Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers (31 views)
Mol Ther Nucleic Acids (ISSN: 2162-2531linking), 2023 Dec 12; 34: 102039-102039.
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Paper type: Journal Article
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Keywords: Mt: Oligonucleotides: Therapies And Applications , Remd Simulation , Rna Conformational Distribution , Aptamer , Flexibility , Nucleic Acids , Plasticity , Rational Design , Sequence-Structure Relationships , Structural Rna Motifs
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*** IBB - CNR ***
Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy.
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Not available.
Mol Ther Nucleic Acids (ISSN: 2162-2531linking), 2023 Dec 12; 34: 102039-102039.
Export to BibTeX Export to EndNote
Paper type: Journal Article
Impact factor: 0, 5-year impact factor: 0
Url: Not available.
Keywords: Mt: Oligonucleotides: Therapies And Applications , Remd Simulation , Rna Conformational Distribution , Aptamer , Flexibility , Nucleic Acids , Plasticity , Rational Design , Sequence-Structure Relationships , Structural Rna Motifs
Affiliations:
*** IBB - CNR ***
Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy.
References:
Not available.
Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers
Intrinsic flexibility and structural modularity are two common features of RNA molecules. Although functionally crucial, RNA plasticity often represents a major complication in high-resolution structural studies. To overcome this problem, RNAs may be rigidified through the complexation with high-affinity partners such as Fab molecules. This approach has been previously used to characterize the DIR2-aptamer. However, possible perturbations induced by the insertion of the Fab binding site on the DIR2-aptamer conformational properties were not investigated. Here, using enhanced molecular dynamics simulations, we compared the dynamics of the DIR2 aptamer holding the Fab binding site with that of the parental sequence. Our results suggest that the L2-loop modification for the Fab recognition leads to a significant increase in local flexibility that also affects the mobility of distant regions. The trajectories provide clear indications of the groups and the interactions mediating the dynamics transfer in DIR2. The effectiveness of our approach in addressing RNA flexibility was further corroborated by showing its ability to reproduce the most important events affecting the NF-κB RNA aptamer upon dissociation from the partner. Therefore, REMD analyses, a rarely adopted technique to unravel the structural/dynamical properties of aptamers, could efficiently complement experimental data guiding the rational design of nucleic acid therapeutics.
Intrinsic flexibility and structural modularity are two common features of RNA molecules. Although functionally crucial, RNA plasticity often represents a major complication in high-resolution structural studies. To overcome this problem, RNAs may be rigidified through the complexation with high-affinity partners such as Fab molecules. This approach has been previously used to characterize the DIR2-aptamer. However, possible perturbations induced by the insertion of the Fab binding site on the DIR2-aptamer conformational properties were not investigated. Here, using enhanced molecular dynamics simulations, we compared the dynamics of the DIR2 aptamer holding the Fab binding site with that of the parental sequence. Our results suggest that the L2-loop modification for the Fab recognition leads to a significant increase in local flexibility that also affects the mobility of distant regions. The trajectories provide clear indications of the groups and the interactions mediating the dynamics transfer in DIR2. The effectiveness of our approach in addressing RNA flexibility was further corroborated by showing its ability to reproduce the most important events affecting the NF-κB RNA aptamer upon dissociation from the partner. Therefore, REMD analyses, a rarely adopted technique to unravel the structural/dynamical properties of aptamers, could efficiently complement experimental data guiding the rational design of nucleic acid therapeutics.
Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers
Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers
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J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic, 0192-8651linking), 2008 Apr 30; 29(6): 957-964.
Impact Factor: 3.39
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Breveglieri G, Pensato S, Salvatori F, Saviano M, Pedone C, Romanelli A, Gambari R
* PNA-mediated alteration of mRNA splicing (448 views)
Minerva Biotecnol (ISSN: 1120-4826), 2008; 20(4): 175-181.
Impact Factor: 0.1
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Marchelli R, Saviano M, Licandro E, Spoto G, Borgatti M, Gambari R
* PNAs targeting the "RNA world": Micro RNA next? (522 views)
Minerva Biotecnol (ISSN: 1120-4826), 2008; 20(4): 183-188.
Impact Factor: 0.1
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Zanoli L, Dagata R, Spoto G
* Surface plasmon-based optical detection of DNA peptide nucleic acids (390 views)
Minerva Biotecnol (ISSN: 1120-4826), 2008; 20(4): 165-174.
Impact Factor: 0.1
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Roviello GN, Musumeci D, Moccia M, Castiglione M, Sapio R, Valente M, Bucci EM, Perretta G, Pedone C
* Dabpna: Design, Synthesis And Nucleic Acids Binding Studies (483 views)
Nucleosides Nucleotides Nucleic Acids (ISSN: 1525-7770), 2007; 26(10-12): 1307-1310.
