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Anticipating intramolecular excited-state proton-coupled electron transfer (PCET) process within dinuclear Ir 2 -photocatalytic system via the covalent linkage is seminal, yet challenging. Indeed, the development of various dinuclear complexes is also promising for studying integral photophysics and facilitating applications in catalysis or biology. Herein, this study reports dinuclear [Ir 2 (bis{imidazo-phenanthrolin-2-yl}-hydroquinone)(ppy) 4 ] 2+ (1 2+ ) complex by leveraging both ligand-centered redox property and intramolecular H-bonding for exploring dual excited-state proton-transfer assisted PCET process. The vital role of covalently placed hydroquinone in bridged ligand is investigated as electron-proton transfer (ET-PT) mediator in intramolecular PCET and validated from triplet spin density plot. Moreover, bimolecular photoinduced ET reaction is studied in acetonitrile/water medium, forging the lowest energy triplet charge separated ( 3 CS Phen-Im ) state of 1 2+ with methyl viologen via favorably concerted-PCET pathway. The result indicates strong donor-acceptors coupling, which limits charge recombination and enhances catalytic efficiency. To showcase the potential application, this bioinspired PCET-based photocatalytic platform is studied for phototherapeutics, indicating significant mitochondrial localization and leading to programmed cell death (apoptosis) through futile redox cycling. Indeed, the consequences of effective internalization (via energy-dependent endocytosis), better safety profile, and higher photoinduced antiproliferative activity of 1 2+ compared to Cisplatin, as explored in 3D tumor spheroids, this study anticipates it to be a potential lead compound., (© 2024 The Author(s). Small published by Wiley‐VCH GmbH.)

Red fluorescent protein (RFP)-based fluorescent probes that can selectively interact with specific nucleic acids are of great importance for therapeutic and bioimaging applications. Herein, we have reported the synthesis of RFP chromophores for selective recognition of G-quadruplex nucleic acids in vitro and ex vivo. We identified DFHBI-DM as a fluorescent turn-on probe that binds to the dimeric NG16 parallel quadruplex with superior selectivity and sensitivity over various parallel, antiparallel, and hybrid topologies. The binding of DFHBI-DM to NG16 exhibited excellent photophysical properties, including high binding affinity, large Stokes shift, high photostability, and quantum yield. The MD simulation study supports the 1:1 binding stoichiometry. It confirms the planar conformation of DFHBI-DM , which makes strong binding interactions with a flat quartet of NG16 compared to other antiparallel and hybrid topologies. The cell imaging and MTT assays revealed that DFHBI-DM is a biocompatible and efficient fluorescent probe for intracellular imaging of NG16. Overall, these results demonstrated that DFHBI-DM could be an effective fluorescent G4-stabilizing agent for the dimeric NG16 parallel quadruplex, and it could be a promising candidate for further exploration of bioimaging and therapeutic applications.

In this article, we describe the synthesis of N 3 -methyluridine (m 3 U) and 2'-O-alkyl/2'-fluoro-N 3 -methyluridine (2'-O-alkyl/2'-F-m 3 U) phosphoramidites as well as their incorporation into a 14-mer DNA and RNA oligonucleotide sequence. Synthesis of the 2'-O-alkyl-m 3 U phosphoramidite starts with commercially available uridine to achieve a tritylated m 3 U intermediate, followed by 2'-O-alkylation and finally phosphitylation. Synthesis of the 2'-F-m 3 U phosphoramidite is obtained from a commercially available 2'-F-uridine nucleoside. These phosphoramidite monomers are compatible with DNA and RNA oligonucleotide synthesis using conventional phosphoramidite chemistry. This strategy offers efficient synthetic access to various modifications at the 2'-position of m 3 U that can be employed in numerous nucleic acid-based therapeutic applications, including antisense technologies, small interfering RNAs, CRISPR-Cas9, and aptamers. The data presented in this article are based on our previously published reports. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 2'-O-alkyl-N 3 -methyluridine analogs and their corresponding phosphoramidites Alternate Protocol 1: Synthesis of 2'-O-TBDMS-N 3 -methyluridine and its phosphoramidite Alternate Protocol 2: Synthesis of 2'-fluoro-N 3 -methyluridine and its phosphoramidite Basic Protocol 2: Solid-phase synthesis of N 3 -methyluridine-modified DNA and RNA oligonucleotides., (© 2024 Wiley Periodicals LLC.)

