molecules

Editorial
Special Issue “Frontiers in Nucleic Acid Chemistry—In
Memory of Professor Enrique Pedroso for His Outstanding
Contributions to Nucleic Acid Chemistry”
Montserrat Terrazas 1, * , Ramon Eritja 2,3, * and Daniela Montesarchio 4, *

1 Department of Inorganic and Organic Chemistry, Organic Chemistry Section, Institute of Biomedicine of the
University of Barcelona (IBUB), University of Barcelona, 08028 Barcelona, Spain
2 Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, 08034 Barcelona, Spain
3 Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN),
Instituto de Salud Carlos III, 28029 Madrid, Spain
4 Department of Chemical Sciences, University of Naples Federico II, I-80126 Napoli, Italy
* Correspondence: [email protected] (M.T.); [email protected] (R.E.);
[email protected] (D.M.)

This Special issue is dedicated to the memory of Enrique Pedroso, Professor Emeritus
of Organic Chemistry at University of Barcelona, who passed away at the age of 72 in
September 2020. Professor Enrique Pedroso has been one of the pioneers of Nucleic Acids
Chemistry in Spain, significantly contributing to the development of this highly interdis-
ciplinary field which combines organic chemistry, biochemistry, pharmacology, materials
chemistry, and biophysics. His major research achievements have been accomplished in
the synthesis of modified oligonucleotides and especially conjugates and cyclic oligonu-
cleotides, as well as their analogues, which opened new avenues in the search for novel
applications of oligonucleotides.
His research activity started in 1981 at the Department of Organic Chemistry of
University of Barcelona, where he spent all his intense academic and scientific career,
covering almost four decades. After having deeply investigated the methods of solid phase
Citation: Terrazas, M.; Eritja, R.; peptide synthesis, providing significant progress in the field also in collaboration with
Montesarchio, D. Special Issue Ernest Giralt, Fernando Albericio and Ramon Eritja of the same University, in 1990, he
“Frontiers in Nucleic Acid published his first article on the solid-phase synthesis of oligonucleotides [1]. This work was
Chemistry—In Memory of Professor immediately followed by an important contribution on the synthesis and characterization of
Enrique Pedroso for His Outstanding oligodeoxynucleotides containing the mutagenic base analogue 4-O-ethylthymine, carried
Contributions to Nucleic Acid out in collaboration with Ramon Eritja [2], with whom he always maintained strict research
Chemistry”. Molecules 2023, 28, 7278. relationships.
https://doi.org/10.3390/ After an enlightening research stay in University of Colorado in Boulder, hosted in the
molecules28217278 group of prof. Marvin H. Caruthers, he grew a solid and active research group starting from
Received: 13 October 2023 the early 1990s in collaboration with Anna Grandas—his closest collaborator in research
Accepted: 24 October 2023 and beloved partner in life. Together, they developed efficient approaches for the synthesis
Published: 26 October 2023 of hybrid compounds, such as nucleopeptides and peptide–oligonucleotide conjugates,
among others (see: [3–6]).
In 1997, he published an effective method for the solid-phase synthesis of cyclic
oligodeoxyribonucleotides, successfully engineering the functionalized solid support so
Copyright: © 2023 by the authors.
to exploit phosphotriester chemistry for the crucial cyclization step of the target oligonu-
Licensee MDPI, Basel, Switzerland.
cleotide, previously assembled via standard phosphoramidite chemistry protocols [7].
This article is an open access article
Later, this approach was extended to the synthesis of cyclic oligoribonucleotides [8]. Using
distributed under the terms and
this methodology, his group synthesized several small and medium-sized cyclic oligonu-
conditions of the Creative Commons
Attribution (CC BY) license (https://
cleotides, studying their peculiar properties and discovering unusual conformational
creativecommons.org/licenses/by/
motifs, also in collaboration with the research group of Carlos Gonzalez [9–11]. A more
4.0/).