Impact Factor: 0.723
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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 (333 views)
Nucleosides Nucleotides Nucleic Acids (ISSN: 1525-7770), 2007; 26(8-9): 1173-1176.
Impact Factor: 0.723
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Santoro F, Gustavsson T, Lami S, Barone V, Improta R
* Towards the understanding of the excited state dynamics of nucleic acids: Solvent and stacking effect on the photophysical behavior of nucleobases (361 views)
Aip Conf Proc (ISSN: 0094-243x), 2007; 963(2): 631-634.
Impact Factor: 0
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Santoro F, Barone V, Gustavsson T, Improta R
* Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water (1041 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2006 Dec 20; 128(50): 16312-16322.
Impact Factor: 7.696
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Roviello GN, Moccia M, Sapio R, Valente M, Bucci EM, Castiglione M, Pedone C, Perretta G, Benedetti E, Musumeci D
* Synthesis, Characterization And Hybridization Studies Of New Nucleo-Gamma-Peptides Based On Diaminobutyric Acid (610 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2006 Dec; 12(12): 829-835.
Impact Factor: 1.801
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Borgatti M, Boyd DD, Lampronti I, Bianchi N, Fabbri E, Saviano M, Romanelli A, Pedone C, Gambari R
* Decoy molecules based on PNA-DNA chimeras and targeting Sp1 transcription factors inhibit the activity of urokinase-type plasminogen activator receptor (uPAR) promoter (513 views)
Oncology Research (ISSN: 0965-0407), 2005; 15(7-8): 373-383.
Impact Factor: 1.844
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Borgatti M, Finotti A, Romanelli A, Saviano M, Bianchi N, Lampronti I, Lambertini E, Penolazzi L, Nastruzzi C, Mischiati C, Piva R, Pedone C, Gambari R
* Peptide nucleic acids (PNA)-DNA chimeras targeting transcription factors as a tool to modify gene expression (683 views)
Curr Drug Targets (ISSN: 1389-4501), 2004 Nov; 5(8): 735-744.
Impact Factor: 4.104
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Esposito G, Vitagliano L, Costanzo P, Borrelli L, Barone R, Pavone L, Izzo P, Zagari A, Salvatore F
* Human aldolase A natural mutants: relationship between flexibility of the C-terminal region and enzyme function (468 views)
Biochem J (ISSN: 0264-6021, 1470-8728electronic, 0264-6021linking), 2004 May 15; 380: 51-56.
Impact Factor: 4.278
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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 (487 views)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2004 Apr 2; 5(4): 541-544.
Impact Factor: 3.474
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Cortesi R, Mischiati C, Borgatti M, Breda L, Romanelli A, Saviano M, Pedone C, Gambari R, Nastruzzi C
* Formulations for natural and peptide nucleic acids based on cationic polymeric submicron particles (451 views)
The Aaps Journal (ISSN: 1522-1059, 1550-7416), 2004 Jan 20; 6(1): N/D-N/D.
Impact Factor: 1.938
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Musumeci D, Roviello GN, Valente M, Sapio R, Pedone C, Bucci EM
* New synthesis of PNA-3′DNA linker monomers, useful building blocks to obtain PNA/DNA chimeras (494 views)
Biopolymers, 2004; 76(6): 535-542.
Impact Factor: 2.248
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Borgatti M, Lampronti I, Romanelli A, Pedone C, Saviano M, Bianchi N, Mischiati C, Gambari R
* Transcription factor decoy molecules based on a peptide nucleic acid (PNA)-DNA chimera mimicking Sp1 binding sites (913 views)
Jbc Papers (ISSN: 0021-9258, 1083-351x, 0021-9258linking), 2003 Feb 28; 278(9): 7500-7509.
Impact Factor: 6.482
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Gambari R, Borgatti M, Romanelli A, Capasso D, Saviano M, Bianchi N, Lampronti I, Mischiati C, Pedone C
* Transcription factor decoy (TFD) activity of peptide nucleic acids (PNA)-DNA chimeras (373 views)
International Journal Of Molecular Medicine (ISSN: 1107-3756), 2003; 12(Supplement1): N/D-N/D.
Impact Factor: 1.94
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Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
* Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites (576 views)
Eur J Biochem (ISSN: 0014-2956, 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.
Impact Factor: 2.849
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Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
* Molecular interactions with nuclear factor kappaB (NF-kappaB) transcription factors of a PNA-DNA chimera mimicking NF-kappaB binding sites (510 views)
Eur J Biochem (ISSN: 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.
