Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
Sugimoto, Naoki, Nakano, Shu-ichi, Katoh, Misa, Matsumura, Akiko, Nakamuta, Hiroyuki, Ohmichi, Tatsuo, Yoneyama, Mari, Sasaki, Muneo·1995·Biochemistry
Cited by (696)
Items 201–300 of 696
- Remarkably Stable Parallel-Stranded Oligonucleotides Containing 5-Methylisocytosine and IsoguanineHiroshi Sugiyama, Shuji Ikeda, Isao Saito · 1996 · Journal of the American Chemical Society
- Association of Short-Strand DNA Oligomers with Guanidinium-Linked Nucleosides. A Kinetic and Thermodynamic StudyAndrei Blaskó, Robert O. Dempcy, Elvira E. Minyat · 1996 · Journal of the American Chemical Society
- Reovirus Protein ςNS Binds in Multiple Copies to Single-Stranded RNA and Shares Properties with Single-Stranded DNA Binding ProteinsAnne Lynn Gillian, Stephen C. Schmechel, Jonathan Livny · 2000 · Journal of Virology
- Contributions of Stacking, Preorganization, and Hydrogen Bonding to the Thermodynamic Stability of Duplexes between RNA and 2′- O -Methyl RNA with Locked Nucleic AcidsElżbieta Kierzek, Anna Pasternak, Karol Pasternak, Zofia Gdaniec, Ilyas Yildirim, Douglas H. Turner, Ryszard Kierzek · 2009 · Biochemistry
- A Cross-Platform Comparison of Affymetrix and Agilent Microarrays Reveals Discordant miRNA Expression in Lung Tumors of c-Raf Transgenic MiceValerio Del Vescovo, Tatiana Meier, Alberto Inga, Michela A. Denti, Juergen Borlak · 2013 · PLoS ONE
- Oligonucleotide Probes for RNA‐Targeted Fluorescence In Situ HybridizationAdam P. Silverman, Eric T. Kool · 2006 · Advances in clinical chemistry
- Oligonucleotide properties determination and primer designing: a critical examination of predictionsS. Chavali, A. Mahajan, Rubina Tabassum, S. Maiti, D. Bharadwaj · 2005 · Bioinform.
- Base Pair Interactions and Hybridization Isotherms of Matched and Mismatched Oligonucleotide Probes on MicroarraysHans Binder, Stephan Preibisch, Toralf Kirsten · 2005 · Langmuir
- New insights into repeat instabilityElizabeth McIvor, Urszula Polak, Марек Напиерала · 2010 · RNA Biology
- Bottom‐Up‐Assembled Nanostar Colloids of Gold Cores and Tubes Derived From Tobacco Mosaic VirusFabian J. Eber, Sabine Eiben, Holger Jeske · 2013 · Angewandte Chemie International Edition
- Magnesium and molecular crowding of the cosolutes stabilize the i‐motif structure at physiological pHSarika Saxena, Savita Joshi, Jadala Shankaraswamy · 2017 · Biopolymers
- Key Concepts and Challenges in Archaeal TranscriptionFabian Blombach, Dorota Matelska, Thomas Fouqueau, Gwenny Cackett, Finn Werner · 2019 · Journal of Molecular Biology
- Controllable self-assembly of RNA dendrimersAshwani Kumar Sharma, Farzin Haque, Fengmei Pi · 2015 · Nanomedicine Nanotechnology Biology and Medicine
- Nearest neighbor parameters for Watson–Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotidesE. Kierzek, D. Mathews, A. Ciesielska, D. Turner, R. Kierzek · 2006 · Nucleic Acids Research
- Computational antisense oligo prediction with a neural network modelAlistair Morgan Chalk, Erik L. L. Sonnhammer · 2002 · Bioinformatics
- Effect of selected aldehydes on the growth and fermentation of ethanologenicEscherichia coliJesus Zaldivar, Alfredo Martı́nez, Lonnie O'Neal Ingram · 1999 · Biotechnology and Bioengineering
- Keeping CRISPR/Cas on-TargetMuhammad Jamal, Faheem Ahmed Khan, Da Lin, Zeshan Habib, Jinxia Dai, Gang Cao · 2016 · Current Issues in Molecular Biology
- Facilitating RNA Structure Prediction with MicroarraysElżbieta Kierzek, Ryszard Kierzek, Douglas H. Turner, Irina E. Catrina · 2005 · Biochemistry
- Thermodynamic dependence of DNA/DNA and DNA/RNA hybridization reactions on temperature and ionic strength.Brian E. Lang, F. Schwarz · 2007 · Biophysical Chemistry
