/science/article/pii/S0167478198001328
6) https://en.wikipedia.org/wiki/DNA_supercoil
7) http://www.ncbi.nlm.nih.gov/pubmed/12142526
8 )http://reasonandscience.heavenforum.org/t2086-chromosome-condensation-amazing-evidence-of-design
9) http://foresight.org/Conference/MNT6/Abstracts/Knoch/index.html
10) http://www.ncbi.nlm.nih.gov/pubmed/17293019



Last edited by Admin on Tue Jan 19, 2016 4:12 pm; edited 21 times in total

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Bacteria typically possess two type II topoisomerases: DNA gyrase, which maintains DNA in a slightly unwound (negatively supercoiled) state, and topoisomerase IV (Topo IV), which is primarily responsible for unlinking newly replicated DNA 2


Bacterial DNA replication is bidirectional since the chromosome is circular.  It begins from a central origin and proceeds around the chromosome until the two polymerase enzymes meet.  The torsion placed on the separated strands by the untwisting activity of helicase is relaxed by the enzyme topoisomerase by cutting the twisting sections and re-joining them opposite to the direction of the supercoil. 1



1) http://academic.pgcc.edu/~kroberts/Lecture/Chapter%207/replication.html
2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012485/

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Structure of type IIA topoisomerases 1


Type IIA topoisomerases consist of several key motifs: an

N-terminal GHKL ATPase domain

Toprim domain
 
central DNA-binding core

C-terminal domain

Each of these key motifs are essential for the proper function of the enzyme. No part can be reduced, and neither is it possible any of the subparts to emerge by natural means. Not only had the enzyme to emerge prior to the first cell being formed, and so could not be the result of evolution, but the sub parts by themself, and the enzyme by itself even fully formed,  would have no use, unless the DNA double helix molecules were already existing as well, and so the whole process of cell division, mitosis, and catenation, which happens through DNA replication. The enzyme is however essential for life, so if Topo II is removed, life could not exist. So we have here one of inumerous essential seemingly tiny and aparently unimportant parts, which by closer looking reveal to be life essential. This provides another big question mark in regard of naturalistic explanations, provides on the other part once more a powerful argument for design.

ATPase domains dimerize to form a closed conformation.

Linking the ATPase domain to the Toprim fold is a helical element known as the transducer domain. This domain is thought to communicate the nucleotide state of the ATPase domain to the rest of the protein.

The central core of the protein contains a Toprim fold and a DNA-binding core that contains a winged helix domain (WHD), often referred to as a CAP domain, since it was first identified to resemble the WHD of catabolite activator protein. The catalytic tyrosine lies on this WHD. The Toprim fold is a Rossmann fold that contains three invariant acidic residues that coordinate magnesium ions involved in DNA cleavage and DNA religation (Avarind, Leipe, Konin, Nucleic Acids Research 1998). The DNA-binding core consists of the WHD, which leads to a tower domain. A coiled-coil region leads to a C-terminal domain that forms the main dimer interface for this crystal state (often termed the C-gate). While the original topoisomerase II structure shows a situation where the WHDs are separated by a large distance, the structure of gyrase shows a closed conformation, where the WHD close.

Picture below: Structure of yeast topoisomerase II bound to a doubly nicked 34-mer duplex DNA . The Toprim fold is colored cyan; the DNA is colored orange; the HTH is colored magenta; and the C-gate is colored purple. Notice that the DNA is bent by ~160 degrees through an invariant isoleucine (Ile833 in yeast).




The Fass structure shows that the Toprim domain is flexible and that this flexibility can allow the Toprim domain to coordinate with the WHD to form a competent cleavage complex.

The C-terminal region of the prokaryotic topoisomerases  formed a novel beta barrel, which bends DNA by wrapping the nucleic acid around itself. The bending of DNA by gyrase has been proposed as a key mechanism in the ability of gyrase to introduce negative supercoils into the DNA. This is consistent with footprinting data that shows that gyrase has a 140-base-pair footprint. Both gyrase and topoisomerase IV CTDs bend DNA, but only gyrase introduces negative supercoils.
Unlike the function of the C-terminal domain of prokaryotic topoisomerases, the function of the C-terminal region of eukaryotic topoisomerase II is still not clear. Studies have suggested that this region is regulated by phosphorylation and this modulates topoisomerase activity, however more research needs to be done to investigate this.