Impact Factor: 4.779
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* Flexibility of brain dynamics is increased and predicts clinical impairment in relapsing-remitting but not in secondary progressive multiple sclerosis (7 views)
Brain Commun (ISSN: 2632-1297linking), 2024 Apr 2; 6 (2 ): fcae112-N/D.
Impact Factor:
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F
* Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies (6 views)
Int J Mol Sci (ISSN: 1422-0067linking), 2023 Nov 14; 24 (22 ): N/D-N/D.
Impact Factor:
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Falanga AP, Terracciano M, Oliviero G, Roviello GN, Borbone N
* Exploring the relationship between G-quadruplex nucleic acids and plants: from plant G-quadruplex function to phytochemical G4 ligands with pharmaceutic potential (57 views)
Pharmaceutics, 2022 Nov 4; N/D: N/D-N/D.
Impact Factor: 6.525
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Mosseri A, Sancho-albero M, Leone M, Nava D, Secundo F, Maggioni D, De Cola L, Romanelli A
* Chiral Fibers Formation Upon Assembly of Tetraphenylalanine Peptide Conjugated to a PNA Dimer (108 views)
Chemistry (ISSN: 0947-6539linking, 1521-3765electronic), 2022 Jul 1; 28 (37 ): e202200693-N/D.
Impact Factor: 5.476
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Borbone N, Piccialli I, Falanga AP, Piccialli V, Roviello GN, Oliviero G
* Nucleic Acids as Biotools at the Interface between Chemistry and Nanomedicine in the COVID-19 Era (93 views)
International Journal Of Molecular Sciences, 2022 Jun; 23: 4359-4375.
Impact Factor: 5.924
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Greco F, Musumeci D, Borbone N, Falanga AP, D , #xerrico S, Terracciano M, Piccialli I, Roviello GN, Oliviero G
* Exploring the Parallel G-Quadruplex Nucleic Acid World: A Spectroscopic and Computational Investigation on the Binding of the c-myc Oncogene NHE III1 Region by the Phytochemical Polydatin (200 views)
Molecules (ISSN: 1420-3049linking, 1420-3049electronic), 2022 May 7; 27(9): 2997-3006.
Impact Factor: 4.412
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Scognamiglio PL, Platella C, Napolitano E, Musumeci D, Roviello GN
* From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides (146 views)
Molecules (ISSN: 1420-3049linking, 1420-3049electronic), 2021 Jun 10; 26(12): 3558-3558.
Impact Factor: 4.411
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Avitabile C, Diaferia C, Roviello V, Altamura D, Giannini C, Vitagliano L, Accardo A, Romanelli A
* Fluorescence and Morphology of Self-Assembled Nucleobases and Their Diphenylalanine Hybrid Aggregates (277 views)
Chemistry (ISSN: 0947-6539linking, 1521-3765electronic), 2019 Nov 22; 25(65): 14850-14857.
Impact Factor: 5.476
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Piacenti V, Langella E, Autiero I, Nolan JC, Piskareva O, Adamo MFA, Saviano M, Moccia M
* A combined experimental and computational study on peptide nucleic acid (PNA) analogues of tumor suppressive miRNA-34a (279 views)
Bioorg Chem (ISSN: 0045-2068linking, 1090-2120electronic), 2019 Oct; 91: 103165-103165.
Impact Factor: 3.9
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Balasco N, Barone D, Iaccarino E, Sandomenico A, De Simone A, Ruvo M, Vitagliano L
* Intrinsic structural versatility of the highly conserved 412-423 epitope of the Hepatitis C Virus E2 protein (343 views)
Int J Biol Macromol (ISSN: 1879-0003electronic, 0141-8130linking), 2018 Sep; 116: 620-632.
Impact Factor: 1.427
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Smaldone G, Berisio R, Balasco N, D'Auria S, Vitagliano L, Ruggiero A
* Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization (343 views)
Bba-Gen Subjects (ISSN: 1570-9639print, 1570-9639linking, 0005-2728), 2018 May 31; 1866(9): 952-962.
Impact Factor: 2.773
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Chattopadhyay A, Cogdell R, Crespo-hernandez CE, Datta A, De A, Haacke S, Hariharan M, Helliwell J, Hughes A, Improta R, Jones M, Joseph J, Karsili T, Kohler B, Krishnan R, Kuriakose A, L , M , Markovitsi D, Medhi H, Periyasamy G, Pradeepkumar PI, Roy Chowdhury P, Sarangi M, Schapiro I, Schertler GFX, Schlichting I, Segarra-marti J, Swaminathan R, V , V , Van Grondelle R, Venkatraman RK, Venkatramani R, Watts A
* Light induced charge and energy transport in nucleic acids and proteins: general discussion (231 views)
Faraday Discuss (ISSN: 1359-6640print, 1359-6640linking), 2018 Apr 1; 207: 153-180.