Molecules 2023, 28, 7278. https://doi.org/10.3390/molecules28217278 https://www.mdpi.com/journal/molecules

Molecules 2023, 28, 7278 2 of 5

recent contribution revisited the thiol–maleimide condensation reaction to obtain cyclic

oligonucleotide constructs [12].
If most of his scientific collaborations were with eminent Spanish researchers, rele-
vant was also his international profile, being an invited speaker in many international
conferences, Visiting Professor in many Universities outside Spain and having a number of
fruitful international collaborations, e.g., with Eric T. Kool [13], Daniela Montesarchio [14]
and Keith Fox [15], among others. In his last contribution, always collaborating with
Anna Grandas, he explored the synthesis of oligonucleotide, peptide or PNA conjugates,
successfully obtained via inverse electron-demand Diels−Alder cycloaddition [16].
In all his career, Enrique was deeply involved in the research and promotion of
Nucleic Acid Chemistry. He was indeed an active member of the International Society for
Nucleosides, Nucleotides and Nucleic Acids (IS3NA, www.is3na.org), which organizes
International Roundtables on a biannual basis to present and discuss advances in chemistry
and biology of nucleosides, nucleotides and nucleic acids, as well as of the Spanish Society
for Nucleic Acids and Nucleosides, which gathers researchers every two years in the
Spanish Nucleosides Nucleotides and Nucleic Acids meetings (RANN).
This Special issue comprises a collection of twelve research or review articles prepared
by international experts in nucleic acids, including nucleoside and oligonucleotide syn-
thesis, nucleic acids structural studies, DNA repair, and biophysical characterization of
DNA-targeting ligands, especially G-quadruplex binding drugs.
A novel route for the synthesis of 20 ,30 -dideoxy and 20 ,30 -didehydro nucleosides,
including several anti-HIV drugs such as stavudine, zalcitabine and didanosine, was pre-
sented by the group of Dr. Ferrero and Dr. Fernández (contribution 1) from the University
of Oviedo. Starting from the protection at the 50 -hydroxyl group of the corresponding ri-
bonucleotides followed by the formation of the corresponding 20 ,30 -bisxanthates, a key step
in the synthesis of the target compounds was the radical deoxygenation of the bisxanthates,
successfully realized using environmentally friendly and low-cost reagents.
Phosphorodiamidate morpholino oligomer (PMO) derivatives are extensively used
in exon-skipping strategies for the treatment of Duchenne muscular dystrophy, but the
preparation of these derivatives is not trivial at all. Prof. Caruthers provided a compre-
hensive review on the synthesis and properties of modified morpholino oligonucleotides
developed by his group at the University of Colorado in Boulder (contribution 2). This
work is a masterpiece in the field of nucleic acid chemistry showing the state-of-the art of
phosphoramidite chemistry, nucleoside chemistry and development of novel protecting
groups for oligonucleotide synthesis.
An exceptional development in siRNA therapeutics is the discovery and use of oligonu-
cleotide conjugates carrying trivalent N-acetyl galactosamine (GalNAc) residues. These
oligonucleotides are rapidly internalized via the clathrin-mediated pathway in hepatocytes
due to the presence of an asialoglycoprotein receptor with high affinity for galactose glyco-
proteins and trivalent GalNAc oligonucleotides. Eritja et al. at the IQAC-CSIC in Barcelona
demonstrated that the tetramerization of G-rich oligonucleotides may be a novel and simple
route to obtain the beneficial effects of multivalent N-acetylgalactosamine functionalization
(contribution 3,4).
Meschaninova et al. from Novosibirsk State University described novel methods for
the 50 -functionalization of oligonucleotides through acid labile phosphoramidate linkages
(contribution 5). A wide variety of oligonucleotides 50 -conjugated with ligands, such as
cholesterol, oleylamine, and p-anisic acid, was described. The methodology was success-
fully applied to DNA, RNA, and 20 -O-methyl-RNA oligonucleotides.
The possibility of using enzymes for the preparation of modified oligonucleotides
was addressed by Hollenstein et al. from the University of Paris (contribution 6). In this
work, the enzymatic synthesis of a modified nucleoside triphosphate equipped with a
vancomycin moiety on the nucleobase was described, demonstrating that this nucleotide
analogue is suitable for polymerase-mediated synthesis of modified DNA and compatible
Molecules 2023, 28, 7278 3 of 5

