Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study
Abstract
:1. Introduction
2. Materials and Methods
2.1. DNA Extraction
2.2. Surface-Enhanced Raman Spectroscopy
2.2.1. Preparation of DNA-Nanoparticle Complexes
2.2.2. Instrumentation
2.3. Femtosecond Laser System
2.4. UV-Vis Characterization of DNA-Silver Nanoparticle Complexes
2.5. Computational Details
3. Results and Discussion
3.1. Surface-Enhanced Raman Spectroscopy of DNA Extracted from Grapevine Leaf Tissues
3.2. Effects of Femtosecond IR Laser Pulses on Genomic DNA Structure
3.3. Principal Component Analysis on the SERS Spectra Recorded from Non-Irradiated Grapevine DNAs
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Feteasca Neagra | Tamaioasa Romaneasca | Gordan | Feteasca Regala | Coarna Neagra | Ardeleanca | Braghina | Carloganca | Francuse | Cramposie | Tentative Assignment a |
---|---|---|---|---|---|---|---|---|---|---|
360 m | 359 w | 356 vw | 363 w | 354 w | 362 m | 359 vw | dG, dT, dA str | |||
378 w | 421 vw | 410 w | str dG, dT, dA | |||||||
452 m | 451 vw | 448 w | 449 w | 456 w | 448 m | str deoxyribose | ||||
480 w | 481 w | str deoxyribose | ||||||||
525 m | 528 w | 526 w | 517 vw | 530 w | dC/dT (ring def) | |||||
571 w | 570 w | 577 w | dA (C2–H, N9–H wagging) | |||||||
613 s | 613 s | 613 m | 613 m | 613 m | deoxyribose (C3′-endo-anti) | |||||
660 w | 657 w | 663 w | dG (ring breathing) | |||||||
707 vw | 706 w | 706 w | dA (ring breathing) | |||||||
732 s | 725 m | 721 w | 723 vw | dA (ring breathing) | ||||||
741 vw | dT (ring breathing) | |||||||||
773 s | 773 s | 773 m | 773 m | 772 m | 771 vw | dC, C2′-endo-anti | ||||
795 m | 796 m | 790 w | bk 5′C–O–P–O–C3′ sym str | |||||||
829 w | deoxyribose C2′-endo | |||||||||
928 w | 929 w | 913 w | 911 m | 915 m | 907 w | deoxyribose | ||||
958 w | dA/dC/dG (NH2 rk) | |||||||||
1016 vw | 988 vw | 1008 w | dT (out-of-plane NH2 wagging) | |||||||
1029 vw | 1055 vw | 1031 w | 1059 w | dA (N- deoxyribose str) | ||||||
1086 w | 1087 w | 1085 vw | 1088 vw | 1084 vw | 1084 w | 1084 w | bk PO2− sym str | |||
1127 m | 1127 m | 1129 m | 1122 w | 1136 vw | 1126 m | 1127 m | 1127 m | 1119 vw | 1127 m | dA (C8–N9 str, N9–H, C8–H def) |
1182 s | 1180 m | 1175 m | 1175 m | 1176 s | 1174 w | 1170 m | 1174 s | 1172 m | dA, dG (C5–C6 str) | |
1228 w | 1230 w | dT (in-plane ring - CH3 str) | ||||||||
1280 sh | dC (C–NH2 str + ring str) | |||||||||
1311 s | 1310 s | 1308 m | 1310 m | 1308 s | 1306 m | 1304 m | 1300 m | 1305 m | dA, dG (C–N str (Im)) | |
1331 m | dA, dG (ring mode) | |||||||||
1363 vs | 1363 vs | 1363 s | 1363 vs | 1383 w | 1363 vs | 1359 s | 1361 m | 1370 s | 1362 m | dT, dA, dG (C–N str (Py)) |
1421 w | 1422 m | 1425 w | 1423 vw | 1432 w | 1434 vw | Deoxyribose C2′H2 scissoring | ||||
1468 vw | 1451 vw | 1465 w | 1450 w | 1452 w | Deoxyribose CH2 | |||||
1510 vs | 1510 vs | 1510 vs | 1509 vs | 1510 vs | 1508 m | 1510 w | 1512 w | dA (NH2 def) | ||
1545 vw | 1534 m | 1532 w | dT (in-plane ring str) | |||||||
1575 s | 1574 s | 1575 m | 1574 m | 1575 vw | 1576 m | 1575 m | dG, dA (C2=N3 of guanine) | |||
1601 sh | 1621 w | 1621 s | 1602 s | 1604 s | 1621 s | 1623 m | dA, dG, dC (NH2 def) | |||
1651 vs | 1650 vs | 1651 vs | 1650 s | 1650 s | 1648 m | dT, δ(H2O) (C=O str, C=C str) | ||||
1700 w | dG (C–O), C–C |
Feteasca Regala IR | Braghina IR | Francuse IR | Carloganca IR | Feteasca Neagra IR | Tamaioasa Romaneasca IR | Ardeleanca IR | Tentative Assignment a |
---|---|---|---|---|---|---|---|
354 w | dG, dT, dA str | ||||||
453 w | 454 m | 462 m | 441 w | 459 m | str deoxyribose | ||
473 w | 482 w | 480 m | 482 m | 481 w | 480 m | str deoxyribose | |