Impact Factor: 4.194
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Chandra A, Cogdell R, Crespo-hernandez CE, Datta A, Giussani A, Haacke S, Helliwell J, Improta R, Jayasree RS, Jones M, Karsili T, Kohler B, L , M , Mandal I, Markovitsi D, Medhi H, Mishra PP, Pradeepkumar PI, Roy Chowdhury P, Sarangi M, Schapiro I, Schlichting I, Segarra-marti J, Sharma A, V , V , Van Grondelle R, Watts A
* Light induced damage and repair in nucleic acids and proteins: general discussion (179 views)
Faraday Discuss (ISSN: 1359-6640print, 1359-6640linking), 2018 Apr 1; 207: 389-408.
Impact Factor: 4.194
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Autiero I, Ruvo M, Improta R, Vitagliano L
* The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition (440 views)
Bba-Gen Subjects (ISSN: 0304-4165print, 0304-4165linking, 1872-8006electronic), 2018 Apr; 1862(4): 1006-1016.
Impact Factor: 3.829
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Avitabile C, Diaferia C, Della Ventura B, Mercurio FA, Leone M, Roviello V, Saviano M, Velotta R, Morelli G, Accardo A, Romanelli A
* Self-Assembling of Fmoc-GC Peptide Nucleic Acid Dimers into Highly Fluorescent Aggregates (1296 views)
Chemistry (ISSN: 1521-3765electronic, 0947-6539linking), 2018 Mar 26; 24(18): 4729-4735.
Impact Factor: 5.476
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Bhat V, Cogdell R, Crespo-hernández CE, Datta A, De A, Haacke S, Helliwell J, Improta R, Joseph J, Karsili T, Kohler B, Krishnan R, Mahil LM, Lewis F, Mandal I, Markovitsi D, Mishra PP, Paul S, Periyasamy G, Pradeepkumar PI, Roy Chowdhury P, Sarangi M, Sasikumar D, Schapiro I, Schertler GFX, Schlichting I, Segarra-martí J, Swaminathan R, Vishnu V, Van Grondelle R, Varghese R, Venkatramani R
* Photocrosslinking between nucleic acids and proteins: general discussion (182 views)
Faraday Discussions, 2018; N/D: N/D-N/D.
Impact Factor: 3.427
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Piras L, Avitabile C, D'Andrea LD, Saviano M, Romanelli A
* Detection of oligonucleotides by PNA-peptide conjugates recognizing the biarsenical fluorescein complex FlAsH-EDT2 (359 views)
Biochem Bioph Res Co (ISSN: 0006-291x), 2017 Sep 15; N/D: N/D-N/D.
Impact Factor: 2.559
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Barone D, Balasco N, Autiero I, Vitagliano L
* The dynamic properties of the Hepatitis C Virus E2 envelope protein unraveled by molecular dynamics (6 views)
J Biomol Struct Dyn (ISSN: 0739-1102linking), 2017 Mar; 35 (4 ): 805-816.
Impact Factor:
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Barone D, Balasco N, Autiero I, Vitagliano L
* The dynamic properties of the Hepatitis C Virus E2 envelope protein unraveled by molecular dynamics (366 views)
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 2016 Dec; N/D: 1-12.
Impact Factor: 3.123
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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 (411 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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Roviello GN, Roviello V, Autiero I, Saviano M
* Solid phase synthesis of TyrT, a thymine-tyrosine conjugate with poly(A) RNA-binding ability (669 views)
Rsc Adv (ISSN: 2046-2069, 2046-2069electronic, 2046-2069linking), 2016 Mar 15; 6(33): 27607-27613.
Impact Factor: 3.108
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Improta R, Santoro F, Blancafort L
* Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases (1605 views)
Chem Rev (ISSN: 0009-2665), 2016; 116(6): 3540-3593.
Impact Factor: 47.928
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Paladino A, Morra G, Colombo G
Structural Stability and Flexibility Direct the Selection of Activating Mutations in Epidermal Growth Factor Receptor Kinase (73 views)
J Chem Inf Model (ISSN: 1549-9596linking), 2015 Jul 27; 55 (7 ): 1377-1387.
Impact Factor:
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Galdiero S, Falanga A, Berisio R, Grieco P, Morelli G, Galdiero M
* Antimicrobial peptides as an opportunity against bacterial diseases (870 views)
Curr Med Chem (ISSN: 0929-8673, 1875-533x, 1875-533xelectronic), 2015 Mar 11; 22(14): 1665-1677.
