Study of the interaction between UV light and nucleic acids: elucidating the molecular mechanisms responsible of the genetic stability and of the oxidative damaging processes by using computational methods

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Research areas: Structural and electronic properties of nucleic acids,

Keywords: Quantum Mechanical Calculations, Photophysics, Photochemistry, Dna Oxidative Damage

Contact person: Roberto Improta, robimp

unina.it

Actors: Roberto Improta, robimp

unina.it, Luciana Esposito, luciana.esposito

cnr.it,

Description:
Absorption of UV light by DNA is a very importantbiological process, since it can lead to the damage of the genetic code and is relatedto aging, apoptosis and carcinogenesis. Thisresearch line, based on our experience in the development and the applicationof quantum mechanical computational methods to study the reactivity ofbiomacromolecules, aims to understand the molecular mechanism responsible ofthe photostability of nucleic acids or, on the opposite, involved in theoxidative photodamage. Our activity is organized in different researchpackages:

1) Molecular processes responsible of DNAphotostability: photophsyics of isolated bases, including epigenetic bases.

2) Molecular processes responsible of DNAphotostability: collective photophysical processes in single and doublestrands.

3) Molecular process responsible of photodamage:photodimerization in NA

4) Molecular processresponsible of photodamage: One photon ionization in NA.

Figures:

Selected papers:

1) Quantum mechanical studies on the photophysics and the photochemistry ofnucleic acids and nucleobases R Improta, F Santoro, L Blancafort

Chemicalreviews (2016), 116, 3540-3593,

2) What makes thienoguanosine an outstanding fluorescent DNA probe?

J Kuchlyan, L Martinez-Fernandez, M Mori, K Gavvala, S Ciaco, C. Boudier, L.Richert, P. Didier, Y. Tor, R. Improta, Y. Mély

Journal of the American Chemical Society (2020), 142, 16999-17014

3) Comprehensive study of guanine excited state relaxation and photoreactivityin G-quadruplexes L Martinez-Fernandez, P Changenet, A Banyasz, T Gustavsson,D. Markovitsi, R. Improta The Journal of Physical Chemistry Letters (2019) 10,6873-6877

4) Absorption of low-energy uv radiation by human telomere G-quadruplexesgenerates long-lived guanine radical cations A Banyasz, L Martinez-Fernandez, CBalty, M Perron, T Douki, R Improta, D. Markovitsi

Journal of the American Chemical Society (2017), 139,10561-10568

Study of the interaction between UV light and nucleic acids: elucidating the molecular mechanisms responsible of the genetic stability and of the oxidative damaging processes by using computational methods Your query: ([atitle, adesc, keywords] "Quantum Mechanical Calculations" OR [atitle, adesc, keywords] "Photophysics" OR [atitle, adesc, keywords] "Photochemistry" OR [atitle, adesc, keywords] "Dna Oxidative Damage") AND NOT [id] = 164

Your query: ([atitle, adesc, keywords] "Quantum Mechanical Calculations" OR [atitle, adesc, keywords] "Photophysics" OR [atitle, adesc, keywords] "Photochemistry" OR [atitle, adesc, keywords] "Dna Oxidative Damage") AND NOT [id] = 164

▼ Molecular dynamics simulation approach to study UV-induced DNA damage

Improta Roberto

Esposito Luciana

Study of the interaction between UV light and nucleic acids: elucidating the molecular mechanisms responsible of the genetic stability and of the oxidative damaging processes by using computational methods Your query: [btitle, abstract, keywords] "Quantum Mechanical Calculations" OR [btitle, abstract, keywords] "Photophysics" OR [btitle, abstract, keywords] "Photochemistry" OR [btitle, abstract, keywords] "Dna Oxidative Damage"

Your query: [btitle, abstract, keywords] "Quantum Mechanical Calculations" OR [btitle, abstract, keywords] "Photophysics" OR [btitle, abstract, keywords] "Photochemistry" OR [btitle, abstract, keywords] "Dna Oxidative Damage"