544 w | dC/dT (ring def) | ||||||
558 w | 569 w | dA (C2–H, N9–H wagging) | |||||
612 m | 612 m | 612 m | 620 w | Deoxyribose (C3′-endo-anti) | |||
661 w | 641 w | dG (ring breathing) | |||||
723 w | 707 w | 706 w | 706 w | dA (ring breathing) | |||
756 vw | dT (ring breathing) | ||||||
772 m | 773 m | 775 m | 778 w | 769 w | dC, C2′-endo-anti | ||
807 w | 815 w | 818 w | 803 w | bk 5′C–O–P–O–C3′ sym str | |||
851 w | deoxyribose C3′-endo | ||||||
911 m | 915 w | 924 w | 915 w | 911 m | Deoxyribose | ||
1083 m | 1083 w | 1086 w | 1083 w | 1084 w | 1087 w | bk PO2− sym str | |
1126 m | 1127 m | 1127 s | 1126 m | 1127 w | 1123 w | dA (C8–N9 str, N9–H, C8–H def) | |
1177 s | 1191 m | 1172 m | 1180 m | 1172 w | 1181 m | 1171 m | dA, dG (C5–C6 str) |
1220 vw | 1239 vw | 1240 w | dT (ring str), dA, dC, dG (C8–N9 str) | ||||
1278 w | 1266 w | dC (C-NH2 str + ring str) | |||||
1310 m | 1314 m | 1314 m | 1303 w | 1304 m | dA, dG (C–N str (Im)) | ||
1363 vs | 1364 vs | 1363 m | 1363 s | 1361 w | 1365 m | 1365 m | dT, dA, dG (C–N str (Py)) |
1425 w | 1423 w | Deoxyribose C2′H2 scissoring | |||||
1442 w | Deoxyribose CH2 | ||||||
1510 s | 1510 s | 1512 s | 1509 w | 1509 w | 1513 m | dA (NH2 def) | |
1553 sh | dT (in-plane ring str) | ||||||
1578 m | 1574 m | 1590 m | 1578 m | 1587 vw | 1581 m | dG, dA (C2=N3 of guanine) | |
1623 s | 1626 s | 1625 s | 1624 s | dA, dG, dC (NH2 def) | |||
1650 s | 1651 vs | 1651 s | 1653 w | 1651 w | 1650 s | dT, δ(H2O) (C=O str, C=C str) | |
1683 vw | dA (NH2 scissoring) |
Grapevine Varieties DNA (cm−1) | Shift (cm−1) | Grapevine varieties IR Irradiated DNA (cm−1) | Tentative Assignments a |
---|---|---|---|
Feteasca Regala | Feteasca Regala IR | ||
1423 | +19 | 1442 | Deoxyribose C2′H2 scissoring |
Braghina | Braghina IR | ||
1174 | +17 | 1191 | dA, dG (C5–C6 str) |
1228 | −8 | 1220 | dT (in-plane ring –CH3 str) |
1306 | +8 | 1314 | dA, dG (C–N str (Im)) |
1602 | −28 | 1574 | dA, dG, dC (NH2 def) |
Francuse | Francuse IR | ||
721 | −15 | 706 | dA (ring breathing) |
741 | +15 | 756 | dT (ring breathing) |
796 | +19 | 815 | bk 5′C–O–P–O–C3′ sym str |
1119 | +8 | 1127 | dA (C8–N9 str, N9–H, C8–H def) |
1532 | +21 | 1553 | dT (in-plane ring str) |
1575 | +15 | 1590 | dG, dA (C2=N3 of guanine) |
Carloganca | Carloganca IR | ||
1170 | +10 | 1180 | dA, dG (C5–C6 str) |
1230 | +10 | 1240 | dT (in-plane ring –CH3 str) |
1304 | +10 | 1314 | dA, dG (C–N str (Im)) |
1604 | −26 | 1578 | dA, dG, dC (NH2 def) |
Feteasca Neagra | Feteasca Neagra IR | ||
452 | −11 | 441 | str deoxyribose |
1182 | −10 | 1172 | dA, dG (C5–C6 str) |
1575 | +12 | 1587 | dG, dA (C2=N3 of guanine) |
Tamaioasa Romaneasca | Tamaioasa Romaneasca IR | ||
929 | −14 | 915 | Deoxyribose |
1601 | +24 | 1625 | dA, dG, dC (NH2 def) |
Ardeleanca | Ardeleanca IR | ||
449 | +10 | 459 | str deoxyribose |
795 | +8 | 803 | bk 5′C–O–P–O–C3′ sym str |
1450 | −27 | 1423 | Deoxyribose CH2 |
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Dina, N.E.; Muntean, C.M.; Leopold, N.; Fălămaș, A.; Halmagyi, A.; Coste, A. Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study. Nanomaterials 2016, 6, 96. https://doi.org/10.3390/nano6060096
Dina NE, Muntean CM, Leopold N, Fălămaș A, Halmagyi A, Coste A. Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study. Nanomaterials. 2016; 6(6):96. https://doi.org/10.3390/nano6060096
Chicago/Turabian StyleDina, Nicoleta E., Cristina M. Muntean, Nicolae Leopold, Alexandra Fălămaș, Adela Halmagyi, and Ana Coste. 2016. "Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study" Nanomaterials 6, no. 6: 96. https://doi.org/10.3390/nano6060096