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Investigation of the Structural Basis for Thermodynamic Stabilities of Tandem GU Mismatches: Solution Structure of (rGAGGUCUC)2 by Two-Dimensional NMR and Simulated Annealing,
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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An all atom force field for simulations of proteins and nucleic acids
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Sequence-dependent DNA Structure
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NMR of macromolecules: A practical approach
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Principles of Nucleic Acid Structure
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Observation of spin-diffusion in biomolecules by three-dimensional NOE-NOE spectroscopy
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Phosphorus-31 NMR Principles and Applications
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Evaluating Hydrogen Bonds and Base Stacking of Single, Tandem and Terminal GU Mismatches in RNA with a Mesoscopic Model
inferred← citeshttps://doi.org/10.1021/acs.joc.2c00812openalex-snapshot
DNA with Purine–Purine Base Pairs: Size and Position of Isoguanine and 8-Aza-7-deazaisoguanine Clickable Residues Control the Molecular Recognition of Guanine and 5-Aza-7-deazaguanine
inferred← citeshttps://doi.org/10.1021/acs.joc.3c01370openalex-snapshot
Purine DNA Constructs Designed to Expand the Genetic Code: Functionalization, Impact of Ionic Forms, and Molecular Recognition of 7-Deazaxanthine–7-Deazapurine-2,6-diamine Base Pairs and Their Purine Counterparts
inferred← citeshttps://doi.org/10.1021/acs.joc.4c00982openalex-snapshot
7-Deazapurine and Pyrimidine Nucleoside and Oligonucleotide Cycloadducts Formed by Inverse Diels–Alder Reactions with 3,6-Di(pyrid-2-yl)-1,2,4,5-tetrazine: Ethynylated and Vinylated Nucleobases for Functionalization and Impact of Pyridazine Adducts on DNA Base Pair Stability and Mismatch…
inferred← citeshttps://doi.org/10.1021/acs.joc.5b00040openalex-snapshot
Duplex DNA and DNA–RNA Hybrids with Parallel Strand Orientation: 2′-Deoxy-2′-fluoroisocytidine, 2′-Deoxy-2′-fluoroisoguanosine, and Canonical Nucleosides with 2′-Fluoro Substituents Cause Unexpected Changes on the Double Helix Stability
inferred← citeshttps://doi.org/10.1021/acs.joc.6b01498openalex-snapshot
7-Deaza-2′-deoxyguanosine: Selective Nucleobase Halogenation, Positional Impact of Space-Occupying Substituents, and Stability of DNA with Parallel and Antiparallel Strand Orientation
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5b06970openalex-snapshot
Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b07369openalex-snapshot
Photophysical Characterization of Enhanced 6-Methylisoxanthopterin Fluorescence in Duplex DNA
inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b00556openalex-snapshot
Formation of a DNA Mini-Dumbbell with a Quasi-Type II Loop
inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b00818openalex-snapshot
Relative Populations of Some Tautomeric Forms of 2′-Deoxyguanosine-5-Fluorouridine Mismatch
inferred← citeshttps://doi.org/10.1021/acschembio.0c00735openalex-snapshot
Base Pairing and Functional Insights into N 3 -Methylcytidine (m 3 C) in RNA
inferred← citeshttps://doi.org/10.1021/acschembio.6b00147openalex-snapshot
Small Molecule Recognition and Tools to Study Modulation of r(CGG)exp in Fragile X-Associated Tremor Ataxia Syndrome
inferred← citeshttps://doi.org/10.1021/acschembio.7b00108openalex-snapshot
Nature’s Selection of Geranyl Group as a tRNA Modification: The Effects of Chain Length on Base-Pairing Specificity
inferred← citeshttps://doi.org/10.1021/acsomega.3c07563openalex-snapshot
Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability
inferred← citeshttps://doi.org/10.1021/acssynbio.6b00224openalex-snapshot
Biophysics of Artificially Expanded Genetic Information Systems. Thermodynamics of DNA Duplexes Containing Matches and Mismatches Involving 2-Amino-3-nitropyridin-6-one (Z) and Imidazo[1,2-a]-1,3,5-triazin-4(8H)one (P)
inferred← citeshttps://doi.org/10.1021/bc020024qopenalex-snapshot
