Biomedical Engineering Reference
In-Depth Information
2800
2400
2000
FIGURE 1.45
DNA fragment peak sizes as a function of digestion
time with micrococcal nuclease. The agarose gel
fragment midpoints are plotted vs. digestion time
for the monomers (circles), dimers (squares), and
trimers (triangle) resulting from spermidine
3
-con-
densed
1600
1200
-174 DNA, the RFII circular (filled sym-
bols) and the linear
Xho
I-digested (open symbols)
complexes. Reprinted from Marx, K.A., Reynolds,
T.C. (1982) Spermidine-Condensed PhiX-174 DNA
Cleavage by Micrococcal Nuclease: Torus Cleavage
Model and Evidence for Unidirectional
Circumferential DNA Wrapping.
Proc. Natl. Acad.
Sci. USA
79:6484-6488. With permission of
National Academy of Science, copyright 1982, and
authors.
800
400
0
0
10
20
30
40
50
Digestion time (min)
condensates, combined with the TEM results, these data presented strong evidence for a
model of toroidal-shaped DNA structure formation by a continuous circumferential wrap-
ping of DNA (138).
We have also used Manning counterion condensation theory (132) to explain the ion
concentration dependence of other experimental DNA physical properties, such as DNA
end-to-end distance changes and the electrophoretic mobilities of noncollapsed DNA in
solution. This was done by a modification of the Manning Theory to apply to two differ-
ent cations, monovalent and divalent, that occur in the electrophoresis experiments below
the critical counterion condensation levels needed for DNA collapse to toroidal structures.
We discovered that the measured length-dependent electrophoretic properties could be
accounted for by the magnitude of the DNA phosphate charge fraction not neutralized as
determined from the calculations (142-145).
Recently, the Seeman lab has pioneered the development of new kinds of self-assem-
bling regular geometric DNA nanoscale structures. They have been formed from short
synthetic DNA sequence constructs by a combination of the concepts of DNA self-assem-
bly along with rationally designed and positioned sequence complementarity. The struc-
tures created include DNA cubes, octahedrons, and dimorphic structures capable of being
switched between states by changes in counterion type and concentration. They also
include tiling structures that can serve as self-assembling DNA computing systems
(146,147). These novel structures with their variable self-assembly properties have the
potential to serve as new types of biological elements in smart biosensors.
1.3.4
Computational Simulation of DNA Melting—Reversing the Self-Assembly Process
of the Double Helix
Melting is an order-disorder phase transition of the DNA double helix that can be driven
to the disordered single-stranded state by increasing the temperature. The melting transi-
tion can be characterized most simply by its
T
m
, the melting temperature at the transition
midpoint. Measured primarily by optical methods,
T
m
values have been obtained for innu-
merable whole genomic DNAs, genomic DNA fractions, and short synthetic DNA
