Biomedical Engineering Reference
In-Depth Information
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FIGURE 1.39
Histogram of the measured surface areas of mouse wounds measured at various times during healing. Wounds
on a number of mice at day 0 were treated with a single application of either PBS releasate from 1 h -0.3 V stim-
ulated ECM (1st bar) or unstimulated control PBS (2nd bar). The '*' indicates healing times where the two con-
ditions have achieved wound-healing areas that are significantly different at the
p
< 0.05 confidence level.
Reprinted from Braunhut, S.J., McIntosh, D., Vorotnikova, K., Zhou, T., Marx, K.A. (2004). Development of a
Smart Bandage Applying Electrical Potential to Selectively Release Wound Healing Growth Factors from Cell
Free Extracellular Matrix. In: Architecture and Applications of Biomaterials and Biomolecular Materials,
Proc.
Mater. Res. Soc.,
EXS-1:403-405. With permission from Elsevier Publishing.
information storage, flow, and control functions within all living cells. Our aim in the
following discussion is to illuminate the advantages of being able to simulate the intelli-
gent properties of molecules such as DNA, prior to their incorporation and testing in
biosensors. In the Center for Intelligent Biomaterials at the University of Massachusetts
Lowell, we have focused efforts on characterizing and simulating certain sequence-spe-
cific properties of DNA as well as attempting to understand DNA-protein complex sta-
bility by investigating computed physical property parameters of the underlying DNA
sequence. This is a far easier task than modeling DNA structure and dynamics using all
atom molecular simulation methods on specific sequences. Such methods provide far
greater detail about the system, but they are greatly limited by computational constraints
on the system size and the time scale that can be modeled. With the physical property
parameter approach, we hope to eventually understand at a meta-level the basis for the
intelligent properties of DNA. Such an understanding will provide insight as well as pre-
dictive capabilities and allow the rational design of specific DNA and DNA-protein com-
plexes into smart biosensor systems.
The DNA double helix is a regular repeating 3-D structure comprising two right-handed
interwound polynucleotide single strands. Each single strand contains a linear string of
nitrogenous bases that form complementary hydrogen bonds to the corresponding bases
on the opposite single strand. Together, these bases create the A-T and C-G base pairs com-
prising the central core of the double helix. At the time of the original publication by
Watson & Crick of the fiber diffraction-based 3-D structure of DNA, and for the following
two decades, little structural variability was imagined for the DNA double helix. However,
we know today primarily from the numerous determinations of 3-D structures for short
DNAs by NMR and x-ray crystallography that DNA forms a variety of repeating second-
ary structure types, some of which are interconvertable. We also know that DNA, while still
considered an overall rigid structure on the length scale of tens of base pairs, and with
a persistence length in solution on the order of
200 bp, is known to be capable of consid-
erable generic as well as sequence-based variation in structure and dynamic motion
(109,110). The sequence-based properties and dynamics of the DNA double helix underlie