- Efficient fluorescence labeling of a large RNA through oligonucleotide hybridizationGlenna J. Smith, Tobin R. Sosnick, Norbert F. Scherer · 2004 · RNA
- Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein functionElżbieta Kierzek, Ryszard Kierzek, Walter N. Moss · 2008 · Nucleic Acids Research
- Characterization of Intracellular Crowding Environments with Topology-Based DNA Quadruplex SensorsShuntaro Takahashi, Johtaro Yamamoto, Akira Kitamura, Masataka Kinjo, Naoki Sugimoto · 2019 · Analytical Chemistry
- The Influence of Arm Length Asymmetry and Base Substitution on the Activity of the 10-23 DNA EnzymeMurray J. Cairns, Toni M. Hopkins, Craig Witherington · 2000 · Antisense and Nucleic Acid Drug Development
- Molecular Cloning, Expression, and Characterization of a β-Agarase Gene,agaD, from a Marine Bacterium,Vibriosp. Strain PO-303Jinhua Dong, Yutaka Tamaru, Toshiyoshi Araki · 2007 · Bioscience Biotechnology and Biochemistry
- Transfer RNA recognition by aminoacyl-tRNA synthetasesPenny J. Beuning, Karin Musier‐Forsyth · 1999 · Biopolymers
- Single-molecule force spectroscopy of toehold-mediated strand displacementAndreas Walbrun, Tianhe Wang, Michael Matthies · 2024 · Nature Communications
- Influence of Substrate Composition on the Helicase Activity of Transcription Termination Factor Rho: Reduced Processivity of Rho Hexamers during Unwinding of RNA–DNA Hybrid RegionsCéline Walmacq, A. Rachid Rahmouni, Marc Boudvillain · 2004 · Journal of Molecular Biology
- In-silico Design of DNA Oligonucleotides: Challenges and ApproachesM. Hendling, I. Barišić · 2019 · Computational and Structural Biotechnology Journal
- Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybridsJiahui Zhang, Ashkan Fakharzadeh, Feng Pan, Christopher Roland, Celeste Sagui · 2020 · Nucleic Acids Research
- Minimum length requirement of the alignment domain of human telomerase RNA to sustain catalytic activity in vitroGérald Gavory · 2002 · Nucleic Acids Research
- Multi-stringency wash of partially hybridized 60-mer probes reveals that the stringency along the probe decreases with distance from the microarray surfaceLena Poulsen, Martin Jensen Søe, Detlef Snakenborg · 2008 · Nucleic Acids Research
- A review of statistical methods for preprocessing oligonucleotide microarraysZhijin J. Wu · 2009 · Statistical Methods in Medical Research
- Nucleic Acid Unwinding by Hepatitis C Virus and Bacteriophage T7 Helicases Is Sensitive to Base Pair StabilityIlker Donmez, Vaishnavi Rajagopal, Yong‐Joo Jeong, Smita S. Patel · 2007 · Journal of Biological Chemistry
- Adsorption models of hybridization and post-hybridization behaviour on oligonucleotide microarraysConrad J. Burden, Yvonne Pittelkow, Susan R. Wilson · 2006 · Journal of Physics Condensed Matter
- Guide-target mismatch effects on dCas9–sgRNA binding activity in living bacterial cellsHuibao Feng, Jiahui Guo, Tianmin Wang, Chong Zhang, Xin‐Hui Xing · 2020 · Nucleic Acids Research
- MELTING, a flexible platform to predict the melting temperatures of nucleic acidsM. Dumousseau, Nicolas Rodriguez, N. Juty, N. Le Novère · 2012 · BMC Bioinformatics
- CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning networkJialiang Sun, Jun Hai Guo, Jian Liu · 2024 · PLoS Computational Biology
- An emergent understanding of strand displacement in RNA biologyHong Bo Fan, Petr Šulc · 2019 · Journal of Structural Biology
- A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2′-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexesAnna Pasternak, Elżbieta Kierzek, Karol Pasternak, Douglas H. Turner, Ryszard Kierzek · 2007 · Nucleic Acids Research
- d-Xylose Isomerase from a Marine Bacterium, Vibrio sp. Strain XY-214, and d-Xylulose Production from β-1,3-XylanYoshiaki Umemoto, Toshiyuki Shibata, Toshiyoshi Araki · 2011 · Marine Biotechnology
