BIOL 201 Lecture Notes - Lecture 4: Shadow Biosphere, D-Loop, Telomere

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Published on 9 Feb 2013
Although the `B-DNA form' is most common under the conditions found in cells, it is not a well-
defined conformation but a family of related DNA conformations that occur at the high hydration
levels present in living cells. Their corresponding X-ray diffraction and scattering patterns are
characteristic of molecular paracrystals with a significant degree of disorder.
Compared to B-DNA, the A-DNA form is a wider right-handed spiral, with a shallow, wide
minor groove and a narrower, deeper major groove. The A form occurs under non-physiological
conditions in partially dehydrated samples of DNA, while in the cell it may be produced in
hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes. Segments of
DNA where the bases have been chemically modified by methylation may undergo a larger
change in conformation and adopt the Z form. Here, the strands turn about the helical axis in
a left-handed spiral, the opposite of the more common B form. These unusual structures can be
recognized by specific Z-DNA binding proteins and may be involved in the regulation of
For a number of years exobiologists have proposed the existence of a shadow biosphere, a
postulated microbial biosphere of Earth that uses radically different biochemical and molecular
processes than currently known life. One of the proposals was the existence of lifeforms that
use arsenic instead of phosphorus in DNA. A report in 2010 of the possibility in
the bacterium GFAJ-1, was announced,though the research was disputed, and evidence suggests
the bacterium actively prevents the incorporation of arsenic into the DNA backbone and other
At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The
main function of these regions is to allow the cell to replicate chromosome ends using the
enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′
ends of chromosomes. These specialized chromosome caps also help protect the DNA ends, and
stop the DNA repair systems in the cell from treating them as damage to be corrected. In human
cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats
of a simple TTAGGG sequence.
These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked
sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four
guanine bases form a flat plate and these flat four-base units then stack on top of each other, to
form a stable G-quadruplexstructure. These structures are stabilized by hydrogen bonding
between the edges of the bases and chelation of a metal ion in the centre of each four-base
unit. Other structures can also be formed, with the central set of four bases coming from either a
single strand folded around the bases, or several different parallel strands, each contributing one
base to the central structure.
In addition to these stacked structures, telomeres also form large loop structures called telomere
loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by
telomere-binding proteins. At the very end of the T-loop, the single-stranded telomere DNA is
held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical
DNA and base pairing to one of the two strands. This triple-stranded structure is called a
displacement loop or D-loop.
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