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Ciaco S, Gavvala K, Greiner V, Mazzoleni V, Didier P, Ruff M, Martinez-fernandez L, Improta R, Mély Y
* Thienoguanosine brightness in DNA duplexes is governed by the localization of itsππ* excitation in the lowest energy absorption band (1362 views)
Methods Appl Fluoresc (ISSN: 2050-6120linking), 2022 May 5; 10(3): N/D-N/D.
Impact Factor: 2.79
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Lizondo-aranda P, Martínez-fernández L, Miranda MA, Improta R, Gustavsson T, Lhiaubet-vallet V
* The Excited State Dynamics of a Mutagenic Cytidine Etheno Adduct Investigated by Combining Time-Resolved Spectroscopy and Quantum Mechanical Calculations (1274 views)
J Phys Chem Lett (ISSN: 1948-7185linking, 1948-7185electronic), 2022 Jan 13; 13(1): 251-257.
Impact Factor: 6.475
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Green JA, Yaghoubi Jouybari M, Asha H, Santoro F, Improta R
* Fragment Diabatization Linear Vibronic Coupling Model for Quantum Dynamics of Multichromophoric Systems: Population of the Charge-Transfer State in the Photoexcited Guanine-Cytosine Pair (1172 views)
J Chem Theory Comput (ISSN: 1549-9618linking, 1549-9626electronic), 2021 Aug 10; 17(8): 4660-4674.
Impact Factor: 5.011
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Asha H, Green JA, Martinez-fernandez L, Esposito L, Improta R
* Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States (1815 views)
Molecules (ISSN: 1420-3049linking, 1420-3049electronic), 2021 Aug 7; 26(16): N/D-N/D.
Impact Factor: 4.411
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Wang X, Martínez-fernández L, Zhang Y, Zhang K, Improta R, Kohler B, Xu J, Chen J
* Solvent-Dependent Stabilization of a Charge Transfer State is the Key to Ultrafast Triplet State Formation in an Epigenetic DNA Nucleoside (1844 views)
Chemistry (ISSN: 0947-6539linking, 1521-3765electronic), 2021 Jul 26; 27(42): 10932-10940.
Impact Factor: 5.236
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Martinez-fernandez L, Gustavsson T, Diederichsen U, Improta R
* Excited State Dynamics of 8-Vinyldeoxyguanosine In Aqueous Solution Studied by Time-Resolved Fluorescence Spectroscopy and Quantum Mechanical Calculations (1807 views)
Molecules (ISSN: 1420-3049linking, 1420-3049electronic), 2020 Feb 13; 25(4): N/D-N/D.
Impact Factor: 3.267
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Schmid M, Martinez-fernandez L, Markovitsi D, Santoro F, Hache F, Improta R, Changenet P
* Unveiling Excited-State Chirality of Binaphthols by Femtosecond Circular Dichroism and Quantum Chemical Calculations (1967 views)
J Phys Chem Lett (ISSN: 1948-7185linking, 1948-7185electronic), 2019 Jul 18; 10(14): 4089-4094.
Impact Factor: 6.687
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Banyasz A, Balanikas E, Martinez-fernandez L, Baldacchino G, Douki T, Improta R, Markovitsi D
* Radicals Generated in Tetramolecular Guanine Quadruplexes by Photoionization: Spectral and Dynamical Features (1231 views)
J Phys Chem B (ISSN: 1520-5207linking, 1520-6106), 2019 Jun 13; 123(23): 4950-4957.
Impact Factor: 3.603
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Martinez-fernandez L, Gavvala K, Sharma R, Didier P, Richert L, Segarra Marti J, Mori M, Mely Y, Improta R
* Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine (1049 views)
Chemistry (ISSN: 0947-6539linking, 1521-3765electronic), 2019 May 28; 25(30): 7375-7386.
Impact Factor: 5.16
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Martinez-fernandez L, Improta R
* Sequence dependence on DNA photochemistry: a computational study of photodimerization pathways in TpdC and dCpT dinucleotides (3011 views)
Photochemical & (ISSN: 1474-9092electronic, 1474-905xlinking), 2018 May 16; 17(5): 586-591.
Impact Factor: 2.939
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Banyasz A, Ketola T, Martinez-fernandez L, Improta R, Markovitsi D
* Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation (1931 views)
Faraday Discuss (ISSN: 1359-6640print, 1359-6640linking), 2018 Jan 26; N/D: N/D-N/D.
Impact Factor: 4.194
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Martinez-fernandez L, Improta R
* Photoactivated proton coupled electron transfer in DNA: Insights from quantum mechanical calculations (1582 views)
Faraday Discuss (ISSN: 1359-6640, 1359-6640print), 2018; 207: 199-216.
Impact Factor: 3.427
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Banyasz A, Martinez-fernandez L, Balty C, Perron M, Douki T, Improta R, Markovitsi D
* Absorption of Low-Energy UV Radiation by Human Telomere G-Quadruplexes Generates Long-Lived Guanine Radical Cations (1232 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 0002-7863print), 2017 Aug 2; 139(30): 10561-10568.
Impact Factor: 14.357
