Differential stability of 2′F-ANA•RNA and ANA•RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility

Hybrids of RNA with arabinonucleic acids 2′F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other biophysical methods together with state-of-the-art theoretical calculations on a fully modified 10-mer hybrid duplex. Comparison between the solution structure of 2′F-ANA•RNA and ANA•RNA hybrids indicates that the increased binding affinity of 2′F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (2′F–purine H8) which contrasts with unfavorable 2′-OH–nucleobase steric interactions in the case of ANA. While both 2′F-ANA and ANA strands maintained conformations in the southern/eastern sugar pucker range, the 2′F-ANA strand’s structure was more compatible with the A-like structure of a hybrid duplex. No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANA•RNA duplex showed lower uptake of counterions than its 2′F-ANA•RNA counterpart. Finally, while the two hybrid duplexes are of similar rigidities, 2′F-ANA single strands may be more suitably preorganized for duplex formation. Thus the dramatically increased stability of 2′F-ANA•RNA and ANA•RNA duplexes is caused by differences in at least four areas, of which structure and pseudohydrogen bonding are the most important

G-quadruplexes with (4n - 1) guanines in the G-tetrad core : formation of a G-triad·water complex and implication for small-molecule binding

G-quadruplexes are non-canonical structures of nucleic acids, in which guanine bases form planar G-tetrads (G·G·G·G) that stack on each other in the core of the structure. G-quadruplexes generally contain multiple times of four (4n) guanines in the core. Here, we study the structure of G-quadruplexes with only (4n - 1) guanines in the core. The solution structure of a DNA sequence containing 11 guanines showed the formation of a parallel G-quadruplex involving two G-tetrads and one G-triad with a vacant site. Molecular dynamics simulation established the formation of a stable G-triad·water complex, where water molecules mimic the position of the missing guanine in the vacant site. The concept of forming G-quadruplexes with missing guanines in the core broadens the current definition of G-quadruplex-forming sequences. The potential ability of such structures to bind different metabolites, including guanine, guanosine and GTP, in the vacant site, could have biological implications in regulatory functions. Formation of this unique binding pocket in the G-triad could be used as a specific target in drug design.MOE (Min. of Education, S’pore)Published versio

Structural Effects of Incorporation of 2'‐Deoxy‐2'2'‐Difluorodeoxycytidine (Gemcitabine) in A‐ and B‐Form Duplexes

We report the structural effect of 2'‐deoxy‐2',2'‐difluorocytidine (dFdC) insertions in the DNA strand of a DNA : RNA hybrid duplex and in a self‐complementary DNA : DNA duplex. In both cases, the modification slightly destabilizes the duplex and provokes minor local distortions that are more pronounced in the case of the DNA : RNA hybrid. Analysis of the solution structures determined by NMR methods show that dFdC is an adaptable derivative that adopts North type sugar conformation when inserted in pure DNA, or a South sugar conformation in the context of DNA : RNA hybrids. In this latter context, South sugar pucker favors the formation of a 2'F⋅⋅H8 attractive interaction with a neighboring purine, which compensates the destabilizing effect of base pair distortions. These interactions share some features with pseudohydrogen bonds described previously in other nucleic acids structures with fluorine modified sugars.This investigation was supported by research grants from the Ministerio de Ciencia e Innovación (BFU2017‐89707‐P, BFU2017‐84415‐R and PID2019‐107158GB‐I00), Piano de Sostegno alla Ricerca 2020‐Linea2 azione B (Defens), Agència de Gestió d′Ajuts Universitaris i de Recerca (AGAUR) Ref. 2017SGR114. We acknowledge the ICTS NANBIOSIS oligonucleotide synthesis platform (U29) from CIBER‐BBN support, and the “Manuel Rico” NMR laboratory (LMR), a node of the ICTS R‐LRB. C. C. acknowledges the FPI contract.Peer reviewe

Structural Effects of Incorporation of 2'‐Deoxy‐2'2'‐Difluorodeoxycytidine (Gemcitabine) in A‐ and B‐Form Duplexes

We report the structural effect of 2'‐deoxy‐2',2'‐difluorocytidine (dFdC) insertions in the DNA strand of a DNA : RNA hybrid duplex and in a self‐complementary DNA : DNA duplex. In both cases, the modification slightly destabilizes the duplex and provokes minor local distortions that are more pronounced in the case of the DNA : RNA hybrid. Analysis of the solution structures determined by NMR methods show that dFdC is an adaptable derivative that adopts North type sugar conformation when inserted in pure DNA, or a South sugar conformation in the context of DNA : RNA hybrids. In this latter context, South sugar pucker favors the formation of a 2'F⋅⋅H8 attractive interaction with a neighboring purine, which compensates the destabilizing effect of base pair distortions. These interactions share some features with pseudohydrogen bonds described previously in other nucleic acids structures with fluorine modified sugars.This investigation was supported by research grants from the Ministerio de Ciencia e Innovación (BFU2017‐89707‐P, BFU2017‐84415‐R and PID2019‐107158GB‐I00), Piano de Sostegno alla Ricerca 2020‐Linea2 azione B (Defens), Agència de Gestió d′Ajuts Universitaris i de Recerca (AGAUR) Ref. 2017SGR114. We acknowledge the ICTS NANBIOSIS oligonucleotide synthesis platform (U29) from CIBER‐BBN support, and the “Manuel Rico” NMR laboratory (LMR), a node of the ICTS R‐LRB. C. C. acknowledges the FPI contract.Peer reviewe

Estableciendo "puentes" entre la Universidad y el tejido social madrileño : cómo los estudiantes de la Asignatura Ciudad y Urbanismo pueden colaborar en la búsqueda de soluciones urbanísticas a históricas reclamaciones vecinales en el entorno de Puente de Vallecas

Publicación de los trabajos elaborados por los estudiantes del curso 2022/23 de la asignatura Ciudad y Urbanismo (35001304) de la Escuela Técnica Superior de Arquitectura de la Universidad Politécnica de Madrid en el marco de un proyecto de Aprendizaje-Servicio y reflexiones sobre el proceso tanto de los agentes sociales que formaron parte del mismo, como de los profesores que ha participado en la docencia