375
13 Vibrational Spectroscopy: Disease Diagnostics and Beyond
include the fingerprint of the interaction of the cisplatin with the nuclear dNA, but
also evident are a multitude of other changes associated with exposure and changes
in cellular physiology. In an effort to identify the most important spectral features,
feature selection was performed using the PLS—Jack knifing analysis described
earlier. the regression co-efficients were obtained forseparate regressions against
cisplatin concentrations and against cell viability with the nuclear spectral data.
to elucidate spectral changes that are most statistically significant with respect to
regression against either endpoint, a t-test ( p < 0.001) was applied on the PLS-Jack
knifing results. the spectral features identified by this process are highlighted by
vertical bands in Fig. 13.11.
the PLS regression of the nuclear data against cisplatin concentration
(Fig. 13.11a), identifies many features but, for the purpose of this discussion, only
the changes which are related to the known action of cisplatin are highlighted. Features identified include the thymine (737–742 cm
−1
, 1,589–1,595 cm
−1
), guanine
(1,548–1,553 cm
−1
) and adenine (1,578 cm
−1
, 1,604–1,611 cm
−1
) bands. the regression co-efficients of guanine and thymine are stronger than that of adenine, indicating that cisplatin binds preferably with guanine as compared to adenine [111].
Another interesting observation is that the bands at (877–883 cm
−1
) and at (899–
900 cm
−1
), both assigned to deoxyribose ring breathing, are significantly changed,
indicating a change in the conformation of B-form dNA [112–114]. Changes in the
Raman bands of the proteins are also highlighted, as indicated by the regression
co-efficients which can be assigned to tryptophan ring breathing (761–765 cm
−1
),
(889–891 cm
−1
), C-N stretching (1,128–1,132 cm
−1
), C-h deformation (1,315–
1,316 cm
−1
, 1,351–1,354 cm
−1
), amide-I (1,668–1,679 cm
−1
). these changes may
indicate some structural changes in the nuclear proteins. the spectroscopic features
selected by the PLS regression against drug concentration are consistent with the
known direct interaction of the drug with the dNA and thus are identified as spectroscopic markers of the direct chemical interaction of the drug.
the regression against cell viability (Fig. 13.11b), shows the features which are
correlated with the change in cell physiology. these include the conformational
changes of the dNA B-form (832–833 cm
−1
) and dNA A-form (798–813 cm
−1
).
these changes in the Raman bands of the dNA can be taken as markers for the
conformational changes in the dNA caused by cisplatin binding to the guanine and
thymine dNA bases (vrana et al. 2007) and also confirm the observations from the
mean difference spectra. Changes related to protein secondary and tertiary structures are indicated by the selection of amide-III random coil (1,225–1,228 cm
−1
),
amide-III β-sheet (1250–1259), amide-III α helix, tryptophan ring breathing
(711–721 cm
−1
, 758–763 cm
−1
, 767–772 cm
−1
) and phenyl ring stretching modes
(1,202–1,210 cm
−1
) together with the C-C skeletal vibrations (935–937 cm
−1
,
1,159–1,163 cm
−1
), C-N stretching vibrations (1,065–1,068, 1,073–1,075) and C-h
bending (1,178–1,182 cm
−1
) (1,185–1,186 cm
−1
). these features suggest changes in
the Raman bands of proteins and are indicative of structural alterations associated
with protein activation and denaturation during cellular apoptosis and nucleic acid
repair responses.
13 Vibrational Spectroscopy: Disease Diagnostics and Beyond
include the fingerprint of the interaction of the cisplatin with the nuclear dNA, but
also evident are a multitude of other changes associated with exposure and changes
in cellular physiology. In an effort to identify the most important spectral features,
feature selection was performed using the PLS—Jack knifing analysis described
earlier. the regression co-efficients were obtained forseparate regressions against
cisplatin concentrations and against cell viability with the nuclear spectral data.
to elucidate spectral changes that are most statistically significant with respect to
regression against either endpoint, a t-test ( p < 0.001) was applied on the PLS-Jack
knifing results. the spectral features identified by this process are highlighted by
vertical bands in Fig. 13.11.
the PLS regression of the nuclear data against cisplatin concentration
(Fig. 13.11a), identifies many features but, for the purpose of this discussion, only
the changes which are related to the known action of cisplatin are highlighted. Features identified include the thymine (737–742 cm
−1
, 1,589–1,595 cm
−1
), guanine
(1,548–1,553 cm
−1
) and adenine (1,578 cm
−1
, 1,604–1,611 cm
−1
) bands. the regression co-efficients of guanine and thymine are stronger than that of adenine, indicating that cisplatin binds preferably with guanine as compared to adenine [111].
Another interesting observation is that the bands at (877–883 cm
−1
) and at (899–
900 cm
−1
), both assigned to deoxyribose ring breathing, are significantly changed,
indicating a change in the conformation of B-form dNA [112–114]. Changes in the
Raman bands of the proteins are also highlighted, as indicated by the regression
co-efficients which can be assigned to tryptophan ring breathing (761–765 cm
−1
),
(889–891 cm
−1
), C-N stretching (1,128–1,132 cm
−1
), C-h deformation (1,315–
1,316 cm
−1
, 1,351–1,354 cm
−1
), amide-I (1,668–1,679 cm
−1
). these changes may
indicate some structural changes in the nuclear proteins. the spectroscopic features
selected by the PLS regression against drug concentration are consistent with the
known direct interaction of the drug with the dNA and thus are identified as spectroscopic markers of the direct chemical interaction of the drug.
the regression against cell viability (Fig. 13.11b), shows the features which are
correlated with the change in cell physiology. these include the conformational
changes of the dNA B-form (832–833 cm
−1
) and dNA A-form (798–813 cm
−1
).
these changes in the Raman bands of the dNA can be taken as markers for the
conformational changes in the dNA caused by cisplatin binding to the guanine and
thymine dNA bases (vrana et al. 2007) and also confirm the observations from the
mean difference spectra. Changes related to protein secondary and tertiary structures are indicated by the selection of amide-III random coil (1,225–1,228 cm
−1
),
amide-III β-sheet (1250–1259), amide-III α helix, tryptophan ring breathing
(711–721 cm
−1
, 758–763 cm
−1
, 767–772 cm
−1
) and phenyl ring stretching modes
(1,202–1,210 cm
−1
) together with the C-C skeletal vibrations (935–937 cm
−1
,
1,159–1,163 cm
−1
), C-N stretching vibrations (1,065–1,068, 1,073–1,075) and C-h
bending (1,178–1,182 cm
−1
) (1,185–1,186 cm
−1
). these features suggest changes in
the Raman bands of proteins and are indicative of structural alterations associated
with protein activation and denaturation during cellular apoptosis and nucleic acid
repair responses.