Over the last few decades, chemically modified sugars have been incorporated into nucleic acid-based therapeutics to improve their pharmacological potential. Chemical modification can influence the sugar conformation, Watson-Crick hydrogen (W-C) bonding, and nucleobase stacking interactions, which play major roles in the structural integrity and dynamic properties of nucleic acid duplexes. In this study, we categorized 33 uridine (U*) and cytidine (C*) sugar modifications and calculated their sugar conformational parameters. We also calculated the Watson-Crick hydrogen bond energies of the modified RNA-type base pairs (U*:A and C*:G) using DFT and sSAPT0 methods. The W-C base pairing energy calculations suggested that the South -type modified sugar strengthens the C*:G base pair and weakens the U*:A base pair compared to the unmodified one. In contrast, the North -type sugar modifications form weaker C*:G base pair and marginally stronger U*:A base pair compared to the South -type modified sugars. Moreover, intrastrand base stacking energies were calculated for 15 modifications incorporated at the fourth position in 7-mer non-self-complementary RNA duplexes [(GCAU*GAC) 2 and (GCAC*GAC) 2 ], utilizing molecular dynamics simulation and quantum mechanical (DFT and sSAPT0) methods. The sugar modifications were found to have minimal effect on the intrastrand base-stacking interactions. However, the glycol nucleic acid modification disturbs the intrastrand base-stacking significantly, corroborating the experimental data.

Herein, we have demonstrated that the siRNA activity could be enhanced by incorporating the guide strand in the RISC complex through thermodynamic asymmetry caused by m 3 U-based destabilizing modifications. A nuclease stability study revealed that 2'-OMe-m 3 U and 2'-OEt-m 3 U modifications slightly improved the half-lives of siRNA strands in human serum. In the in vitro gene silencing assay, 2'-OMe-m 3 U modification at the 3'-overhang and cleavage site of the passenger strand in anti-renilla and anti-Bcl-2 siRNA duplexes were well-tolerated and exhibited improved gene silencing activity. However, gene silencing activity was attenuated when these modifications were incorporated at position 3 in the seed region of the antisense strand. The molecular modeling studies using these modifications at the seed region with the MID domain of hAGO2 explained that the 2'-alkoxy group makes steric interactions with the amino acid residues of the hAGO2 protein., Competing Interests: The authors declare no competing financial interest., (© 2024 American Chemical Society.)

In this study, we designed the 4'- C -acetamidomethyl-2'- O -methoxyethyl (4'- C -ACM-2'- O -MOE) uridine and thymidine modifications, aiming to test them into small interfering RNAs. Thermal melting studies revealed that incorporating a single 4'- C -ACM-2'- O -MOE modification in the DNA duplex reduced thermal stability. In contrast, an increase in thermal stability was observed when the modification was introduced in DNA:RNA hybrid and in siRNAs. Thermal destabilization in DNA duplex was attributed to unfavorable entropy, which was mainly compensated by the enthalpy factor to some extent. A single 4'- C -ACM-2'- O -MOE thymidine modification at the penultimate position of the 3'-end of dT 20 oligonucleotides in the presence of 3'-specific exonucleases, snake venom phosphodiesterase (SVPD), demonstrated significant stability as compared to monomer modifications including 2'- O -Me, 2'- O -MOE, and 2'-F. In gene silencing studies, we found that the 4'- C -ACM-2'- O -MOE uridine or thymidine modifications at the 3'-overhang in the passenger strand in combination with two 2'-F modifications exhibited superior RNAi activity. The results suggest that the dual modification is well tolerated at the 3'-end of the passenger strand, which reflects better siRNA stability and silencing activity. Interestingly, 4'- C -ACM-2'- O -MOE-modified siRNAs showed considerable gene silencing even after 96 h posttransfection; it showed that our modification could induce prolonged gene silencing due to improved metabolic stability. Molecular modeling studies revealed that the introduction of the 4'- C -ACM-2'- O -MOE modification at the 3'-end of the siRNA guide strand helps to anchor the strand within the PAZ domain of the hAgo2 protein. The overall results indicate that the 4'- C -ACM-2'- O -MOE uridine and thymidine modifications are promising modifications to improve the stability, potency, and hAgo2 binding of siRNAs.