Impact Factor: 3.455
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Calvanese L, Falcigno L, D'Auria G
* Essential Dynamics Analysis Captures the Concerted Motion of the Integrin-Binding Site in Jerdostatin, an RTS Disintegrin (542 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2015 Mar; 103(3): 158-166.
Impact Factor: 2.248
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Autiero I, Saviano M, Langella E
* Conformational studies of chiral D-Lys-PNA and achiral PNA system in binding with DNA or RNA through a molecular dynamics approach (629 views)
Eur J Med Chem (ISSN: 0223-5234, 1768-3254, 0223-5234linking), 2015 Feb 16; 91: 109-117.
Impact Factor: 3.902
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Avitabile C, Accardo A, Ringhieri P, Morelli G, Saviano M, Montagner G, Fabbri E, Gallerani E, Gambari R, Romanelli A
* Incorporation of Naked Peptide Nucleic Acids into Liposomes Leads to Fast and Efficient Delivery (573 views)
Bioconjug Chem (ISSN: 1043-1802, 1520-4812), 2015; 26(8): 1533-1541.
Impact Factor: 4.5
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Roviello GN, Musumeci D, Roviello V, Pirtskhalava M, Egoyan A, Mirtskhulava M
* Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure (487 views)
Beilstein J Nanotech (ISSN: 2190-4286), 2015; 6(1): 1338-1347.
Impact Factor: 2.778
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Cohen SS, Riven I, Cortajarena AL, De Rosa L, D'Andrea LD, Regan L, Haran G
* Probing the molecular origin of native-state flexibility in repeat proteins (439 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 0002-7863print), 2015; 137(32): 10367-10373.
Impact Factor: 13.038
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Fahleson T, Kauczor J, Norman P, Santoro F, Improta R, Coriani S
* TD-DFT investigation of the magnetic circular dichroism spectra of some purine and pyrimidine bases of nucleic acids (620 views)
J Phys Chem A (ISSN: 1089-5639, 1520-5215electronic, 1089-5639linking), 2015; 119(21): 5476-5489.
Impact Factor: 2.883
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Autiero I, Saviano M, Langella E
* Molecular Dynamics Simulations Of Pna-Pna And Pna-Dna Duplexes By The Use Of New Parameters Implemented In The Gromacs Package: A Conformational And Dynamics Study (1015 views)
Phys Chem Chem Phys (ISSN: 1463-9076, 1463-3907, 1463-9084electronic), 2014 Feb 7; 16(5): 1868-1874.
Impact Factor: 4.493
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Roviello GN, Musumeci D, D'Alessandro C, Pedone C
* Binding ability of a thymine-functionalized oligolysine towards nucleic acids (400 views)
Bioorg Med Chem (ISSN: 0968-0896, 1464-3391, 0968-0896linking), 2014 Feb 1; 22(3): 997-1002.
Impact Factor: 2.793
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Russo Krauss I, Parkinson GN, Merlino A, Mattia CA, Randazzo A, Novellino E, Mazzarella L, Sica F
* A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex (780 views)
Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 2014 Feb; 70(2): 362-370.
Impact Factor: 7.232
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Zanoli LM, Spoto G
* Isothermal amplification methods for the detection of nucleic acids in microfluidic devices (480 views)
Biosensors (ISSN: 2079-6374), 2013 Mar; 3(1): 18-43.
Impact Factor: 0
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Causa F, Della Moglie R, Iaccino E, Mimmi S, Marasco D, Scognamiglio PL, Battista E, Palmieri C, Cosenza C, Sanguigno L, Quinto I, Scala G, Netti PA
* Evolutionary screening and adsorption behavior of engineered M13 bacteriophage and derived dodecapeptide for selective decoration of gold interfaces (528 views)
J Colloid Interface Sci (ISSN: 0021-9797, 1095-7103electronic, 0021-9797linking), 2013 Jan 1; 389(1): 220-229.
Impact Factor: 1.646
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Zanoli LM, Licciardello M, D'Agata R, Lantano C, Calabretta A, Corradini R, Marchelli R, Spoto G
* Peptide nucleic acid molecular beacons for the detection of PCR amplicons in droplet-based microfluidic devices (501 views)
Anal Bioanal Chem (ISSN: 1618-2642), 2013 Jan; 405(2-3): 615-624.