Origin and evolution of DNA topoisomerases. 10

The DNA topoisomerases are essential for DNA replication, transcription, recombination, as well as for chromosome compaction and segregation. They may have appeared early during the formation of the modern DNA world. Several families and subfamilies of the two types of DNA topoisomerases (I and II) have been described in the three cellular domains of life (Archaea, Bacteria and Eukarya), as well as in viruses infecting eukaryotes or bacteria. The main families of DNA topoisomerases, Topo IA, Topo IB, Topo IC (Topo V), Topo IIA and Topo IIB (Topo VI) are not homologous, indicating that they originated independently. However, some of them share homologous modules or subunits that were probably recruited independently to produce different topoisomerase activities. The puzzling phylogenetic distribution of the various DNA topoisomerase families and subfamilies cannot be easily reconciled with the classical models of early evolution describing the relationships between the three cellular domains. A possible scenario is based on a Last Universal Common Ancestor (LUCA) with a RNA genome (i.e. without the need for DNA topoisomerases). Different families of DNA topoisomerases (some of them possibly of viral origin) would then have been independently introduced in the different cellular domains.

The molecular basis for these differences and their evolutionary origins remains speculative  11

1) https://en.wikipedia.org/wiki/Type_II_topoisomerase
11) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012485/



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http://www.ncbi.nlm.nih.gov/pubmed/7783632
DNA topoisomerases are essential to the cell for the regulation of DNA supercoiling levels and for chromosome decatenation.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC18654/
Mammalian DNA topoisomerase IIIα is essential in early embryogenesis

http://www.ncbi.nlm.nih.gov/pubmed/20939813
DNA topoisomerases (topos) are essential enzymes that regulate the topological state of DNA during cellular processes such as replication, transcription, recombination, and chromatin remodeling.

http://www.annualreviews.org/doi/abs/10.1146/annurev.pa.34.040194.001203
DNA Topoisomerases: Essential Enzymes and Lethal Targets

http://nar.oxfordjournals.org/content/early/2009/02/09/nar.gkp032.full
Topoisomerases are essential enzymes that solve topological problems arising from the double-helical structure of DNA.

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One of the most remarkable new papers giving evolution the glory for complex design is a piece by Forterre and Gadelle1 about DNA-processing molecular machines called topoisomerases . 1 They used the E-word evolution 18 times in an attempt to explain how these machines evolved.  Surprisingly, there is very little homology to hang a phylogeny on: similarities crop up between different kingdoms, and differences are seen where there should be homologies.  “Topoisomerases are essential enzymes that solve topological problems arising from the double-helical structure of DNA,” they explained.  “As a consequence, one should have naively expected to find homologoustopoisomerases in all cellular organisms, dating back to their last common ancestor.  However, as observed for other enzymes working with DNA, this is not the case.”  Has Darwinian universal common ancestry, therefore, been falsified?  Not so fast.  In the evolutionary “scenario,” evidence is no longer a requirement.  The story is the thing:

Topoisomerases could have originated by combining protein modules previously involved in RNA metabolism, such as RNA-binding proteins, RNA endonucleases or RNA ligases.  Alternatively, they could have evolved from protein modules that were already working with DNA, if the first steps in the evolution of DNA genomes occurred in the absence of any topoisomerase activity, i.e. before the emergence of long double-stranded DNA genomes.  Twoarguments favour the latter hypothesis: first, whereas RNA polymerases and RNA-binding proteins are obvious candidates to be direct ancestors of DNA polymerases and single-stranded DNA-binding proteins, ‘RNA topoisomerases’ that could be direct ancestor of DNA topoisomerases are unknown.  Secondly, it is likely that double-stranded DNA genomes with complex DNA-replication mechanisms (i.e. concurrent symmetric DNA replication) were precededby single-stranded or even short double-stranded DNA genomes replicated by simpler mechanisms, such as asymmetric DNA replication, and/or rolling circle (RC) replication (75) (Figure 3).  These simple systems probably did not require topoisomerases, as it is still the case for their modern counterparts (the RC replication of some replicons require supercoiled DNA, hence gyrase activity, but only for the recognition step of the initiator protein).  If this scenario is correct, topoisomerases probably originated when more complex DNA genomes (long linear or circular DNA molecules) were selected in the course of evolution, together with more elaborate replication machineries.

Their viral-origin hypothesis required the word suggest 26 times, possible 16 times, could 14 times, and might 10 times.  Of one thing they were sure, however.  These complex molecular machines were not intelligently designed.  It’s rare for a scientific paper to even mention intelligent design.  Here’s what they said about it: “An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists.”  Whimsical as that statement is, it represents a remarkable turnaround.  Usually, evolutionists claim that similarities disprove intelligent design.  These scientists are claiming that differences disprove it.  ID can’t win for losing.

1) http://creationsafaris.com/crev200902.htm

further readings : http://nar.oxfordjournals.org/content/37/3/679.full

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An Untangled Problem for Evolution: DNA Topoisomerase.


