Structural response of genomic DNA from grapevine ( Vitis vinifera L.) varieties to microwaves irradiation: A Fourier transform infrared spectroscopy assessment

Abstract

In this work, Fourier transform infrared (FT-IR) spectra of untreated and microwaves irradiated genomic DNAs extracted from leaves of different grapevine varieties, respectively, have been analyzed between 1800–800 cm⁻¹, in order to investigate their screening characteristic features and their structural response to microwaves treatment at 869–894 MHz frequency band. FT-IR vibrational modes for each of these cases, spectroscopic band assignments and structural interpretations of genomic DNAs are reported. No significant microwaves damage, concerning DNA bases structure, base pairing and base unstacking was found. Conformational changes of specific DNA segments and effects on deoxyribose seem to appear after microwaves irradiation. Grapevine varieties dependent microwaves influence on the structure of DNA has been found. Best nucleic acids structural tolerance upon microwave irradiation, as compared with the non-exposed DNA has been found in the case of genomic DNA isolated from ‘Chasselas Doré’ grapevine variety.

Keywords

Genomic DNA grapevine varieties FT-IR spectroscopy microwaves irradiation

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References

Green

Liu

F.M.

Cohen

Köllensperger

and Cass

, SERS platforms for high density DNA arrays, Faraday Discuss. 132 (2006), 269–280.

Kneipp

Wittig

Bohr

and Kneipp

, Surface-enhanced Raman scattering: A new optical probe in molecular biophysics and biomedicine, Theor. Chem. Acc. 125 (2010), 319–327.

Muntean

C.M.

Stefan

Bindea

and Cozma

, Fourier transform infrared spectroscopy of DNA from Borrelia burgdorferi sensu lato and Ixodes ricinus ticks, Spectrochim. Acta, Part A, Mol. Biomol. Spectrosc. 110 (2013), 185–192.

Stefan

Muntean

C.M.

Tripon

Halmagyi

and Valimareanu

, UV degradation of genomic DNA from in vitro grown plant species: A Fourier transform infrared spectroscopic assessment, Polym. Degrad. Stab. 108 (2014), 35–40.

Song

S.Y.

Jie

E.Y.

Ahn

M.S.

Lee

I.H.

Nou

I.S.

Min

B.W.

and Kim

S.W.

, Fourier transform infrared (FT-IR) spectroscopy of genomic DNA to discriminate F1 progenies from their paternal lineage of Chinese cabbage (Brassica rapa subsp. pekinensis), Mol. Breed. 33 (2014), 453–464.

Emura

Yamanaka

Isoda

and Watanabe

K.N.

, Estimation for different genotypes of plants based on DNA analysis using near-infrared (NIR) and Fourier-transform infrared (FT-IR) spectroscopy, Breed. Sci. 56 (2006), 399–403.

Lipiec

Kowalska

Lekki

Wiechec

and Kwiatek

W.M.

, FTIR microspectroscopy in studies of DNA damage induced by proton microbeam in single PC-3 cell, Acta Phys. Pol. A 121 (2012), 506–509.

Le-Tien

Lafortune

Shareck

and Lacroix

, DNA analysis of a radiotolerant bacterium Pantoea agglomerans by FT-IR spectroscopy, Talanta 71 (2007), 1969–1975.

Gomes

P.J.

Ribeiro

P.A.

Shaw

Mason

N.J.

and Raposo

, UV degradation of deoxyribonucleic acid, Polym. Degrad. Stab. 94 (2009), 2134–2141.

10.

Wood

B.R.

, The importance of hydration and DNA conformation in interpreting infrared spectra of cells and tissues, Chem. Soc. Rev. (2016). doi:10.1039/C5CS00511F.

11.

Surducan

Keul

and Halmagyi

, Microwaves irradiation experiments on biological samples, Stud. Univ. Babes-Bolyai Biol. 58 (2013), 83–98.

12.

Ragha

Mishra

Ramachandran

and Bhatia

M.S.

, Effects of low-power microwave fields on seed germination and growth rate, J. Electromagn. Anal. Appl. 3 (2011), 165–171.

13.

Viliche Balint

Surducan

and Oroian

I.G.

, Plant irradiation device in microwave field with controlled envinronment, Comput. Electron. Agric. 121 (2016), 48–56.

14.

Vian

Roux

Girard

Bonnet

Paladian

Davies

and Ledoigt

, Microwave irradiation affects gene expression in plants, Plant Signal. Behav. 1 (2006), 67–70.