Impact Factor: 3.578
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Poletto M, Vascotto C, Scognamiglio PL, Lirussi L, Marasco D, Tell G
* Role Of The Unstructured N-Terminal Domain Of The Human Apurinic/Apyrimidinic Endonuclease 1 (hape1) In The Modulation Of Its Interaction With Nucleic Acids And Nucleophosmin (npm1) (554 views)
Biochem J (ISSN: 0264-6021, 1470-8728electronic, 0264-6021linking), 2013; 452(3): 545-557.
Impact Factor: 4.779
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Roviello GN, Musumeci D, Bucci EM, Pedone C
* Synthesis of a diaminopropanoic acid-based nucleoamino acid and assembly of cationic nucleopeptides for biomedical applications (557 views)
Amino Acids (ISSN: 0939-4451, 1438-2199, 1438-2199electronic), 2012 Dec; 43(6): 2537-2543.
Impact Factor: 3.914
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Roviello GN, Roviello G, Musumeci D, Bucci EM, Pedone C
* Dakin-West reaction on 1-thyminyl acetic acid for the synthesis of 1, 3-bis(1-thyminyl)-2-propanone, a heteroaromatic compound with nucleopeptide-binding properties (614 views)
Amino Acids (ISSN: 1438-2199, 0939-4451, 1438-2199electronic), 2012 Oct; 43(4): 1615-1623.
Impact Factor: 3.914
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Avitabile C, Saviano M, D'Andrea LD, Bianchi N, Fabbri E, Brognara E, Gambari R, Romanelli A
* Targeting pre-miRNA by peptide nucleic acids: a new strategy to interfere in the miRNA maturation (899 views)
Artif Dna Pna Xnaartificial Dna Pna & Xna (ISSN: 1949-9096, 1949-0968, 1949-095x), 2012 Apr; 3(2): 88-96.
Impact Factor: 0
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Improta R, Barone V
* Interplay between "neutral" and "charge-transfer" excimers rules the excited state decay in adenine-rich polynucleotides (744 views)
Angew Chem Int Ed (ISSN: 1433-7851, 1521-3773electronic, 1433-7851linking), 2011 Dec 9; 50(50): 12016-12019.
Impact Factor: 13.455
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Roviello GN, Musumeci D, Bucci EM, Pedone C
* Synthesis and characterization of a novel ester-based nucleoamino acid for the assembly of aromatic nucleopeptides for biomedical applications (607 views)
Int J Pharm (ISSN: 0378-5173, 1873-3476), 2011 Sep 30; 415(1-2): 206-210.
Impact Factor: 3.35
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Roviello GN, Musumeci D, Bucci EM, Pedone C
* Nucleobase-containing peptides: a spectroscopic study of their properties and nucleic acids recognition ability (461 views)
Eur Biophys J (ISSN: 0175-7571, 1432-1017, 0175-7571linking), 2011 Sep; 40: N/D-N/D.
Impact Factor: 2.139
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Merlino A, Russo Krauss I, Castellano I, De Vendittis E, Rossi B, Conte M, Vergara A, Sica F
* Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis (616 views)
J Struct Biol (ISSN: 1047-8477, 1047-8477linking), 2010 Dec; 172(3): 343-352.
Impact Factor: 3.5
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Moccia M, Roviello GN, Bucci EM, Pedone C, Saviano M
* Synthesis of a l-lysine-based alternate alpha, epsilon-peptide: A novel linear polycation with nucleic acids-binding ability (587 views)
Int J Pharm (ISSN: 0378-5173, 1873-3476), 2010 Sep 15; 397(1-2): 179-183.
Impact Factor: 3.607
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Roviello GN, Crescenzo C, Capasso D, Di Gaetano S, Franco S, Bucci EM, Pedone C
* Synthesis of a novel Fmoc-protected nucleoaminoacid for the solid phase assembly of 4-piperidyl glycine/L-arginine-containing nucleopeptides and preliminary RNA interaction studies (510 views)
Amino Acids (ISSN: 0939-4451, 1438-2199, 1438-2199electronic), 2010 Sep; 39(3): 795-800.
Impact Factor: 4.106
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D'Agata R, Corradini R, Ferretti C, Zanoli L, Gatti M, Marchelli R, Spoto G
* Ultrasensitive detection of non-amplified genomic DNA by nanoparticle-enhanced surface plasmon resonance imaging (641 views)
Biosens Bioelectron (ISSN: 0956-5663, 1873-4235electronic), 2010 May 15; 25(9): 2095-2100.
Impact Factor: 5.361
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Orsi S, De Capua A, Guarnieri D, Marasco D, Netti PA
* Cell recruitment and transfection in gene activated collagen matrix (489 views)
Biomaterials (ISSN: 0142-9612, 1878-5905electronic, 0142-9612linking), 2010 Jan; 31(3): 570-576.