- Natural antisense RNA/target RNA interactions: Possible models for antisense oligonucleotide drug designNicholas Delihas, Steven E. Rokita, Ping Zheng · 1997 · Nature Biotechnology
- Reciprocal Self‐Assembly of Peptide–DNA Conjugates into a Programmable Sub‐10‐nm Supramolecular DeoxyribonucleoproteinMahnseok Kye, Yong‐beom Lim · 2016 · Angewandte Chemie International Edition
- Development of thermodynamic models for simulating probe dissociation profiles in fluorescence in situ hybridizationLutfu Safak Yilmaz, Daniel R. Noguera · 2006 · Biotechnology and Bioengineering
- Thermodynamic prediction of RNA-DNA duplex-forming regions in the human genome.J. Huppert · 2008 · Molecular Biosystems
- Noncanonical Structures and Their Thermodynamics of DNA and RNA Under Molecular CrowdingNaoki Sugimoto · 2014 · International review of cytology
- 2 – Thermodynamics of RNA Secondary Structure FormationT. Xia, D. Mathews, D. Turner · 2001 · RNA
- Bistability of an In Vitro Synthetic Autoregulatory SwitchPakpoom Subsoontorn, Jongmin Kim, Erik Winfree · 2011 · arXiv (Cornell University)
- G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibrationMario Fasold, Peter Florian Stadler, Hans Binder · 2010 · BMC Bioinformatics
- Prediction of melting temperatures in fluorescencein situhybridization (FISH) procedures using thermodynamic modelsSílvia Fontenete, Nuno Guimarães, Jesper Wengel, Nuno F. Azevedo · 2015 · Critical Reviews in Biotechnology
- Effects of Polyethylene Glycol on DNA Duplex Stability at Different NaCl ConcentrationsHisae Tateishi Karimata, Shu‐ichi Nakano, Naoki Sugimoto · 2007 · Bulletin of the Chemical Society of Japan
- Cloning and Characterization of a β-1,4-Mannanase 5C Possessing a Family 27 Carbohydrate-Binding Module from a Marine Bacterium,Vibriosp. Strain MA-138Megumi Tanaka, Yoshiaki Umemoto, Hidenori OKAMURA · 2009 · Bioscience Biotechnology and Biochemistry
- Induced tRNA Import into Human Mitochondria: Implication of a Host Aminoacyl-tRNA-SynthetaseA. Gowher, Alexandre Smirnov, I. Tarassov, N. Entelis · 2013 · PLoS ONE
- A Small Post-Translocation Energy Bias Aids Nucleotide Selection in T7 RNA Polymerase TranscriptionJin Hui Yu, GEORGE F. OSTER · 2012 · Biophysical Journal
- Biochemical Characterization of the RNA Helicase UPF1 Involved in Nonsense-Mediated mRNA DecayFrancesca Fiorini, Fabien Bonneau, Hervé Le Hir · 2012 · Methods in enzymology on CD-ROM/Methods in enzymology
- Conformational Flexibility Influences Degree of Hydration of Nucleic Acid HybridsSmritimoy Pramanik, Satoru Nagatoishi, Sarika Saxena, Jhimli Bhattacharyya, Naoki Sugimoto · 2011 · The Journal of Physical Chemistry B
- Software to Determine Optimal Oligonucleotide Sequences Based on Hybridization Simulation DataDavid L. Hyndman, Allan Cooper, S. Pruzinsky · 1996 · BioTechniques
- Human Telomerase RNA Template Sequence Is a Determinant of Telomere Repeat Extension RateWilliam C. Drosopoulos, Roberto DiRenzo, Vinayaka R. Prasad · 2005 · Journal of Biological Chemistry
- Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid proteinKlara Post, Besik I. Kankia, Swathi Gopalakrishnan, Victoria Yang, Elizabeth M. Cramer, Pilar H. Saladores, Robert J. Gorelick, Jianhui Guo, Karin Musier‐Forsyth, Judith G. Levin · 2009 · Nucleic Acids Research
- Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in DictyosteliumGue Su Chang, Angelika Anna Noegel, Travis N. Mavrich, Rolf Müller, Lynn Tomsho, Elissa Ward, Marius Felder, Cizhong Jiang, Ludwig Eichinger, Gernot Glöckner et al. · 2012 · Genome Research
- ASOptimizer: Optimizing antisense oligonucleotides through deep learning for IDO1 gene regulationGyeongjo Hwang, Mincheol Kwon, Dongjin Seo, Dae Hoon Kim, Daehwan Lee, Ki‐Won Lee, Eunyoung Kim, Mingeun Kang, Jin‐Hyeob Ryu · 2024 · Molecular Therapy — Nucleic Acids