DNA replicates itself. That is Biology 101. The process is quite complex and any biology student required to rattle off the procedure on an exam can confirm. Although there are separate kinds of topoisomerase,1 they perform the same essential function within the process of replication.

What is topoisomerase?

In each human cell, there are approximately 2 meters of DNA compacted within a nucleus of the diameter of about 10 micrometers.2 For perspective, imagine that the nucleus is represented by a standard basketball. The length of all the DNA compacted into the ball would go round-trip between the earth and the moon just shy of twice. Topoisomerase has the job of ensuring that the shape of DNA is manageable. Add in the fact that DNA is not just a helix, but a double-helix. As one might imagine, the task of trying to do anything productive with this material presents very serious concerns that need to be dealt with. During replication, the topology (i.e. the shape and structure) of DNA and the movement in unzipping result in issues like tangling and kinking, so the process faces a formidable and complex challenge of bioengineering.3 It’s topoisomerase’s job to alleviate those issues so they don’t halt the replication process.4 If DNA cannot replicate, then an organism cannot grow. Additionally, DNA doesn’t just unzip for replication. It unzips in a process called transcription, which, with the help of RNA, is the first half of producing vital proteins in the cell.


Two examples might help illustrate some of the mechanical concerns that arise. Without even trying, the ordinary use of a wired phone produces coiling in the helical cord. No extraordinary spinning or energy is required to produce the effect, but it doesn’t take long for the cable to go from fresh and neat to knotted spaghetti, which seem to never come out. Even if the tangle is gone, there always seems to be a small bend or a missing turn were the tangle was. The second illustration may serve to demonstrate the problem of kinking just prior to cutting the DNA strand in two. To demonstrate the concept, you can take a piece of twine and try to unwind it by pulling away both its twisted strands away from each other. A "Y"-shape forms: the two strands being pulled apart are each the top segments of the "Y" and the rest of the twine is the bottom. Now at some point, enough tension will build up at the center of the "Y" to where you can no longer pull the strands apart. Fortunately, topoisomerase is there to work out these sorts of problems. Its process is so vital and complex that some have referred to topoisomerase as the "magicians of the DNA world"5 because of their uncanny ability to manipulate the DNA strand and master its topology. 

The Problems for evolution

1: Does not fit early evolutionary models for an ancestral topoisomerase

It is still unclear how exactly topoisomerase originated on an evolutionary model, particularly because all the different types of topoisomerase appear to have originated independently of one another.6 A core tenet of evolutionary biology is that all life can be traced to a common ancestor (more technically, LUCA: last universal common ancestor). It is natural to assume that LUCA would have some master topoisomerase that would have developed into the varying domains7 of natural life: Achaea, Bacteria, and Eukaryota. But, this seems to be an incorrect inference that does not align with the actual data.8It is speculated that topoisomerase might have emerged with either an ancient viral lineage or a LUCA that began with RNA genetic information or a combination of the two.9


These RNA-infused models would be controversial, because such scenarios involve the already contested10 (among researchers in that field) RNA-world hypothesis for the origin of life. And, the progressive introduction of topoisomerase and other necessary replication proteins into the evolutionary lineup seems an inventive proposition, but requires massive amounts of biological informational leaps that are unfounded, especially within the limited time window for the emergence of life on earth that evolution demands. 

2: Conceptual Paradox11

Most of all, the origin of topoisomerase presents a chick-and-egg paradox. To replicate itself the DNA molecule needs topoisomerase to unwind it. And, DNA would need to code for a protein to do the unwinding (in order to pass on the genes to code for topoisomerase). It’s like having a car with no gas. You need to drive to the gas station to get gas, but you need gas to get to the gas station. DNA might have obtained topoisomerase from somewhere else, but the instant it makes a copy of itself, the other strand needs topoisomerase also. The scenario requires the leap to the reality, where DNA actually codes for this protein itself. That is not to mention that the actual mechanics of unwinding get even more complicated, because topoisomerase is able to cut and re-join small sections of DNA, which require precise biochemistry to ensure the right pieces get linked back up with each other and at the proper speed. Too slow, and the DNA doesn’t unwind fast enough for cell division (mitosis) and the cell dies before replication can occur.12 Too quickly, and the cell can set off its own self-destruct sequence (apoptosis) or cause irreversible damage to the genes that results in cancer.13

Conclusion

Lastly, it is also important to keep in mind that this is only a piece of a wider issue for evolutionary biology to explain DNA replication in general: proteins that function as stabilizing clamps, ones that actually unzip the DNA strand, others that error-check the new copies, or the fact that one side of the DNA is duplicated backwards and in sections…


http://apologetics-notes.comereason.org/2014/04/an-untangled-problem-for-evolution-dna.html

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