15.

Pavel

Ungureanu Bara

C.E.

Gassner

and Creangă

D.E.

, Cytogenetic changes induced by low-intensity microwaves in the species Triticum aestivum , Rev. Med.-Chir. Soc. Med. Nat. Iasi 102 (1998), 89–92.

16.

Wan

Schwaninger

H.R.

Baldo

A.M.

Labate

J.A.

Zhong

G.Y.

and Simon

C.J.

, A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change, BMC Evol. Biol. 13(141) (2013), 1–20.

17.

This

Lacombe

and Thomas

M.R.

, Historical origins and genetic diversity of wine grapes, Trends Genet. 22 (2006), 511–519.

18.

Reisch

B.I.

and Pratt

, Grapes, in: Fruit Breeding. Vol. II. Vine and Small Fruits Crops, 2nd edn Janick

and Moore

J.N.

, eds, Wiley, New York, 1996, pp. 297–369.

19.

Thomas

M.R.

Matsumoto

Cain

and Scott

N.S.

, Repetitive DNA of grapevine: Classes present and sequences suitable for cultivar identification, Theor. Appl. Genet. 86 (1993), 173–180.

20.

Lodhi

M.A.

and Reisch

B.I.

, In situ hybridization in Vitis vinifera L, Theor. Appl. Genet. 90 (1995), 11–16.

21.

Rathnayake

A.J.

Allue

Llugany

Puig-Pujol

Hirimburegama

and Poschenrieder

, High quality DNA obtained from a single seed of Vitis vinifera L. using rapid DNA extraction method, Am. J. Plant. Sci. 5 (2014), 2023–2030.

22.

Jaillon

Aury

J.M.

Noel

Policriti

Clepet

Casagrande

Choisne

Aubourg

Vitulo

Jubin

Vezzi

Legeai

Hugueney

Dasilva

Horner

Mica

Jublot

Poulain

Bruyère

Billault

Segurens

Gouyvenoux

Ugarte

Cattonaro

Anthouard

Vico

Del Fabbro

Alaux

Di Gaspero

Dumas

Felice

Paillard

Juman

Moroldo

Scalabrin

Canaguier

Le Clainche

Malacrida

Durand

Pesole

Laucou

Chatelet

Merdinoglu

Delledonne

Pezzotti

Lecharny

Scarpelli

Artiguenave

Pè

M.E.

Valle

Morgante

Caboche

Adam-Blondon

A.F.

Weissenbach

Quétier

and Wincker

(for The French-Italian Public Consortium for Grapevine Genome Characterization), The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature 449 (2007), 463–467.

23.

Velasco

Zharkikh

Troggio

Cartwright

D.A.

Cestaro

Pruss

Pindo

FitzGerald

L.M.

Vezzulli

Reid

Malacarne

Iliev

Coppola

Wardell

Micheletti

Macalma

Facci

Mitchell

J.T.

Perazzolli

Eldredge

Gatto

Oyzerski

Moretto

Gutin

Stefanini

Chen

Segala

Davenport

Demattè

Mraz

Battilana

Stormo

Costa

Tao

Si-Ammour

Harkins

Lackey

Perbost

Taillon

Stella

Solovyev

Fawcett

J.A.

Sterck

Vandepoele

Grando

S.M.

Toppo

Moser

Lanchbury

Bogden

Skolnick

Sgaramella

Bhatnagar

S.K.

Fontana

Gutin

Van de Peer

Salamini

and Viola

, A high quality draft consensus sequence of the genome of a heterozygous grapevine variety, PLoS ONE 2 (2007), e1326.

24.

Surducan

Butic-Keul

and Halmagyi

, Microwaves irradiation experiments on biological samples, Stud. Univ. Babes-Bolyai Biol. 1 (2013), 83–98.

25.

Surducan

and Halmagyi

, Process and installation for stimulating plant growth in microwave field, Patent RO-125068, 2012.

26.

ICNIRP, Guidelines for limiting exposure to time – Varying electric, magnetic and electromagnetic fields (up to 300 GHz), Health Phys. 74 (1998), 494–522.

27.

Muntean

C.M.

Leopold

Halmagyi

and Valimareanu

, Surface-enhanced Raman spectroscopy of genomic DNA from in vitro grown plant species, J. Raman Spectrosc. 42 (2011), 1925–1931.