Herein, we report the synthesis of 2'-O-alkyl/2'-fluoro-N 3 -methyluridine (2'-O-alkyl/2'-F-m 3 U) phosphoramidites and their incorporation in DNA and RNA oligonucleotides. The duplex binding affinity and base discrimination studies showed that all 2'-O-alkyl/2'-F-m 3 U modifications significantly decreased the thermal stability and base-pairing discrimination ability. Serum stability study of dT 20 with 2'-O-alkyl-m 3 U modification exhibited excellent nuclease resistance when incubated with 3'-exonucleases (SVPD) or 5'-exonucleases (PDE-II) as compared to m 3 U, 2'-F, 2'-OMe modified oligonucleotides. MD simulation studies with RNA tetradecamer duplexes illustrated that the m 3 U and 2'-O-methyl-m 3 U modifications reduce the duplex stabilities by disrupting the Watson-Crick hydrogen bonding and base-stacking interactions. Further molecular modelling investigations demonstrated that the 2'-O-propyl-m 3 U modification exhibits steric interactions with amino acid residues in the active site of 3'- and 5'-exonuclease, leading to enhanced stability. These combined data indicate that the 2'-modified-m 3 U nucleotides can be used as a promising tool to enhance the stability, silencing efficiency, and drug-like properties of antisense/siRNA-based therapeutics., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Here, we report vinyl substituted triphenylamine (TPA-alk) fluorescent probe for the rapid and efficient detection of mercury ion (Hg 2+ ) in water and biological environment. TPA-alk detects Hg 2+ selectively over a wide range of competitive metal ions with a blue shift of 43 nm in the UV absorbance spectrum. The detection limit is found to be 0.146 µM (29.2 ppb) with high selectivity over a wide range of competitive metal ions. DFT study explains the blue shift in the UV-vis absorption band of the optical probe upon the addition of Hg 2+ . Cell viability assay illustrates that the probe is biocompatible and it has low cytotoxicity even at its higher concentration. Cell imaging studies demonstrate the efficiency of the TPA-alk probe for the micromolar detection of mercury (II) in live BMG1 cells., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties., (© 2022 The Chemical Society of Japan & Wiley-VCH GmbH.)

The Complementary Learning Systems (CLS) theory provides a powerful framework for considering the acquisition, consolidation, and generalization of new knowledge. We tested this proposed neural division of labor in adults through an investigation of the consolidation and long-term retention of newly learned native vocabulary with post-learning functional neuroimaging. Newly learned items were compared with two conditions: 1) previously known items to highlight the similarities and differences with established vocabulary and 2) unknown/untrained items to provide a control for non-specific perceptual and motor speech output. Consistent with the CLS, retrieval of newly learned items was supported by a combination of regions associated with episodic memory (including left hippocampus) and the language-semantic areas that support established vocabulary (left inferior frontal gyrus and left anterior temporal lobe). Furthermore, there was a shifting division of labor across these two networks in line with the items' consolidation status; faster naming was associated with more activation of language-semantic areas and lesser activation of episodic memory regions. Hippocampal activity during naming predicted more than half the variation in naming retention 6 months later., (© The Author(s) 2021. Published by Oxford University Press.)

Nucleic acid-based therapeutics that control gene expression have been steadily progressing towards achieving their full clinical potential throughout the last few decades. Rapid progress has been achieved in RNAi-based therapy by optimizing high specificity and gene silencing efficiency using chemically modified siRNAs. Since 2018, four siRNA drugs - patisiran, givosiran, lumasiran, and inclisiran, were approved by the US FDA, providing a testament to the promise of RNAi therapeutics. Despite these promising results, safe and efficient siRNA delivery at the target site remains a major obstacle for efficient siRNA-based therapeutics. In this review, we have outlined the synergistic effects of emerging dual ribose modifications, including 2',4'- and 2',5'-modifications, 5'- E/Z- vinylphosphonate, and northern methanocarbacyclic (NMC) modifications that have contributed to drug-like effects in siRNA. These modifications enhance nuclease stability, prolong gene silencing efficiency, improve thermal stability, and exhibit high tissue accumulation. We also highlight the current progress in siRNA clinical trials. This review will help to understand the potential effects of dual ribose modifications and provides alternative ways to use extensive 2'-modifications in siRNA drugs. Moreover, the minimal number of these dual ribose modifications could be sufficient to achieve the desired therapeutic effect. In future, detailed in vivo studies using these dual ribose modifications could help to improve the therapeutic effects of siRNA. Rational design could further open doors for the rapid progress in siRNA therapeutics. [Figure: see text].

