Solid Phase Synthesis and RNA-binding Activity of an Arginine-containing Nucleopeptide

Overview

Journal RSC Adv

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2017 Oct 24

PMID 29057071

Citations 11

Authors

G N Roviello

C Vicidomini

S Di Gaetano

D Capasso

D Musumeci

V Roviello

Affiliations

Soon will be listed here.

Abstract

Here we report the solid phase synthesis and characterization (LC-ESIMS, CD) of a cationic nucleobase-containing α-peptide, composed of both l-arginine residues and l-lysine-based nucleoamino acids sequentially present in the structure. The binding properties of this novel basic nucleopeptide towards nucleic acids were investigated by CD spectroscopy which revealed the ability of the thymine-containing oligomer to bind both adenine-containing DNA (dA) and RNA (poly rA) molecules inducing high conformational variations in the nucleic acid structures. Moreover, the artificial oligonucleotide inhibited the enzymatic activity of HIV reverse transcriptase, opening the door to the exploitation of novel antiviral strategies inspired to this molecular tool.

Citing Articles

Solid Phase Synthesis and TAR RNA-Binding Activity of Nucleopeptides Containing Nucleobases Linked to the Side Chains via 1,4-Linked-1,2,3-triazole.

Mucha P, Pieszko M, Bylinska I, Wiczk W, Ruczynski J, Prochera K Biomedicines. 2024; 12(3).

PMID: 38540183 PMC: 10968536. DOI: 10.3390/biomedicines12030570.

Willardiine and Its Synthetic Analogues: Biological Aspects and Implications in Peptide Chemistry of This Nucleobase Amino Acid.

Palumbo R, Omodei D, Vicidomini C, Roviello G Pharmaceuticals (Basel). 2022; 15(10).

PMID: 36297355 PMC: 9611319. DOI: 10.3390/ph15101243.

Discovery of a novel small molecular peptide that disrupts helix 34 of bacterial ribosomal RNA.

Gc K, To D, Jayalath K, Abeysirigunawardena S RSC Adv. 2022; 9(69):40268-40276.

PMID: 35542650 PMC: 9076165. DOI: 10.1039/c9ra07812f.

carba-Nucleopeptides (cNPs): A Biopharmaceutical Modality Formed through Aqueous Rhodamine B Photoredox Catalysis.

Immel J, Bloom S Angew Chem Int Ed Engl. 2022; 61(28):e202205606.

PMID: 35507689 PMC: 9256812. DOI: 10.1002/anie.202205606.

Nucleic Acids as Biotools at the Interface between Chemistry and Nanomedicine in the COVID-19 Era.

Borbone N, Piccialli I, Falanga A, Piccialli V, Roviello G, Oliviero G Int J Mol Sci. 2022; 23(8).

PMID: 35457177 PMC: 9031702. DOI: 10.3390/ijms23084359.

References

Scognamiglio P, Di Natale C, Leone M, Poletto M, Vitagliano L, Tell G . G-quadruplex DNA recognition by nucleophosmin: new insights from protein dissection. Biochim Biophys Acta. 2014; 1840(6):2050-9. DOI: 10.1016/j.bbagen.2014.02.017. View

Simeone L, Milano D, De Napoli L, Irace C, Di Pascale A, Boccalon M . Design, synthesis and characterisation of guanosine-based amphiphiles. Chemistry. 2011; 17(49):13854-65. DOI: 10.1002/chem.201101827. View

Roviello G, Musumeci D, DAlessandro C, Pedone C . Binding ability of a thymine-functionalized oligolysine towards nucleic acids. Bioorg Med Chem. 2014; 22(3):997-1002. DOI: 10.1016/j.bmc.2013.12.053. View

Avitabile C, Cimmino A, Romanelli A . Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs): emerging therapeutics applications. J Med Chem. 2014; 57(24):10220-40. DOI: 10.1021/jm5006594. View

Roviello G, Roviello G, Musumeci D, Bucci E, 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. Amino Acids. 2012; 43(4):1615-23. DOI: 10.1007/s00726-012-1237-7. View

Calabretta A, Tedeschi T, Di Cola G, Corradini R, Sforza S, Marchelli R . Arginine-based PNA microarrays for APOE genotyping. Mol Biosyst. 2009; 5(11):1323-30. DOI: 10.1039/b909912n. View