Oligonucleotides Incorporating 7-(Aminoalkynyl)-7-deaza-2‘-deoxyguanosines: Duplex Stability and Phosphodiester Hydrolysis by Exonucleases
inferred← citeshttps://doi.org/10.1021/bc900386wopenalex-snapshot
Binding of Europium(III) to a Non-Nucleosidic Phenanthroline Linker in DNA
inferred← citeshttps://doi.org/10.1021/bi011033+openalex-snapshot
C5-(1-Propynyl)-2‘-deoxy-Pyrimidines Enhance Mismatch Penalties of DNA:RNA Duplex Formation
inferred← citeshttps://doi.org/10.1021/bi047561dopenalex-snapshot
Determining the Origin of the Stabilization of DNA by 5-Aminopropynylation of Pyrimidines
inferred← citeshttps://doi.org/10.1021/bi048079yopenalex-snapshot
Solution Structure of an RNA Internal Loop with Three Consecutive Sheared GA Pairs,
inferred← citeshttps://doi.org/10.1021/bi048213eopenalex-snapshot
Folding Thermodynamics and Kinetics of YNMG RNA Hairpins: Specific Incorporation of 8-Bromoguanosine Leads to Stabilization by Enhancement of the Folding Rate
inferred← citeshttps://doi.org/10.1021/bi049168dopenalex-snapshot
Factors Affecting Thermodynamic Stabilities of RNA 3 × 3 Internal Loops
inferred← citeshttps://doi.org/10.1021/bi051409+openalex-snapshot
Facilitating RNA Structure Prediction with Microarrays
inferred← citeshttps://doi.org/10.1021/bi052060topenalex-snapshot
Consecutive GA Pairs Stabilize Medium-Size RNA Internal Loops
inferred← citeshttps://doi.org/10.1021/bi0524464openalex-snapshot
An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA,
inferred← citeshttps://doi.org/10.1021/bi0605787openalex-snapshot
The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from Its Structure in Crystals of 50S Ribosomal Subunits,
inferred← citeshttps://doi.org/10.1021/bi061350mopenalex-snapshot
NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs,
inferred← citeshttps://doi.org/10.1021/bi062169gopenalex-snapshot
Probing the Role of a Secondary Structure Element at the 5‘- and 3‘-Splice Sites in Group I Intron Self-Splicing: The Tetrahymena L-16 Sca I Ribozyme Reveals a New Role of the G·U Pair in Self-Splicing
inferred← citeshttps://doi.org/10.1021/bi100393ropenalex-snapshot
Nuclear Magnetic Resonance Structure of the Prohead RNA E-Loop Hairpin,
inferred← citeshttps://doi.org/10.1021/bi101470nopenalex-snapshot
Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters
inferred← citeshttps://doi.org/10.1021/bi101521popenalex-snapshot
Consecutive Terminal GU Pairs Stabilize RNA Helices
inferred← citeshttps://doi.org/10.1021/bi101724hopenalex-snapshot
Molecular Recognition of 6′-N-5-Hexynoate Kanamycin A and RNA 1x1 Internal Loops Containing CA Mismatches
inferred← citeshttps://doi.org/10.1021/bi200710mopenalex-snapshot
Effects of a Protecting Osmolyte on the Ion Atmosphere Surrounding DNA Duplexes
inferred← citeshttps://doi.org/10.1021/bi3001227openalex-snapshot
Thermodynamic Characterization of RNA 2 × 3 Nucleotide Internal Loops
inferred← citeshttps://doi.org/10.1021/bi3002709openalex-snapshot
Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters
inferred← citeshttps://doi.org/10.1021/bi3010347openalex-snapshot
The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/bi3013005openalex-snapshot
Kinetics and Thermodynamics of DNA, RNA, and Hybrid Duplex Formation
inferred← citeshttps://doi.org/10.1021/bi4008275openalex-snapshot
Effect of Sodium Ions on RNA Duplex Stability
inferred← citeshttps://doi.org/10.1021/bi500611jopenalex-snapshot
Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA
inferred← citeshttps://doi.org/10.1021/bi700736fopenalex-snapshot
Non-Nearest-Neighbor Dependence of the Stability for RNA Bulge Loops Based on the Complete Set of Group I Single-Nucleotide Bulge Loops
inferred← citeshttps://doi.org/10.1021/bi701024wopenalex-snapshot
Thermodynamic Characterization of RNA Duplexes Containing Naturally Occurring 1 × 2 Nucleotide Internal Loops
inferred← citeshttps://doi.org/10.1021/bi7020876openalex-snapshot
Thermodynamic Characterization of the Complete Set of Sequence Symmetric Tandem Mismatches in RNA and an Improved Model for Predicting the Free Energy Contribution of Sequence Asymmetric Tandem Mismatches
inferred← citeshttps://doi.org/10.1021/bi800210topenalex-snapshot
The Dynamic Structural Basis of Differential Enhancement of Conformational Stability by 5′- and 3′-Dangling Ends in RNA