RNA interference (RNAi), a gene regulatory process mediated by small interfering RNAs (siRNAs), has made remarkable progress as a potential therapeutic agent against various diseases. However, RNAi is associated with fundamental challenges such as poor systemic delivery and susceptibility to the nucleases. Targeting ligand-bound delivery vehicles has improved the accumulation of drug at the target site, which has resulted in high transfection efficiency and enhanced gene silencing. Recently, folate receptor (FR)-mediated targeted delivery of siRNAs has garnered attention due to their enhanced cellular uptake and high transfection efficiency toward tumor cells. Folic acid (FA), due to its small size, low immunogenicity, high in vivo stability, and high binding affinity toward FRs, has attracted much attention for targeted siRNA delivery. FRs are overexpressed in a large number of tumors, including ovarian, breast, kidney, and lung cancer cells. In this review, we discuss recent advances in FA-mediated siRNA delivery to treat cancers and inflammatory diseases. This review summarizes various FA-conjugated nanoparticle systems reported so far in the literature, including liposome, silica, metal, graphene, dendrimers, chitosan, organic copolymers, and RNA nanoparticles. This review will help in the design and development of potential delivery vehicles for siRNA drug targeting to tumor cells using an FR-mediated approach.

Conversion efforts constitute any attempt to align an individual's behavior or identity with cisgender and heterosexual norms. The majority of empirical literature on conversion efforts focuses on the experiences of White cisgender gay men. Drawing on a review of the literature, archives, and interviews with local community leaders and stakeholders, this article highlights a broader set of conversion strategies targeted toward Black transgender individuals in Memphis, a community at the heart of the civil rights movement. In addition to the role of ex-gay ministries like Love In Action, this investigation produced themes highlighting the roles of Christian organizations promulgating "church hurt," structural violence, and gatekeeping to access affirmative care as forms of conversion. We further describe how lack of inclusion within the lesbian, gay, bisexual, transgender, and queer community, in terms of race, class, and gender identity, has resulted in unequal support for Black transgender individuals and the obscuring of the central role that many transgender individuals, especially those with intersectional marginalized identities, have played in social justice movements. We end with ideas for moving toward affirmation and liberation. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Large Stokes shift (LSS) fluorescent proteins (FPs) exploit excited state proton transfer pathways to enable fluorescence emission from the phenolate intermediate of their internal 4-hydroxybenzylidene imidazolone (HBI) chromophore. An RNA aptamer named Chili mimics LSS FPs by inducing highly Stokes-shifted emission from several new green and red HBI analogues that are non-fluorescent when free in solution. The ligands are bound by the RNA in their protonated phenol form and feature a cationic aromatic side chain for increased RNA affinity and reduced magnesium dependence. In combination with oxidative functionalization at the C2 position of the imidazolone, this strategy yielded DMHBO + , which binds to the Chili aptamer with a low-nanomolar K D . Because of its highly red-shifted fluorescence emission at 592 nm, the Chili-DMHBO + complex is an ideal fluorescence donor for Förster resonance energy transfer (FRET) to the rhodamine dye Atto 590 and will therefore find applications in FRET-based analytical RNA systems., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Since the evolutionary discovery of RNA interference and its utilization for gene knockdown in mammalian cell, a remarkable progress has been achieved in small interfering RNA (siRNA) therapeutics. siRNA is a promising tool, utilized as therapeutic agent against various diseases. Despite its significant potential benefits, safe, efficient, and target oriented delivery of siRNA is one of the major challenges in siRNA therapeutics. This review covers major achievements in clinical trials and targeted delivery of siRNAs using various targeting ligand-receptor pair. Local and systemically administered siRNA drug candidates at various phases in clinical trials are described in this review. This review also provides a deep insight in development of targeted delivery of siRNA. Various targeting ligand-siRNA pair with complexation and conjugation approaches are discussed in this review. This will help to achieve further optimization and development in targeted delivery of siRNAs to achieve higher gene silencing efficiency with lowest siRNA dose availability.

N(2)-Furfuryl-deoxyguanosine (fdG) is carcinogenic DNA adduct that originates from furfuryl alcohol. It is also a stable structural mimic of the damage induced by the nitrofurazone family of antibiotics. For the structural and functional studies of this model N(2)-dG adduct, reliable and rapid access to fdG-modified DNAs are warranted. Toward this end, here we report the synthesis of fdG-modified DNAs using phosphoramidite chemistry involving only three steps. The functional integrity of the modified DNA has been verified by primer extension studies with DNA polymerases I and IV from E. coli. Introduction of fdG into a DNA duplex decreases the Tm by ∼1.6 °C/modification. Molecular dynamics simulations of a DNA duplex bearing the fdG adduct revealed that though the overall B-DNA structure is maintained, this lesion can disrupt W-C H-bonding, stacking interactions, and minor groove hydrations to some extent at the modified site, and these effects lead to slight variations in the local base pair parameters. Overall, our studies show that fdG is tolerated at the minor groove of the DNA to a better extent compared with other bulky DNA damages, and this property will make it difficult for the DNA repair pathways to detect this adduct.

