Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8‐oxo‐7,8‐dihydropurine, and 8‐bromopurine analogues within A‐form duplexes of RNA
Sign Up to like & getrecommendations! Published in 2020 at "Biopolymers"
DOI: 10.1002/bip.23410
Abstract: Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function.… read more here.
Keywords: pairing abilities; corresponding oxo; base pairing; base ... See more keywords
Cyano Modification on Uridine Decreases Base‐Pairing Stability and Specificity through Neighboring Disruption in RNA Duplex
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DOI: 10.1002/cbic.201800399
Abstract: 5‐Cyanomethyluridine (cnm5U) and 5‐cyanouridine (cn5U), the two uridine analogues, were synthesized and incorporated into RNA oligonucleotides. Base‐pairing stability and specificity studies in RNA duplexes indicated that cnm5U slightly decreased the stability of the duplex but… read more here.
Keywords: rna; base pairing; pairing stability; base ... See more keywords
DNA Base Pairing-Inspired Supramolecular Nanodrug Camouflaged by Cancer-Cell Membrane for Osteosarcoma Treatment.
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DOI: 10.1002/smll.202202337
Abstract: Osteosarcoma (OS) is one of the most common bone malignant tumors which mainly develops in adolescents. Although neoadjuvant chemotherapy has improved the prognosis of patients, numerous chemotherapeutic challenges still limit their use. Here, inspired by… read more here.
Keywords: cell; cell membrane; base pairing; cancer cell ... See more keywords
Interrogation of Base Pairing of the Spiroiminodihydantoin Diastereomers Using the α-Hemolysin Latch.
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DOI: 10.1021/acs.biochem.6b01175
Abstract: Spiroiminodihydantoin (Sp) is a hyperoxidized form of guanine (G) resulting from oxidation by reactive oxygen species. The lesion is highly mutagenic, and the stereocenter renders the two isomers with distinct behaviors in chemical, spectroscopic, enzymatic,… read more here.
Keywords: base pairing; hemolysin latch; base; base pairs ... See more keywords
Alchemical Free-Energy Calculations of Watson–Crick and Hoogsteen Base Pairing Interconversion in DNA
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DOI: 10.1021/acs.jctc.2c00848
Abstract: Hoogsteen (HG) base pairs have a transient nature and can be structurally similar to Watson–Crick (WC) base pairs, making their occurrence and thermodynamic stability difficult to determine experimentally. Herein, we employed the restrain–free-energy perturbation–release (R-FEP-R)… read more here.
Keywords: base pairing; free energy; watson crick; hoogsteen base ... See more keywords
Photoisomerizable Guanosine Derivative as a Probe for DNA Base-Pairing in Langmuir Monolayers
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DOI: 10.1021/acs.langmuir.9b00429
Abstract: Mixtures of azo-functionalized amphiphilic derivatives of guanosine and of amphiphilic derivatives of other DNA nucleobases were deposited at an air–water interface and repeatedly irradiated with light of 340 and 440 nm wavelengths. The consequent switching… read more here.
Keywords: langmuir monolayers; probe; photoisomerizable guanosine; pairing langmuir ... See more keywords
Nature's Selection of Geranyl Group as a tRNA Modification: The Effects of Chain Length on Base-Pairing Specificity.
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DOI: 10.1021/acschembio.7b00108
Abstract: The recently discovered geranyl modification on the 2-thio position of wobble U34 residues in tRNAGlu, tRNALys, and tRNAGln in several bacteria has been found to enhance the U:G pairing specificity and reduce the frameshifting error… read more here.
Keywords: chain length; pairing specificity; geranyl; base pairing ... See more keywords
Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets
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DOI: 10.1021/acsomega.7b00291
Abstract: Chemical modifications of 2′-O-methyl (2′-OMe) and locked nucleic acid (LNA) of the nucleotides in the seed region (positions 2–8) of the small interfering RNA (siRNA) guide strand significantly reduced seed-matched (SM) off-target effects. The siRNA… read more here.
Keywords: target effects; seed; target; seed region ... See more keywords
DNA Condensation-Inspired Assembly of DNA Nanotubes into Reversible Superstructures: A Base Pairing-Orthogonal Way to Create Rings, Bundles, or Vast Networks
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DOI: 10.1021/jacs.5c10921
Abstract: By offering exquisite programmability, sequence-specific DNA self-assembly is the foundation of structural DNA nanotechnology but necessitates custom-designed DNA strands. Finding assembly principles orthogonal to base pairing is thus desirable not only to organize DNA in… read more here.
Keywords: dna nanotubes; base pairing; dna condensation; inspired assembly ... See more keywords
Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of the American Society for Mass Spectrometry"
DOI: 10.1021/jasms.2c00137
Abstract: DNA nanotechnology has been employed to develop devices based on i-motif structures. The protonated cytosine-cytosine base pairs that stabilize i-motif conformations are favored under slightly acidic conditions. This unique property has enabled development of the… read more here.
Keywords: nanotechnology; base pairs; base pairing; halogenation ... See more keywords
An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode
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DOI: 10.1038/s41467-024-54918-3
Abstract: By targeting the essential viral RNA-dependent RNA polymerase (RdRP), nucleoside analogs (NAs) have exhibited great potential in antiviral therapy for RNA virus-related diseases. However, most ribose-modified NAs do not present broad-spectrum features, likely due to… read more here.
Keywords: base pairing; rna; adenosine analog; base ... See more keywords