Moggio L, Romanelli A, Gambari R, Bianchi N, Borgatti M, Fabbri E . Alternate PNA-DNA chimeras (PNA-DNA)(n): synthesis, binding properties and biological activity. Biopolymers. 2007; 88(6):815-22. DOI: 10.1002/bip.20857. View

Roviello G, Musumeci D, DAlessandro C, Pedone C . Synthesis of a thymine-functionalized nucleoamino acid for the solid phase assembly of cationic nucleopeptides. Amino Acids. 2013; 45(4):779-84. DOI: 10.1007/s00726-013-1520-2. View

Roviello G, Moccia M, Sapio R, Valente M, Bucci E, Castiglione M . Synthesis, characterization and hybridization studies of new nucleo-gamma-peptides based on diaminobutyric acid. J Pept Sci. 2006; 12(12):829-35. DOI: 10.1002/psc.819. View

10.

Zatsepin T, Romanova E, Stetsenko D, Gait M, Oretskaya T . Synthesis of 2'-modified oligonucleotides containing aldehyde or ethylenediamine groups. Nucleosides Nucleotides Nucleic Acids. 2003; 22(5-8):1383-5. DOI: 10.1081/NCN-120022971. View

11.

Bell N, Micklefield J . Chemical modification of oligonucleotides for therapeutic, bioanalytical and other applications. Chembiochem. 2009; 10(17):2691-703. DOI: 10.1002/cbic.200900341. View

12.

Roviello G, Di Gaetano S, Capasso D, Franco S, Crescenzo C, Bucci E . RNA-binding and viral reverse transcriptase inhibitory activity of a novel cationic diamino acid-based peptide. J Med Chem. 2011; 54(7):2095-101. DOI: 10.1021/jm1012769. View

13.

Nielsen P, Egholm M, Berg R, Buchardt O . Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science. 1991; 254(5037):1497-500. DOI: 10.1126/science.1962210. View

14.

Roviello G, Di Gaetano S, Capasso D, Cesarani A, Bucci E, Pedone C . Synthesis, spectroscopic studies and biological activity of a novel nucleopeptide with Moloney murine leukemia virus reverse transcriptase inhibitory activity. Amino Acids. 2009; 38(5):1489-96. DOI: 10.1007/s00726-009-0361-5. View

15.

Dragulescu-Andrasi A, Rapireddy S, He G, Bhattacharya B, Hyldig-Nielsen J, Zon G . Cell-permeable peptide nucleic acid designed to bind to the 5'-untranslated region of E-cadherin transcript induces potent and sequence-specific antisense effects. J Am Chem Soc. 2006; 128(50):16104-12. DOI: 10.1021/ja063383v. View

16.

Poletto M, Malfatti M, Dorjsuren D, Scognamiglio P, Marasco D, Vascotto C . Inhibitors of the apurinic/apyrimidinic endonuclease 1 (APE1)/nucleophosmin (NPM1) interaction that display anti-tumor properties. Mol Carcinog. 2015; 55(5):688-704. PMC: 4600639. DOI: 10.1002/mc.22313. View

17.

Roviello G, Musumeci D, Bucci E, Pedone C . Evidences for supramolecular organization of nucleopeptides: synthesis, spectroscopic and biological studies of a novel dithymine L-serine tetrapeptide. Mol Biosyst. 2011; 7(4):1073-80. DOI: 10.1039/c0mb00214c. View

18.

Roviello G, Musumeci D, De Cristofaro A, Capasso D, Di Gaetano S, Bucci E . Alternate dab-aegPNAs: synthesis, nucleic acid binding studies and biological activity. Mol Biosyst. 2009; 6(1):199-205. DOI: 10.1039/b910278g. View

19.

Avitabile C, Moggio L, Malgieri G, Capasso D, Di Gaetano S, Saviano M . γ Sulphate PNA (PNA S): highly selective DNA binding molecule showing promising antigene activity. PLoS One. 2012; 7(5):e35774. PMC: 3346730. DOI: 10.1371/journal.pone.0035774. View

20.

Vicidomini C, Panico M, Greco A, Gargiulo S, Coda A, Zannetti A . In vivo imaging and characterization of [(18)F]DPA-714, a potential new TSPO ligand, in mouse brain and peripheral tissues using small-animal PET. Nucl Med Biol. 2014; 42(3):309-16. DOI: 10.1016/j.nucmedbio.2014.11.009. View