with the SELEX methodology for the production of aptamers suitable to fight bacterial
resistance.
The impact of the duplex-G-quadruplex equilibrium in DNA Base Excision Re-
pair was studied by Sowers et al. from the University of Texas Medical Branch
(contribution 7), suggesting that DNA damage and repair intermediates can alter
duplex-quadruplex equilibrium. To corroborate this hypothesis, the authors used
G-quadruplex stabilizing compounds, such as pyridostatin, modified oligonucleotides
containing uracil, 5-hydroxymethyluracil, 5-fluorouracil, as well as abasic sites as
building blocks inserted into the loop region of a 22-base telomeric repeat sequence
known to form stable and well-characterized G-quadruplex structure.
In addition to G-quadruplex structures formed by G-tetrads, other tetrads can be
formed. These structures found in some constrained oligonucleotides are more frequent
than expected. An excellent review by Gonzalez et al. summarized the present state-of-the-
art on our knowledge on novel non-G-tetrads including homotetrads, as well as major and
minor groove tetrads, emphasizing their peculiar structural features (contribution 8).
Strand-invading approaches using chemically modified oligonucleotides and nucleic
acid mimics capable of unzipping Watson–Crick base pairs of dsDNA targets and forming
new Watson–Crick base pairs between probe strands and the complementary DNA (cDNA)
regions have been explored by Hrdlicka et al. from the University of Idaho (contribution
9). The use of densely modified oligonucleotides with 20 -O-(pyren-1-yl)methyl RNA
pyrimidine building blocks is highly recommended to achieve satisfactory results.
Aptamers are nucleic acid molecules able to selectively recognize several substrates,
including small molecules and proteins, acting in a similar way as antibodies. Liu et al.
analyzed the intrinsic fluorescent properties of DNA for the characterization of the binding
of several model aptamers to their targets, such as cortisol, Hg2+ , adenosine or caffeine (con-
tribution 10). They found that some aptamers may induce changes in intrinsic fluorescence,
but these changes cannot be used for the determination of binding constants.
G-quadruplexes are important non-canonical DNA structures that are present in G-rich
regions such as telomeres and some promoter regions of oncogenes. The polymorphism
of these structures and the possibility of stabilizing them using planar heterocyclic small
molecules is one of the most intense areas of research in nucleic acid chemistry. Dallavalle
et al. from the University of Milan explored the interaction of several G-quadruplex ligands
such as Curaxin, CX 5461, BA41, TPHS 4, Pyridostatin or BMH 21 with a G-quadruplex
sequence found in the PARP1 promoter region (contribution 11). Pyridostatin was found to
be the best binder for this sequence, being able to adapt its planar but flexible conformation
to the dynamic nature of the G-quadruplex, especially the hybrid 3 + 1 G-quadruplex
structure found in the PARP 1 promoter region.
Oliviero et al. studied the interaction of the c-myc oncogene NHE III1 region with the
3-β-D-glucoside of trans-resveratrol (Polydatin) (contribution 12). The experimental and
modelling data show that this compound may be involved in partial end-stacking to the
terminal G-quartet. Moreover, H-bonding interactions between the sugar moiety of the
ligand and deoxynucleotides not included in the G-tetrads are possible.
Expansion of short nucleotide repeats is one of the causes of genetic diseases and is
dramatically crucial for neurological diseases such as amyotrophic lateral sclerosis and
frontal temporal dementia. Wang et al. described the state-of-the art knowledge of the
structural properties of GGGGCC repeats in RNA and their interaction with small molecules
and proteins specifically binding to these repeats (contribution 13).
By collecting in these scientific works this Special Issue, prepared by international
leaders in the fields of chemistry and biochemistry of nucleosides, nucleotides and nucleic
acids, we hope to contribute to advance knowledge on these fascinating molecules and
their almost infinite applications, following Enrique Pedroso’s lifelong commitment and
example.

Conflicts of Interest: The authors declare no conflict of interest.