Impact Factor: 7.883
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Roviello GN, Musumeci D, Pedone C, Bucci EM
* Synthesis, Characterization And Hybridization Studies Of An Alternate Nucleo-Epsilon/Gamma-Peptide: Complexes Formation With Natural Nucleic Acids (683 views)
Amino Acids (ISSN: 0939-4451, 1438-2199, 1438-2199electronic), 2010 Jan; 38(1): 103-111.
Impact Factor: 4.106
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Improta R, Santoro F, Barone V, Lami A
* Vibronic model for the quantum dynamical study of the competition between bright and charge-transfer excited states in single-strand polynucleotides: the adenine dimer case (355 views)
J Phys Chem A (ISSN: 1089-5639, 1520-5215electronic, 1089-5639linking), 2009 Dec 31; 113(52): 15346-15354.
Impact Factor: 2.899
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Ruggiero A, Di Maro A, Severino V, Chambery A, Berisio R
* Crystal structure of PD-L1, a ribosome inactivating protein from Phytolacca dioica L. leaves with the property to induce DNA cleavage (506 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2009 Dec; 91(12): 1135-1142.
Impact Factor: 2.605
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Merlino A, Russo Krauss I, Perillo M, Mattia CA, Ercole C, Picone D, Vergara A, Sica F
* Toward an Antitumor Form of Bovine Pancreatic Ribonuclease: The Crystal Structure of Three Noncovalent Dimeric Mutants (498 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2009 Dec; 91(12): 1029-1037.
Impact Factor: 2.605
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Santoro F, Barone V, Improta R
* The Excited States Decay Of The A-T Dna: A Pcm/Td-Dft Study In Aqueous Solution Of The (9-Methyl-Adenine) 2 (1-Methyl-Thymine) 2 Stacked Tetramer (320 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2009; 131(42): 15232-15245.
Impact Factor: 8.58
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Merlino A, Varriale S, Coscia MR, Mazzarella L, Oreste U
* Structure and dimerization of the teleost transmembrane immunoglobulin region (561 views)
Journal Of Molecular Graphics & Modelling (ISSN: 1093-3263), 2008 Oct; 27(3): 401-407.
Impact Factor: 2.347
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Roviello GN, Musumeci D, Bucci EM, Castiglione M, Cesarani A, Pedone C, Piccialli G
* Evidences for complex formation between l-dabPNA and aegPNA (426 views)
Bioorg Med Chem Lett (ISSN: 0960-894x, 1464-3405, 1464-3405electronic), 2008 Sep 1; 18(17): 4757-4760.
Impact Factor: 2.531
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D'Agata R, Corradini R, Grasso G, Marchelli R, Spoto G
* Ultrasensitive detection of DNA by PNA and nanoparticle-enhanced surface plasmon resonance imaging (479 views)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2008 Sep 1; 9(13): 2067-2070.
Impact Factor: 3.322
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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 (327 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, Improta R
* Can TD-DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case (404 views)
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic, 0192-8651linking), 2008 Apr 30; 29(6): 957-964.
Impact Factor: 3.39
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Breveglieri G, Pensato S, Salvatori F, Saviano M, Pedone C, Romanelli A, Gambari R
* PNA-mediated alteration of mRNA splicing (448 views)
Minerva Biotecnol (ISSN: 1120-4826), 2008; 20(4): 175-181.
Impact Factor: 0.1
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Marchelli R, Saviano M, Licandro E, Spoto G, Borgatti M, Gambari R
* PNAs targeting the "RNA world": Micro RNA next? (522 views)
Minerva Biotecnol (ISSN: 1120-4826), 2008; 20(4): 183-188.
Impact Factor: 0.1
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Zanoli L, Dagata R, Spoto G
* Surface plasmon-based optical detection of DNA peptide nucleic acids (390 views)
Minerva Biotecnol (ISSN: 1120-4826), 2008; 20(4): 165-174.
Impact Factor: 0.1
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Roviello GN, Musumeci D, Moccia M, Castiglione M, Sapio R, Valente M, Bucci EM, Perretta G, Pedone C
* Dabpna: Design, Synthesis And Nucleic Acids Binding Studies (483 views)
Nucleosides Nucleotides Nucleic Acids (ISSN: 1525-7770), 2007; 26(10-12): 1307-1310.
Impact Factor: 0.723
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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 (333 views)
Nucleosides Nucleotides Nucleic Acids (ISSN: 1525-7770), 2007; 26(8-9): 1173-1176.