- Programmable Computational RNA Droplets Assembled via Kissing-Loop InteractionHirotake Udono, Min‐Zhi Fan, Yoko Saito · 2024 · ACS Nano
- Identification of a 35S U4/U6.U5 tri-small nuclear ribonucleoprotein (tri-snRNP) complex intermediate in spliceosome assemblyZhe Chen, Bin Gui, Yu Zhang, Guojia Xie, Wanjin Li, Shumeng Liu, Bosen Xu, Chongyang Wu, Lin He, Jianguo Yang et al. · 2017 · Journal of Biological Chemistry
- Profiled support vector machines for antisense oligonucleotide efficacy predictionGustau Camps‐Valls, Alistair Morgan Chalk, Antonio José Serrano-López · 2004 · BMC Bioinformatics
- Effect of divalent cations and cytosine protonation on thermodynamic properties of intermolecular DNA double and triple helicesPeng Wu, Yasunori Kawamoto, Hideyuki Hara · 2002 · Journal of Inorganic Biochemistry
- Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplexYu-mi Ueda, Yu-ki Zouzumi, Atsushi Maruyama, Shu‐ichi Nakano, Naoki Sugimoto, Daisuke Miyoshi · 2016 · Science and Technology of Advanced Materials
- Bisbenzimidazole to benzobisimidazole: from binding B-form duplex DNA to recognizing different modes of telomereG-quadruplexJing Huang, Guorui Li, Zhiguo Wu, Zhibin Song, Yangyang Zhou, Liang Shuai, Xiaocheng Weng, Xiang Zhou, Guang‐Fu Yang · 2009 · Chemical Communications
- Kinetic Property of Bulged Helix Formation: Analysis of Kinetic Behavior Using Nearest-Neighbor ParametersTatsuo Ohmichi, Hiroyuki Nakamuta, Kyohko Yasuda · 2000 · Journal of the American Chemical Society
- Tiny Molecular Beacons for in vivo mRNA DetectionDiana P. Bratu, Irina E. Catrina, Salvatore A. E. Marras · 2011 · Methods in molecular biology
- A CRISPR/Cas12a-assisted in vitro diagnostic tool for identification and quantification of single CpG methylation sitesJeanne E. van Dongen, Johanna Theodora Wilhelmina Berendsen, Jan C. T. Eijkel, Loes Irene Segerink · 2021 · Biosensors and Bioelectronics
- Isolation and Expression of the xynB Gene and Its Product, XynB, a Consistent Component of the Clostridium cellulovorans CellulosomeSung Ok Han, Hideaki Yukawa, Masayuki Inui · 2004 · Journal of Bacteriology
- "Hook"-calibration of GeneChip-microarrays: Theory and algorithmHans Binder, Stephan Preibisch · 2008 · Algorithms for Molecular Biology
- Emerging role of RNA•DNA hybrids inC9orf72-linked neurodegenerationJiou Wang, Aaron R. Haeusler, Eric A.J. Simko · 2015 · Cell Cycle
- Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”N. Sugimoto, T. Endoh, Shuntaro Takahashi, Hisae Tateishi-Karimata · 2021 · Bulletin of the Chemical Society of Japan
- PCR Primer DesignDavid L. Hyndman, Masato Mitsuhashi · 2003 · Humana Press eBooks
- Use of Deoxyribozymes in RNA ResearchScott K. Silverman, Dana A. Baum · 2009 · Methods in enzymology on CD-ROM/Methods in enzymology
- Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variantsQiong Liu, Jiang Zhou, Shengli Li, Yinfeng Li, Yingfei Wan, Zhenyu Hu, Shimeng Ma, Zhen Zou, Ronghua Yang · 2025 · Nucleic Acids Research
- AIoptamer: Artificial Intelligence-Driven Aptamer Optimization Pipeline for Targeted Therapeutics in HealthcareTushar Gupta, Priyanka Sharma, Sheeba Malik · 2025 · Molecular Pharmaceutics
- Dynamic DNA-controlled "stop-and-go" assembly of well-defined protein domains on RNA-scaffolded TMV-like nanotubes.Angela Schneider, Fabian J. Eber, Nana L Wenz, Klara Altintoprak, H. Jeske, Sabine Eiben, C. Wege · 2016 · Nanoscale
- Initiation of New DNA Strands by the Herpes Simplex Virus-1 Primase-Helicase Complex and Either Herpes DNA Polymerase or Human DNA Polymerase αNisha A. Cavanaugh, Robert D. Kuchta · 2008 · Journal of Biological Chemistry
- Sustainable development of a surface-functionalized mesoporous aluminosilicate with ultra-high ion exchange efficiencyPejman Hadi, Chao Ning, James D. Kubicki · 2016 · Inorganic Chemistry Frontiers
- Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide designZhijie Lu, David H. Mathews · 2008 · Nucleic Acids Research
- Design and analysis of mismatch probes for long oligonucleotide microarraysYe Deng, Z. He, J. V. Van Nostrand, J. Zhou · 2008 · BMC Genomics
- Effect of metal ions and sequence of deoxyribozymes on their RNA cleavage activityN. Sugimoto, Y. Okumoto, T. Ohmichi · 1999 · Journal of the Chemical Society Perkin Transactions 2
- Intermittent Transcription Dynamics for the Rapid Production of Long Transcripts of High FidelityMartin Depken, Juan M. R. Parrondo, Stephan W. Grill · 2013 · Cell Reports
- R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. HydeSidrit Uruci, Calvin Shun Yu Lo, David Lee Wheeler, Nitika Taneja · 2021 · International Journal of Molecular Sciences
- Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditionsSaptarshi Ghosh, Shuntaro Takahashi, Dipanwita Banerjee, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi‐Karimata, Naoki Sugimoto · 2023 · Nucleic Acids Research
- Unleashing inkjet-printed nanostructured electrodes and battery-free potentiostat for the DNA-based multiplexed detection of SARS-CoV-2 genesMarianna Rossetti, Chawin Srisomwat, Massimo Urban, Giulio Rosati, Gabriel Maroli, Hatice Gödze Yaman Akbay, Orawon Chailapakul, Arben Merkoçi · 2024 · Biosensors and Bioelectronics
- The Presence of an RNA:DNA Hybrid That Is Prone to Slippage Promotes Termination by T7 RNA PolymeraseVadim Molodtsov, Michael Anikin, William T. McAllister · 2014 · Journal of Molecular Biology
- Computational biology of RNA interactionsChristoph Dieterich, Peter Florian Stadler · 2012 · Wiley Interdisciplinary Reviews - RNA
- Modular and Chemically Responsive Oligonucleotide “Bonds” in Nanoparticle SuperlatticesStacey N. Barnaby, Ryan V. Thaner, Michael B. Ross · 2015 · Journal of the American Chemical Society
- Transcript Slippage and RecodingMichael Anikin, Vadim Molodtsov, Dmitry Temiakov, William T. McAllister · 2009 · Nucleic acids and molecular biology
- LNA-Modified Primers Drastically Improve Hybridization to Target RNA and Reverse TranscriptionAgata Frątczak, Ryszard Kierzek, Elżbieta Kierzek · 2009 · Biochemistry
- Interactions in Oligonucleotide Hybrid Duplexes on MicroarraysHans Binder, Toralf Kirsten, Ivo L. Hofacker · 2004 · The Journal of Physical Chemistry B
- DNA Complexes Containing Joined Triplex and Duplex Motifs: Melting Behavior of Intramolecular and Bimolecular Complexes with Similar SequencesHui-Ting Lee, Irine Khutsishvili, Luis A. Marky · 2009 · The Journal of Physical Chemistry B
- Systematic evaluation of single mismatch stability predictors for fluorescence in situ hybridizationLutfu Safak Yilmaz, Lindsey Bergsven, Daniel R. Noguera · 2008 · Environmental Microbiology
- Folding of Intramolecular DNA Hairpin Loops: Enthalpy−Entropy Compensations and Hydration ContributionsDionisios Rentzeperis, Ronald A. Shikiya, Souvik Maiti, James Ho, Luis A. Marky · 2002 · The Journal of Physical Chemistry B
- Cell-type-specific transcriptomics in chimeric models using transcriptome-based masksFélix Naef · 2005 · Nucleic Acids Research
- Versatile Method for the Site‐Specific Modification of DNA with Boron Clusters: Anti‐Epidermal Growth Factor Receptor (EGFR) Antisense Oligonucleotide CaseKatarzyna Ebenryter‐Olbińska, Damian Kaniowski, Milena Sobczak · 2017 · Chemistry - A European Journal
- NUPACK: Computational Nucleic Acid Analysis and DesignM. Fornace, Ji-Ning Huang, C. Newman, Avinash Nanjundiah, Nicholas J. Porubsky, Marshall B. Pierce, N. Pierce · 2026 · ACS Synthetic Biology
- Binding of Short Oligonucleotides to RNA: Studies of the Binding of Common RNA Structural Motifs to Isoenergetic MicroarraysElżbieta Kierzek · 2009 · Biochemistry