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Martinez-fernandez L, Pepino AJ, Segarra-marti J, Jovaisaite J, Vaya I, Nenov A, Markovitsi D, Gustavsson T, Banyasz A, Garavelli M, Improta R
* Photophysics of Deoxycytidine and 5-Methyldeoxycytidine in Solution: A Comprehensive Picture by Quantum Mechanical Calculations and Femtosecond Fluorescence Spectroscopy (2166 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 0002-7863print), 2017 Jun 14; 139(23): 7780-7791.
Impact Factor: 14.357
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Cerezo J, Petrone A, Avila Ferrer FJ, Donati G, Santoro F, Improta R, Rega N
* Electronic spectroscopy of a solvatochromic dye in water: comparison of static cluster/implicit and dynamical/explicit solvent models on structures and energies (1829 views)
Theoretical Chemistry Accounts, 2016 Dec; N/D: N/D-N/D.
Impact Factor: 1.806
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Sholokh M, Improta R, Mori M, Sharma R, Kenfack C, Shin D, Voltz K, Stote RH, Zaporozhets OA, Botta M, Tor Y, Mely Y
* Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels (2258 views)
Angew Chem Int Ed (ISSN: 1433-7851, 1521-3773electronic, 1433-7851linking), 2016 Jun 8; N/D: N/D-N/D.
Impact Factor: 11.994
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Banyasz A, Esposito L, Douki T, Perron M, Lepori C, Improta R, Markovitsi D
* Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors (2428 views)
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207linking), 2016 May 12; 120(18): 4232-4242.
Impact Factor: 3.177
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Zhang Y, De La Harpe K, Beckstead AA, Martínez-fernández L, Improta R, Kohler B
* Excited-State Dynamics of DNA Duplexes with Different H-Bonding Motifs (1902 views)
J Phys Chem Lett (ISSN: 1948-7185, 1948-7185electronic, 1948-7185linking), 2016; 7(6): 950-954.
Impact Factor: 9.353
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Improta R, Santoro F, Blancafort L
* Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases (4402 views)
Chem Rev (ISSN: 0009-2665), 2016; 116(6): 3540-3593.
Impact Factor: 47.928
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Zhang Y, de La Harpe K, Beckstead AA, Improta R, Kohler B
* UV-Induced Proton Transfer between DNA Strands (2313 views) (PDF 398 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 0002-7863print), 2015 Jun 10; 137(22): 7059-7062.
Impact Factor: 13.038
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Huix-Rotllant M, Brazard J, Improta R, Burghardt I, Markovitsi D
* Stabilization of mixed frenkel-charge transfer excitons extended across both strands of guanine-cytosine DNA duplexes (1844 views)
J Phys Chem Lett (ISSN: 1948-7185, 1948-7185electronic, 1948-7185linking), 2015; 6(12): 2247-2251.
Impact Factor: 8.539
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Zhang Y, Dood J, Beckstead AA, Li X-B, Nguyen KV, Burrows CJ, Improta R, Kohler B
* Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide (1910 views)
P Natl Acad Sci Usa (ISSN: 0027-8424, 1091-6490, 0027-8424print), 2014 Sep 12; 111(32): 11612-11617.
Impact Factor: 9.674
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Improta R
* Quantum mechanical calculations unveil the structure and properties of the absorbing and emitting excited electronic states of guanine quadruplex (2052 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2014 Jun 23; 20(26): 8106-8115.
Impact Factor: 5.731
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Zhang Y, Improta R, Kohler B
Mode-specific vibrational relaxation of photoexcited guanosine 5'-monophosphate and its acid form: a femtosecond broadband mid-IR transient absorption and theoretical study (2011 views)
Phys Chem Chem Phys (ISSN: 1463-9076, 1463-3907, 1463-9084electronic), 2014 Jan 28; 16(4): 1487-1499.
Impact Factor: 4.493
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Improta R, Vitagliano L, Esposito L
* Correction: Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures (PLoS ONE) (1592 views)
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2014; 9(1): N/D-N/D.
Impact Factor: 3.234
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Hunger K, Buschhaus L, Biemann L, Braun M, Kovalenko S, Improta R, Kleinermanns K
* UV-light-induced hydrogen transfer in guanosine-guanosine aggregates (1857 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2013 Apr; 19(17): 5425-5431.
Impact Factor: 5.696
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Banyasz A, Gustavsson T, Onidas D, Changenet-Barret P, Markovitsi D, Improta R
* Multi-pathway excited state relaxation of adenine oligomers in aqueous solution: A joint theoretical and experimental study (2370 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2013 Mar; 19(11): 3762-3774.
Impact Factor: 5.696
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Merlino A, Fuchs MR, Pica A, Balsamo A, Dworkowski FSN, Pompidor G, Mazzarella L, Vergara A
