Biomedical Engineering Reference
In-Depth Information
The results for deoxyguanosine, deoxyadenosine, and dAMP did not reveal any
dramatic changes in the scattering behavior. However, comparison of the results
for the nucleosides with the static-exchange results for adenine and guanine did
show a slight upward shift, by 0.1 to 0.3 eV, in the positions of the three low-energy
resonances, with negligible further shifts upon attaching a phosphate to form
the nucleotide. Thus, as in the pyrimidines, it appears that the
shape-resonant
behavior is already modeled well at the level at the level of the isolated nucleobases.
5.3.2
The DNA Backbone
Components of the DNA backbone have already appeared in the calculations on
nucleosides and dAMP described above; however, the focus in that work remained
on the
resonances of the bases. It is natural to consider, though, whether
strand-breaking might involve direct attachment of the electron to the backbone,
as proposed early on by Li, Sevilla, and Sanche [
49
], rather than or in addition to
attachment to a base followed by intramolecular electron transfer to the backbone,
as in the model of Simons and coworkers [
50
,
51
,
62
-
64
]. Thus it is of interest to
explore electron scattering by molecular models of the backbone constituents, de-
oxyribose and phosphate. As with the bases, the focus of our SMC calculations has
been on identifying and characterizing low-energy resonances in the elastic cross
section that might trap electrons long enough to promote dissociative attachment.
5.3.2.1
Deoxyribose
The DNA backbone consists of phosphate groups alternating with substituted
furanose rings. If the phosphates connected to a given furanose are replaced by
hydroxyls, and likewise the base bonded to C
1
, the resulting molecule is of course 2-
deoxyribose. However, there are many other ways to extract a plausible model of the
sugar moiety. The simplest is to replace all ring linkages with H, resulting in tetrahy-
drofuran (THF). Retaining the oxygen at C
3
results in 3-hydroxytetrahydrofuran
(3HTHF). These three structures are illustrated in Fig.
5.4
. Obviously other models,
such as tetrahydrofurfuryl alcohol [
91
-
93
], are possible, but in fact the majority of
attention to date has been given to THF.
THF is a saturated system, and its ring is puckered rather than planar. Which
particular puckered geometry is the absolute minimum of energy has been a topic
of past debate, but what it is clear is that the various minima are of nearly equal
energy and are separated by very small barriers [
94
]. Thus, although the geometry
of deoxyribose in DNA is constrained by its phosphate and nucleobase linkages,
the conformation of an isolated THF molecule at room temperature is constantly
changing. One issue that arises, therefore, is whether the electron scattering cross
section of THF is sensitive to its conformation; if so, gas-phase measurements
may not comment directly on the conformation relevant to DNA, and comparison