The reduction in the efficacy of therapeutic antibiotics represents a global problem of increasing intensity and concern. Nitrofuran antibiotics act primarily through the formation of covalent adducts at the N(2) atom of the deoxyguanosine nucleotide in genomic DNA. These adducts inhibit replicative DNA polymerases (dPols), leading to the death of the prokaryote. N(2)-furfuryl-deoxyguanosine (fdG) represents a stable structural analog of the nitrofuran-induced adducts. Unlike other known dPols, DNA polymerase IV (PolIV) from E. coli can bypass the fdG adduct accurately with high catalytic efficiency. This property of PolIV is central to its role in reducing the sensitivity of E. coli toward nitrofuran antibiotics such as nitrofurazone (NFZ). We present the mechanism used by PolIV to bypass NFZ-induced adducts and thus improve viability of E. coli in the presence of NFZ. Our results can be used to develop specific inhibitors of PolIV that may potentiate the activity of nitrofuran antibiotics., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Herein, we report the synthesis of 4'-C-aminomethyl-2'-deoxy-2'-fluorouridine, a therapeutically appealing RNA modification. Conformational analysis by DFT calculations and molecular dynamics simulations using trinucleotide model systems revealed that modified sugar adopts C3'-endo conformation. In this conformer, a weak intramolecular C-H···F H-bond between the hydrogen atom of the 4'-C-CH2 group and the F atom at the 2' position is observed. Comparative studies with unmodified, 2'-fluoro-, 2'-O-methyl-, and 4'-C-aminomethyl-2'-O-methyluridine showed the chemical nature of 2'-substituent dictates the sugar puckering of 2',4'-modified nucleotides.

A novel nucleic acid analogue called acyclic (S)-butyl nucleic acid (BuNA) composed of an acyclic backbone containing a phosphodiester linkage and bearing natural nucleobases was synthesized. Next, (S)-BuNA nucleotides were incorporated in DNA strands and their effect on duplex stability and changes in structural conformation were investigated. Circular dichroism (CD), UV-melting and non-denatured gel electrophoresis (native PAGE) studies revealed that (S)-BuNA is capable of making duplexes with its complementary strands and integration of (S)-BuNA nucleotides into DNA duplex does not alter the B-type-helical structure of the duplex. Furthermore, (S)-BuNA oligonucleotides and (S)-BuNA substituted DNA strands were studied as primer extensions by DNA polymerases. This study revealed that the acyclic scaffold is tolerated by enzymes and is therefore to some extent biocompatible.

The dual modified nucleotide 4'-C-aminomethyl-2'-O-methylthymidine 5'-triphosphate was synthesized and enzymatically incorporated into DNA by the thermophilic DNA polymerases Pfu and Therminator III. The dual ribose modification imparted increased exonuclease resistance to DNA compared to the well-known 2'-O-methyl modification.

The linear syntheses of 4'-C-aminomethyl-2'-O-methyl uridine and cytidine nucleoside phosphoramidites were achieved using glucose as the starting material. The modified RNA building blocks were incorporated into small interfering RNAs (siRNAs) by employing solid phase RNA synthesis. Thermal melting studies showed that the modified siRNA duplexes exhibited slightly lower T(m) (∼1 °C/modification) compared to the unmodified duplex. Molecular dynamics simulations revealed that the 4'-C-aminomethyl-2'-O-methyl modified nucleotides adopt South-type conformation in a siRNA duplex, thereby altering the stacking and hydrogen-bonding interactions. These modified siRNAs were also evaluated for their gene silencing efficiency in HeLa cells using a luciferase-based reporter assay. The results indicate that the modifications are well tolerated in various positions of the passenger strand and at the 3' end of the guide strand but are less tolerated in the seed region of the guide strand. The modified siRNAs exhibited prolonged stability in human serum compared to unmodified siRNA. This work has implications for the use of 4'-C-aminomethyl-2'-O-methyl modified nucleotides to overcome some of the challenges associated with the therapeutic utilities of siRNAs.