* Selective X-ray-induced NO photodissociation in haemoglobin crystals: evidence from a Raman-assisted crystallographic study (2059 views)
Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 2013 Jan; 69: 137-140.
Impact Factor: 7.232
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Santoro F, Improta R, Avila Ferrer FJ, Segado M, Lami A
* The interplay between neutral exciton and charge transfer states in single-strand polyadenine: A quantum dynamical investigation (1904 views)
Photochem Photobiol Sci (ISSN: 1474-905x), 2013; 12(8): 1527-1543.
Impact Factor: 2.939
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Improta R
* Photophysics and photochemistry of thymine deoxy-dinucleotide in water: A PCM/TD-DFT quantum mechanical study (1050 views)
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2012 Dec 13; 116(49): 14261-14274.
Impact Factor: 3.607
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Caruso P, Causà M, Cimino P, Crescenzi O, D'Amore M, Improta R, Pavone M, Rega N
* Effects of molecular dynamics and solvation on the electronic structure of molecular probes (1911 views)
Theor Chem Acc (ISSN: 1432-881x), 2012 Apr; 131(4): 1211-1212.
Impact Factor: 2.233
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Stendardo E, Avila FJA, Santoro F, Improta R
* Vibrationally resolved absorption and emission spectra of dithiophene in the gas phase and in solution by first-principle quantum mechanical calculations (2578 views)
J Chem Theory Comput (ISSN: 1549-9618, 1549-9626electronic, 1549-9618linking), 2012; 8(11): 4483-4493.
Impact Factor: 5.389
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Improta R, Vitagliano L, Esposito L
* Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures (4015 views)
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2011 Sep 16; 6(9): e24533-e24533.
Impact Factor: 4.092
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Improta R, Ferrante C, Bozio R, Barone V
* The polarizability in solution of tetra-phenyl-porphyrin derivatives in their excited electronic states: A PCM/TD-DFT study (1631 views)
Phys Chem Chem Phys (ISSN: 1463-9076, 1463-3907, 1463-9084electronic), 2009; 11(22): 4664-4673.
Impact Factor: 4.116
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Improta R, Barone V
The excited states of adenine and thymine nucleoside and nucleotide in aqueous solution: A comparative study by time-dependent DFT calculations (1641 views)
Theor Chem Acc (ISSN: 1432-881x), 2008 Jul; 120(4-6): 491-497.
Impact Factor: 2.37
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Santoro F, Barone V, Benzi C, Improta R
* Excited state properties of sizable molecules in solution: From structure to reactivity (1898 views)
Theor Chem Acc (ISSN: 1432-881x), 2007 May; 117(5-6): 1073-1084.
Impact Factor: 2.537
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Moccia M, Musumeci D, Valente M, Roviello GN, Sapio R, Pedone C, Bucci EM
* Thermodynamic studies on PNA and PNA/DNA dendrimer formation (1272 views)
Nucleosides Nucleotides Nucleic Acids (ISSN: 1525-7770), 2007; 26(8-9): 1173-1176.
Impact Factor: 0.723
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Nuernberger P, Vogt G, Gerber G, Improta R, Santoro F
* Femtosecond study on the isomerization dynamics of NK88. I. Ground-state dynamics after photoexcitation (2107 views)
J Chem Phys (ISSN: 0021-9606, 0021-9606print, 0897-690online), 2006 Jul 28; 125(4): 44512-44544.
Impact Factor: 3.247
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Vogt G, Nuernberger P, Gerber G, Improta R, Santoro F, Nuernberger P, Vogt G, Gerber G, Improta R, Santoro F
* Femtosecond study on the isomerization dynamics of NK88. II. Excited-state dynamics (2006 views)
J Chem Phys (ISSN: 0021-9606, 0897-690online), 2006 Jul 28; 125(4): 44512-44512.
Impact Factor: 3.166
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Saviano M, Improta R, Benedetti E, Carrozzini B, Cascarano GL, Didierjean C, Toniolo C, Crisma M
* Benzophenone photophore flexibility and proximity: Molecular and crystal-state structure of a Bpa-containing trichogin dodecapeptide analogue (2034 views)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2004 Apr 2; 5(4): 541-544.
Impact Factor: 3.474
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Costanzo LL, De Guidi G, Giuffrida S, Sortino S, Condorelli G, Pappalardo G
Antioxidant effect of copper(II) on photosensitized lipid peroxidation (2295 views)
J Chem Res (ISSN: 0162-0134print, 0162-0134linking, 1873-3344), 1995 Feb; 57(2): 115-125.
Impact Factor: 1.342
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41 Records (37 excluding Abstracts).
Total impact factor: 258.74 (246.893 excluding Abstracts).
Total 5 year impact factor: 259.93 (245.826 excluding Abstracts).

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