March 31, 2005 | David F. Coppedge

Your Linemen at Work: DNA Search and Rescue Machine Imaged in Action

DNA is amazing enough, but its automatic error-correction utilities are enough to stagger the imagination.  There are dozens of repair mechanisms to shield our genetic code from damage; one of them was portrayed in Nature1 March 31 (see also analysis by Sheila David in the same issue2) in terms that should inspire awe.
    Imagine a huge encyclopedia written on beads, in strands many miles long.  The words of the book are inscribed in letter beads along the strand.  Now imagine that, tied to the primary strand, is a twin strand with beads representing the “negatives” of the primary beads, such that when the strands are separated, exact copies can be made.  Every once in awhile, the strands are separated by a machine.  Floating beads are attracted to the negative beads, lining up to form exact copies of the book or portions thereof.  This is a simplified view of DNA transcription and replication.  What happens, however, if the wrong bead, or a defective bead, becomes attached to the negative?  For books, that could misspell a word or produce gibberish, but in living organisms, the consequences could be disastrous.
    Now picture little machines that regularly traverse the string of beads.  Because the shapes of the beads differ according to the letters on them, this machine is able to find typos.  Let’s say that a letter “C” is always supposed to pair with a letter “G” on the strand.  The proofreading machine feels every bead, and if it finds that particular mismatch, it ejects the incorrect bead so that another correct one can be fastened on by another machine.  This is a simplified view of “base-excision repair” (BER) that actually takes place in your body, all the time.
    The strands in a cell are, of course, DNA, and the beads are called nucleotides, or bases.  Of the four bases in DNA (C, G, A, and T) cytosine or C is always supposed to pair with guanine, G, and adenine, A, is always supposed to pair with thymine, T.  The enzyme studied by Banerjee et al. in Nature is one of a host of molecular machines called BER glycosylases; this one is called human oxoG glycosylase repair enzyme (hOGG1), and it is specialized for finding a particular type of error: an oxidized G base (guanine).  Oxidation damage can be caused by exposure to ionizing radiation (like sunburn) or free radicals roaming around in the cell nucleus.  The normal G becomes oxoG, making it very slightly out of shape.  There might be one in a million of these on a DNA strand.  While it seems like a minor typo, it can actually cause the translation machinery to insert the wrong amino acid into a protein, with disastrous results, such as colorectal cancer.  This little machine has an important job.3  How does it work?
    The machine latches onto the DNA double helix and works its way down the strand, feeling every base on the way.  As it proceeds, it kinks the DNA strand into a sharp angle.  It is built to ignore the T and A bases, but whenever it feels a C, it knows there is supposed to be a G attached.  The machine has precision contact points for C and G.  When the C engages, the base paired to it is flipped up out of the helix into a slot inside the enzyme that is finely crafted to mate with a pure, clean G.  If all is well, it flips the G back into the DNA helix and moves on.  If the base is an oxoG, however, that base gets flipped into another slot further inside, where powerful forces yank the errant base out of the strand so that other machines can insert the correct one.
    Now this is all wonderful stuff so far, but as with many things in living cells, the true wonder is in the details.  The thermodynamic energy differences between G and oxoG are extremely slight – oxoG contains only one extra atom of oxygen – and yet this machine is able to discriminate between them to high levels of accuracy.  David says, “DNA-repair enzymes amaze us with their ability to search through vast tracts of DNA to find subtle anomalies in the structure.  The human repair enzyme 8-oxoguanine glycosylase (hOGG1) is particularly impressive in this regard because it efficiently removes 8-oxoguanine (oxoG), a damaged guanine (G) base containing an extra oxygen atom, and ignores undamaged bases” (emphasis added in all quotes).  The team led by Anirban Banerjee of Harvard, using a clever new stop-action method of imaging, caught this little enzyme in the act of binding to a bad guanine, helping scientists visualize how the machinery works.
    Some other amazing details are mentioned about this molecular proofreader.  It checks every C-G pair, but slips right past the A-T pairs.  The enzyme, “much like a train that stops only at certain locations,” pauses at each C and, better than any railcar conductor inspecting each ticket, flips up the G to validate it.  Unless it conforms to the slot perfectly – even though G and oxoG differ in their match by only one hydrogen bond – it is ejected like a freeloader in a Pullman car and tossed out into the desert.  David elaborates:

Calculations of differences in free energy indicate that both favourable and unfavourable interactions lead to preferential binding of oxoG over G in the oxoG-recognition pocket, and of G over oxoG in the alternative site.  This structure [the image resolved by the scientific team] captures an intermediate that forms in the process of finding oxoG, and illustrates that the damaged base must pass through a series of ‘gates’, or checkpoints, within the enzyme; only oxoG satisfies the requirements for admission to the damage-specific pocket, where it will be clipped from the DNA.  Other bases (C, A and T) may be rejected outright without extrusion from the helix because hOGG1 scrutinizes both bases in each pair, and only bases opposite a C will be examined more closely.

How many linemen does it take to repair your strands?  The researchers explain, “Only 50,000 molecules of hOGG1 protect the entire 6 x 109 base-pair nuclear genome of a diploid human cell, hence the enzyme must have developed an efficient mechanism for distinguishing oxoG from the four nucleobases in normal DNA.”  50,000 repairmen for 6 billion bases: that’s one repairman for every 120,000 letters, comparable to a skilled proofreader checking every letter of a 20,000 word document for one specific kind of typo.  Then there are all the other proofreaders that look for other kinds of mistakes.4

1Banerjee et al., “Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA,” Nature 434, 612 – 618 (31 March 2005); doi:10.1038/nature03458.
2Sheila S. David, “Structural biology: DNA search and rescue,” Nature 434, 569 – 570 (31 March 2005); doi:10.1038/434569a.
3See “Life without DNA Repair,” in PNAS, 1997.  It lists 13 BER enzymes including this one.  Studies on mice are described: “mutants show various combinations of defective embryogenesis, tissue-specific dysfunction, hypersensitivity to DNA-damaging agents, premature senescence, genetic instability, and elevated cancer rates.”
4The authors mention another paralogous enzyme, 3-methyladenine DNA glycosylase (AlkA), which is not as “fastidious” as hOGG1, because it “does occasionally excise adenine residues from undamaged DNA.”  But there may be reasons for the differences in fidelity; some may have to work under stressful conditions, and repair as much as they can within constraints of time or other factors.  JBC Online says that AlkA has “a remarkably versatile active site.”  This reminds us that intelligent design does not mean perfection of every detail, but “constrained optimization”: achieving the combination of features that produces a “sweet spot” with best overall performance.  The proof of the pudding for DNA repair is in the performance itself: no one watching a race horse, cormorant (05/24/2004) or champion triathlete in action could argue with the assertion that the suite of repair enzymes in living things appears optimized to achieve an extremely high degree of fidelity under a wide range of conditions and stress factors.

OK, Darwin Party: checkmate.  Natural selection cannot act without accurate replication, yet the protein machinery for the level of accuracy required is itself built by the very genetic code it is designed to protect.  Explain that!  If the Darwinists cannot provide a plausible mechanism whereby nonliving chemicals, by chance, hit upon a means of replicating information-bearing molecules accurately, there would have been no evolution, because any gains would have been drowned in the errors of subsequent generations.
    It would have been challenging enough to explain accurate translation alone in a primordial soup, but now throw in some free radicals and radiation, and any information gained would have quickly been destroyed through accumulation of errors.  So accurate replication and proofreading are required for the origin of life.  How on earth could proofreading enzymes emerge, especially with this degree of fidelity, when they depend on the very information that they are designed to protect?  Think about it.  This is a catch-22 for Darwinists.  No wonder none of the authors of these two articles dared whisper the word evolution.  The gig is up; we might as well not even waste any time arguing about Hobbit man (03/25/2005), peppered mice (04/18/2003) and what IMAX films to show (03/23/2005).  Proofreading codes by chance?  And a complex suite of translation machinery without a designer?  Anyone with a head screwed on is not going to want such nonsense taught in public schools (03/24/2005).
    If we can just sweep away the cobwebs of musty Darwinian thinking out of our minds for a moment, we can begin to enjoy the wonder of these incredible mechanisms.  If the ancients could understand that creation demands a Creator by looking at the sun, or a bird, or a baby, how much more we today with all the revelations about cell biology and molecular machines?  The grand oratorio of creation is being unveiled, a little at a time, into a hallelujah chorus that deserves our most worshipful applause – indeed, a standing ovation.

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Categories: Cell Biology

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