inferred← citeshttps://doi.org/10.1021/bi800471zopenalex-snapshot
Thermodynamic Characterization of Naturally Occurring RNA Single Mismatches with G-U Nearest Neighbors
inferred← citeshttps://doi.org/10.1021/bi801594kopenalex-snapshot
3′ Terminal Nucleotides Determine Thermodynamic Stabilities of Mismatches at the Ends of RNA Helices
inferred← citeshttps://doi.org/10.1021/bi8019405openalex-snapshot
A CA+ Pair Adjacent to a Sheared GA or AA Pair Stabilizes Size-Symmetric RNA Internal Loops
inferred← citeshttps://doi.org/10.1021/bi9002056openalex-snapshot
Contributions of Stacking, Preorganization, and Hydrogen Bonding to the Thermodynamic Stability of Duplexes between RNA and 2′- O -Methyl RNA with Locked Nucleic Acids
inferred← citeshttps://doi.org/10.1021/bi901264vopenalex-snapshot
Binding of Short Oligonucleotides to RNA: Studies of the Binding of Common RNA Structural Motifs to Isoenergetic Microarrays
inferred← citeshttps://doi.org/10.1021/bi901506fopenalex-snapshot
Chemical Synthesis of LNA-2-thiouridine and Its Influence on Stability and Selectivity of Oligonucleotide Binding to RNA
inferred← citeshttps://doi.org/10.1021/bi901541jopenalex-snapshot
Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots
inferred← citeshttps://doi.org/10.1021/bi9809425openalex-snapshot
Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs
inferred← citeshttps://doi.org/10.1021/cb400875uopenalex-snapshot
Targeting the r(CGG) Repeats That Cause FXTAS with Modularly Assembled Small Molecules and Oligonucleotides
inferred← citeshttps://doi.org/10.1021/ic3004245openalex-snapshot
Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA
inferred← citeshttps://doi.org/10.1021/ic501484popenalex-snapshot
Selective Binding of Zn2+ Complexes to Human Telomeric G-Quadruplex DNA
inferred← citeshttps://doi.org/10.1021/jacs.0c00768openalex-snapshot
Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing
inferred← citeshttps://doi.org/10.1021/jp068732mopenalex-snapshot
Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs Are Replaced by isoG−isoC Pairs
inferred← citeshttps://doi.org/10.1021/jp312154dopenalex-snapshot
Effects of Salt, Polyethylene Glycol, and Locked Nucleic Acids on the Thermodynamic Stabilities of Consecutive Terminal Adenosine Mismatches in RNA Duplexes
inferred← citeshttps://doi.org/10.1021/jp404550aopenalex-snapshot
Modeling Stopped-Flow Data for Nucleic Acid Duplex Formation Reactions: The Importance of Off-Path Intermediates
inferred← citeshttps://doi.org/10.1021/jp506703gopenalex-snapshot
Interplay of LNA and 2′- O -Methyl RNA in the Structure and Thermodynamics of RNA Hybrid Systems: A Molecular Dynamics Study Using the Revised AMBER Force Field and Comparison with Experimental Results
inferred← citeshttps://doi.org/10.1021/mp5007008openalex-snapshot
Improved Design of PPRHs for Gene Silencing
inferred← citeshttps://doi.org/10.1021/tx000040gopenalex-snapshot
Differential Destabilization of the DNA Oligonucleotide Double Helix by a T·G Mismatch, 3,N4-Ethenocytosine, 3,N4-Ethanocytosine, or an 8-(Hydroxymethyl)-3,N4-ethenocytosine Adduct Incorporated into the Same Sequence Contexts
inferred← citeshttps://doi.org/10.1021/tx990088yopenalex-snapshot
Sequence-Dependent Repair of Synthetic AP Sites in 15-mer and 35-mer Oligonucleotides: Role of Thermodynamic Stability Imposed by Neighbor Bases
inferred← citeshttps://doi.org/10.1038/nbt0897-751openalex-snapshot
Natural antisense RNA/target RNA interactions: Possible models for antisense oligonucleotide drug design
inferred← citeshttps://doi.org/10.1038/s41467-022-28817-4openalex-snapshot
Secondary structure prediction for RNA sequences including N6-methyladenosine
inferred← citeshttps://doi.org/10.1038/s41589-025-02025-9openalex-snapshot
A Ψ–Ψ codon–anticodon pairing in nonsense suppression and translational recoding
inferred← citeshttps://doi.org/10.1038/s41598-017-12844-zopenalex-snapshot
Influence of mismatched and bulged nucleotides on SNP-preferential RNase H cleavage of RNA-antisense gapmer heteroduplexes
inferred← citeshttps://doi.org/10.1038/s41598-018-36620-9openalex-snapshot
A systematic study on the influence of thermodynamic asymmetry of 5′-ends of siRNA duplexes in relation to their silencing potency