28.

Letellier

Ghomi

and Taillandier

, Interpretation of DNA vibration modes: IV – A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations, J. Biomol. Struct. Dyn. 6 (1989), 755–768.

29.

Rauch

Pichler

Trieb

Wellenzohn

Liedl

K.R.

and Mayer

, Z-DNA’s conformer substrates revealed by FT-IR difference spectroscopy of nonoriented left-handed double helical Poly(dG-dC), J. Biomol. Struct. Dyn. 22 (2005), 595–614.

30.

Lindqvist

and Gräslund

, An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution, J. Mol. Biol. 314 (2001), 423–432.

31.

Polyanichko

A.M.

Andrushchenko

V.V.

Chikhirzhina

E.V.

Vorob’ev

V.I.

and Wieser

, The effect of manganese(II) on DNA structure: Electronic and vibrational circular dichroism studies, Nucleic Acids Res. 32 (2004), 989–996.

32.

Sun

Song

Wang

Guo

Sun

Liu

and Li

, Ethanol-induced formation of silver nanoparticle aggregates for highly active SERS substrates and application in DNA detection, J. Phys. Chem. C 112 (2008), 1415–1422.

33.

Andrushchenko

Van De Sande

J.H.

and Wieser

, Vibrational circular dichroism and IR absorption of DNA complexes with Cu²⁺ ions, Biopolymers 72 (2003), 374–390.

34.

Pevsner

and Diem

, Infrared spectroscopic studies of major cellular components. Part II: The effect of hydration on the spectra of nucleic acids, Appl. Spectrosc. 55 (2001), 1502–1505.

35.

Sfihi

Liquier

Urpi

Verdaguer

Subirana

J.A.

Igolen

and Taillandier

, A and Z canonical conformations in d(C_nGCG_n) crystals characterized by microFTIR and microRaman spectroscopies, Biopolymers 33 (1993), 1715–1723.

36.

Taillandier

and Liquier

, Infrared spectroscopy of DNA, Methods Enzymol. 211 (1992), 307–335.

37.

Taillandier

Liquier

and Ghomi

, Conformational transitions of nucleic acids studied by IR and Raman spectroscopies, J. Mol. Struct. 214 (1989), 185–211.

38.

Taillandier

and Liquier

, in: Handbook of Vibrational Spectroscopy Applications in Life, Pharmaceutical and Natural Sciences, Vibrational Spectroscopy of Nucleic Acids Chalmers

J.M.

and Griffiths

P.R.

, eds, Wiley, Chichester, 2002.

39.

Adam

Ridoux

J.P.

Bourtayre

Taillandier

Pochet

Huynh-Dinh

and Igolen

, IR and UV studies on stability and conformations of short DNA duplexes containing a no-base residue: Coexistence of B and Z conformations, J. Biomol. Struct. Dyn. 6 (1988), 167–179.

40.

Muntean

C.M.

Lapusan

Mihaiu

and Stefan

, Strain dependent UV degradation of Escherichia coli DNA monitored by Fourier transform infrared spectroscopy, J. Photochem. Photobiol. B, Biol. 130 (2014), 140–145.

41.

Mello

M.L.S.

and Vidal

B.C.

, Changes in the infrared microspectroscopic characteristics of DNA caused by cationic elements, different base richness and single-stranded form, PLoS ONE 7 (2012), 1–12.

42.

Alex

and Dupuis

, FT-IR and Raman investigation of cadmium binding by DNA, Inorg. Chim. Acta 157 (1989), 271–281.

43.

Taillandier

Peticolas

W.L.

Adam

Huynh Dinh

and Igolen

, Polymorphism of the d(CCCGCGGG)₂ double helix studied by FT-i.r. spectroscopy, Spectrochim. Acta, Part A, Mol. Biomol. Spectrosc. 46 (1990), 107–112.

44.

Banyay

Sarkar

and Gräslund

, A library of IR bands of nucleic acids in solution, Biophys. Chem. 104 (2003), 477–488.

45.

Andrushchenko

Leonenko

Cramb

Van De Sande

J.H.

and Wieser

, Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr³⁺ ions: VCD and AFM evidence of DNA condensation, Biopolymers 61 (2002), 243–260.

46.

Hatfield

G.W.

and Benham

C.J.

, DNA topology-mediated control of global gene expression in Escherichia coli , Annu. Rev. Genet. 36 (2002), 175–203.