Impact Factor: 0.723
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Santoro F, Gustavsson T, Lami S, Barone V, Improta R
* Towards the understanding of the excited state dynamics of nucleic acids: Solvent and stacking effect on the photophysical behavior of nucleobases (361 views)
Aip Conf Proc (ISSN: 0094-243x), 2007; 963(2): 631-634.
Impact Factor: 0
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Santoro F, Barone V, Gustavsson T, Improta R
* Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water (1041 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2006 Dec 20; 128(50): 16312-16322.
Impact Factor: 7.696
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Roviello GN, Moccia M, Sapio R, Valente M, Bucci EM, Castiglione M, Pedone C, Perretta G, Benedetti E, Musumeci D
* Synthesis, Characterization And Hybridization Studies Of New Nucleo-Gamma-Peptides Based On Diaminobutyric Acid (610 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2006 Dec; 12(12): 829-835.
Impact Factor: 1.801
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Borgatti M, Boyd DD, Lampronti I, Bianchi N, Fabbri E, Saviano M, Romanelli A, Pedone C, Gambari R
* Decoy molecules based on PNA-DNA chimeras and targeting Sp1 transcription factors inhibit the activity of urokinase-type plasminogen activator receptor (uPAR) promoter (513 views)
Oncology Research (ISSN: 0965-0407), 2005; 15(7-8): 373-383.
Impact Factor: 1.844
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Borgatti M, Finotti A, Romanelli A, Saviano M, Bianchi N, Lampronti I, Lambertini E, Penolazzi L, Nastruzzi C, Mischiati C, Piva R, Pedone C, Gambari R
* Peptide nucleic acids (PNA)-DNA chimeras targeting transcription factors as a tool to modify gene expression (683 views)
Curr Drug Targets (ISSN: 1389-4501), 2004 Nov; 5(8): 735-744.
Impact Factor: 4.104
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Esposito G, Vitagliano L, Costanzo P, Borrelli L, Barone R, Pavone L, Izzo P, Zagari A, Salvatore F
* Human aldolase A natural mutants: relationship between flexibility of the C-terminal region and enzyme function (468 views)
Biochem J (ISSN: 0264-6021, 1470-8728electronic, 0264-6021linking), 2004 May 15; 380: 51-56.
Impact Factor: 4.278
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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 (487 views)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2004 Apr 2; 5(4): 541-544.
Impact Factor: 3.474
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Cortesi R, Mischiati C, Borgatti M, Breda L, Romanelli A, Saviano M, Pedone C, Gambari R, Nastruzzi C
* Formulations for natural and peptide nucleic acids based on cationic polymeric submicron particles (451 views)
The Aaps Journal (ISSN: 1522-1059, 1550-7416), 2004 Jan 20; 6(1): N/D-N/D.
Impact Factor: 1.938
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Musumeci D, Roviello GN, Valente M, Sapio R, Pedone C, Bucci EM
* New synthesis of PNA-3′DNA linker monomers, useful building blocks to obtain PNA/DNA chimeras (494 views)
Biopolymers, 2004; 76(6): 535-542.
Impact Factor: 2.248
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Borgatti M, Lampronti I, Romanelli A, Pedone C, Saviano M, Bianchi N, Mischiati C, Gambari R
* Transcription factor decoy molecules based on a peptide nucleic acid (PNA)-DNA chimera mimicking Sp1 binding sites (913 views)
Jbc Papers (ISSN: 0021-9258, 1083-351x, 0021-9258linking), 2003 Feb 28; 278(9): 7500-7509.
Impact Factor: 6.482
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Gambari R, Borgatti M, Romanelli A, Capasso D, Saviano M, Bianchi N, Lampronti I, Mischiati C, Pedone C
* Transcription factor decoy (TFD) activity of peptide nucleic acids (PNA)-DNA chimeras (373 views)
International Journal Of Molecular Medicine (ISSN: 1107-3756), 2003; 12(Supplement1): N/D-N/D.
Impact Factor: 1.94
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Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
* Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites (576 views)
Eur J Biochem (ISSN: 0014-2956, 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.
Impact Factor: 2.849
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Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
* Molecular interactions with nuclear factor kappaB (NF-kappaB) transcription factors of a PNA-DNA chimera mimicking NF-kappaB binding sites (510 views)
Eur J Biochem (ISSN: 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.
Impact Factor: 4.779
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76 Records (73 excluding Abstracts).
Total impact factor: 318.644 (312.627 excluding Abstracts).
Total 5 year impact factor: 323.699 (314.514 excluding Abstracts).
Total impact factor: 318.644 (312.627 excluding Abstracts).
Total 5 year impact factor: 323.699 (314.514 excluding Abstracts).
31 views. Last view on Tuesday 10 September 2024, 22:31:00
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