inferred← citeshttps://doi.org/10.1039/a808769eopenalex-snapshot
Synthesis of oligonucleotides containing pyrazolo[3,4-d ]pyrimidines: The influence of 7-substituted 8-aza-7-deazaadenines on the duplex structure and stability
inferred← citeshttps://doi.org/10.1039/b200077fopenalex-snapshot
Modified purine nucleosides as dangling ends of DNA duplexes: the effect of the nucleobase polarizability on stacking interactions
inferred← citeshttps://doi.org/10.1039/b205734dopenalex-snapshot
Fluoroaromatic universal bases in peptide nucleic acids
inferred← citeshttps://doi.org/10.1039/b309229aopenalex-snapshot
Fluorescence detection of guanine–adenine transition by a hydrogen bond forming small compound
inferred← citeshttps://doi.org/10.1039/b409155hopenalex-snapshot
An analogue of adenine that forms an “A:T” base pair of comparable stability to G:C
inferred← citeshttps://doi.org/10.1039/b510444kopenalex-snapshot
Stabilization of tandem dG–dA base pairs in DNA-hairpins: replacement of the canonical bases by 7-deaza-7-propynylpurines
inferred← citeshttps://doi.org/10.1039/b510846bopenalex-snapshot
Expanding functionality of RNA: synthesis and properties of RNA containing imidazole modified tandem G–U wobble base pairs
inferred← citeshttps://doi.org/10.1039/c0cc04091fopenalex-snapshot
Pyrimidine–pyrimidine base pairs stabilized by silver( i ) ions
inferred← citeshttps://doi.org/10.1039/c2ob06606hopenalex-snapshot
Parallel-stranded DNA: Enhancing duplex stability by the ‘G-clamp’ and a pyrrolo-dC derivative
inferred← citeshttps://doi.org/10.1039/c5cc07479gopenalex-snapshot
Synthesis and base pairing studies of geranylated 2-thiothymidine, a natural variant of thymidine
inferred← citeshttps://doi.org/10.1039/c6ob02560aopenalex-snapshot
Mercury II -mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents
inferred← citeshttps://doi.org/10.1039/d3ob00093aopenalex-snapshot
Synthesis of folate-labeled siRNAs from a folate derivative phosphoramidite
inferred← citeshttps://doi.org/10.1046/j.1432-1033.2002.02970.xopenalex-snapshot
Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation
inferred← citeshttps://doi.org/10.1073/pnas.0337462100openalex-snapshot
Uptake and antifungal activity of oligonucleotides in Candida albicans
inferred← citeshttps://doi.org/10.1073/pnas.172391199openalex-snapshot
Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing
inferred← citeshttps://doi.org/10.1073/pnas.2112496119openalex-snapshot
Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting
inferred← citeshttps://doi.org/10.1074/jbc.273.50.33406openalex-snapshot
Correlation between Sequence-dependent Glycosylase Repair and the Thermal Stability of Oligonucleotide Duplexes Containing 1,N 6-Ethenoadenine
inferred← citeshttps://doi.org/10.1074/jbc.m109.078790openalex-snapshot
Structural Diversity of Triplet Repeat RNAs
inferred← citeshttps://doi.org/10.1074/jbc.m111.239509openalex-snapshot
Biophysical Analysis of Influenza A Virus RNA Promoter at Physiological Temperatures
inferred← citeshttps://doi.org/10.1074/jbc.m115.655092openalex-snapshot
Evidence That Antibiotics Bind to Human Mitochondrial Ribosomal RNA Has Implications for Aminoglycoside Toxicity
inferred← citeshttps://doi.org/10.1080/07328319908044635openalex-snapshot
Incorporation of 2′-Deoxysangivamycin in DNA Duplexes: The Conversion of a Pyrrolo[2, 3-d]Pyrimidine Nitrile to a Carboxamide upon Oligonucleotide Deprotection
inferred← citeshttps://doi.org/10.1080/15257770.2022.2105354openalex-snapshot
Substituent effects on indole universal bases in DNA
inferred← citeshttps://doi.org/10.1080/15257770008033037openalex-snapshot
The Nonenzymatic Hydrolysis of Oligoribonucleotides VII. Structural Elements Affecting Hydrolysis
inferred← citeshttps://doi.org/10.1080/15257770008045448openalex-snapshot
Fluorescence Properties and Base Pair Stability of Oligonucleotides Containing 8-Aza-7-deaza-2′-deoxyisoinosine or 2′-Deoxyisoinosine
inferred← citeshttps://doi.org/10.1080/15257779908043087openalex-snapshot
7-Deaza-2′-deoxyinosine: A Stable Nucleoside with the Ambiguous Base Pairing Properties of 2′-Deoxyinosine
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