Molecules 2023, 28, 7278 4 of 5

List of Contributions
1. Martín-Nieves, V.; Sanghvi, Y.S.; Fernández, S.; Ferrero, M. Sustainable protocol for
the synthesis of 20 ,30 -dideoxynucleoside and 20 ,30 -didehydro-20 ,30 -dideoxynucleoside
derivatives. Molecules 2022, 27, 3993.
2. Paul, S.; Caruthers, M.H. Synthesis of backbone-modified morpholino oligonucleotides
using phosphoramidite chemistry. Molecules 2023, 28, 5380.
3. Clua, A.; Grijalvo, S.; Erande, N.; Gupta, S.; Yucius, K.; Gargallo, R.; Mazzini, S.;
Manoharan, M.; Eritja, R. Properties of parallel tetramolecular G-quadruplex car-
rying N-acetylgalactosamine as potential enhancer for oligonucleotide delivery to
hepatocytes. Molecules 2022, 27, 3944.
4. Clua, A.; Grijalvo, S.; Erande, N.; Gupta, S.; Yucius, K.; Gargallo, R.; Mazzini, S.;
Manoharan, M.; Eritja, R. Correction. Clua et al. Properties of parallel tetramolecular
G-quadruplex carrying N-acetylgalactosamine as potential enhancer for oligonu-
cleotide delivery to hepatocytes. Molecules 2023, 28, 98.
5. Kropacheva, N.O.; Golyshkin, A.A.; Vorobyeva, M.A.; Meschaninova, M.I. Conve-
nient solid-phase attachment of small-molecule ligands to oligonucleotides via a
biodegradable acid-labile P-N-bond. Molecules 2023, 28, 1904.
6. Figazzolo, C.; Bonhomme, F.; Saidjalolov, S.; Ethève-Quelquejeu, M.; Hollenstein, M.
Enzymatic synthesis of vancomycin-modified DNA. Molecules 2022, 27, 8927.
7. Sowers, M.L.; Conrad, J.W.; Chang-Gu, B.; Cherryhomes, E.; Hackfeld, L.C.; Sowers,
L.C. DNA base excision repair intermediates influence duplex–quadruplex equilib-
rium. Molecules 2023, 28, 970.
8. Escaja, N.; Mir, B.; Garavís, M.; González, C. Non-G base tetrads. Molecules 2022, 27,
5287.
9. Shepard, C.P.; Emehiser, R.G.; Karmakar, S.; Hrdlicka, P.J. Factors impacting invader-
mediated recognition of double-stranded DNA. Molecules 2023, 28, 127.
10. Lu, C.; Lopez, A.; Zheng, J.; Liu, J. Using the intrinsic fluorescence of DNA to charac-
terize aptamer binding. Molecules 2022, 27, 7809.
11. Mazzini, S.; Princiotto, S.; Artali, R.; Musso, L.; Aviñó, A.; Eritja, R.; Gargallo, R.;
Dallavalle, S. Exploring the interaction of G-quadruplex binders with a (3 + 1) hybrid
G-quadruplex forming sequence within the PARP1 gene promoter region. Molecules
2022, 27, 4792.
12. Greco, F.; Musumeci, D.; Borbone, N.; Falanga, A.P.; D’Errico, S.; Terracciano, M.;
Piccialli, I.; Roviello, G.N.; 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. Molecules 2022, 27,
2997.
13. Liu, X.; Zhao, X.; He, J.; Wang, S.; Shen, X.; Liu, Q.; Wang, S. Advances in the structure
of GGGGCC repeat RNA sequence and its interaction with small molecules and
protein partners. Molecules 2023, 28, 5801.

References
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large-scale synthesis of small oligodeoxyribonucleotides. Tetrahedron Lett. 1990, 31, 6231–6234. [CrossRef]
2. Fernandez-Fomer, D.; Palom, Y.; Ikuta, S.; Pedroso, E.; Eritja, R. Synthesis and characterization of oligodeoxynucleotides
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linked peptide-oligonucleotide hybrids. Bioconjug. Chem. 1997, 8, 785–788. [CrossRef] [PubMed]
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Molecules 2023, 28, 7278 5 of 5

7. Alazzouzi, E.; Escaja, N.; Grandas, A.; Pedroso, E. A straightforward solid-phase synthesis of cyclic oligodeoxyribonucleotides.
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size. Angew. Chem. Int. Ed. 1999, 38, 3654–3657. [CrossRef]
14. Di Fabio, G.; Randazzo, A.; D’Onofrio, J.; Ausín, C.; Pedroso, E.; Grandas, A.; De Napoli, L.; Montesarchio, D. Cyclic phosphate-
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