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 401–500 of 696
- Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World HypothesisEri Kurihara, Sayuri Uchida, Takuya Umehara, Koji Tamura · 2014 · Biology
- The Size of the Internal Loop in DNA Hairpins Influences Their Targeting with Partially Complementary StrandsIztok Prislan, Hui-Ting Lee, Cynthia S. Y. Lee, Luis A. Marky · 2014 · The Journal of Physical Chemistry B
- Nonspecific Hybridization Scaling of Microarray Expression Estimates: A Physicochemical Approach for Chip-to-Chip NormalizationHans Binder, Jan Brücker, Conrad J. Burden · 2009 · The Journal of Physical Chemistry B
- Physical-Chemistry-Based Analysis of Affymetrix Microarray DataThomas M. Heim, Léon-Charles Tranchevent, Enrico Carlon, G. T. Barkema · 2006 · The Journal of Physical Chemistry B
- Thermodynamic Analysis of Duplex Formation of the Heterochiral DNA with l-DeoxyadenosineJ. Kawakami, Kazuhiko Tsujita, N. Sugimoto · 2005 · Analytical Sciences
- Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription ElongationPedro Rafael Costa, Márcio Luís Acencio, Ney Lemke · 2013 · PLoS ONE
- Photoswitching properties of hairpin ODNs with azobenzene derivatives at the loop positionLi Wu, Ya Wu, Hongwei Jin · 2014 · MedChemComm
- Melting Behavior of a DNA Four-Way Junction Using Spectroscopic and Calorimetric TechniquesCarolyn E. Carr, Luis A. Marky · 2017 · Journal of the American Chemical Society
- Transcriptional accuracy modeling suggests two-step proofreading by RNA polymeraseHarriet Mellenius, Måns Ehrenberg · 2017 · Nucleic Acids Research
- Self-assembled nanoparticles for cellular delivery of peptide nucleic acid using amphiphilic N,N,N-trimethyl-O-alkyl chitosan derivativesChundong Liu, Jianhua Wang, Sheng Huang · 2018 · Journal of Materials Science Materials in Medicine
- Structure and Hybridization Properties of Glycine Morpholine Oligomers in Complexes with DNA and RNA: Experimental and Molecular Dynamics StudiesVictor M. Golyshev, Tatyana V. Abramova, Dmitrii V. Pyshnyi · 2019 · The Journal of Physical Chemistry B
- Intrinsic Terminator Prediction and Its Application in Synechococcus sp. WH8102Xiu‐Feng Wan, Dong He Xu · 2005 · Journal of Computer Science and Technology
- Comment on “Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays”Enrico Carlon, Thomas M. Heim, J. Klein Wolterink · 2006 · Physical Review E
- grID: A CRISPR-Cas9 guide RNA Database and Resource for Genome-EditingVinod Jaskula-Ranga, Donald J. Zack · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- MeltR software provides facile determination of nucleic acid thermodynamicsJacob P. Sieg, Sebastian J. Arteaga, Brent M. Znosko, Philip C. Bevilacqua · 2023 · Biophysical Reports
- GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotesTongjun Xiang, Huibao Feng, Xin‐Hui Xing, Chong Zhang · 2025 · BMC Bioinformatics
- Optimizations of SiRNA Design for the Activation of Gene Transcription by Targeting the TATA-Box MotifMiaomiao Fan, Yijun Zhang, Zhuoqiong Huang, Jun Liu, Xuemin Guo, Hui Zhang, Haihua Luo · 2014 · PLoS ONE
- Loop Contributions to the Folding Thermodynamics of DNA Straight Hairpin Loops and PseudoknotsCalliste Reiling, Irine Khutsishvili, Kai Huang, Luis A. Marky · 2015 · The Journal of Physical Chemistry B
- Unfolding Thermodynamics of DNA Intramolecular Complexes Involving Joined Triple- and Double-Helical MotifsIrine Khutsishvili, Sarah Johnson, Hui-Ting Lee, Luis A. Marky · 2009 · Methods in enzymology on CD-ROM/Methods in enzymology
- Synthesis, physicochemical and biochemical studies of anti-IRS-1 oligonucleotides containing carborane and/or metallacarborane modificationAgnieszka B. Olejniczak, Ryszard Kierzek, Eric Wickstrom · 2013 · Journal of Organometallic Chemistry
- Inhibition of Ampicillin-Resistant Bacteria by Novel Mono-DNAzymes and Di-DNAzyme Targeted to β-Lactamase mRNAFei Chen, Zhe Li, Ruijian Wang · 2004 · Oligonucleotides
- Screening the binding potential of quercetin with parallel, antiparallel and mixed G-quadruplexes of human telomere and cancer protooncogenes using molecular docking approachShikhar Tyagi, Sarika Saxena, Priyansh Srivastava · 2020 · SN Applied Sciences
- Sole and Stable RNA Duplexes of G-Rich Sequences Located in the 5′-Untranslated Region of ProtooncogenesSarika Saxena, Daisuke Miyoshi, Naoki Sugimoto · 2010 · Biochemistry
- Kinetic measurement of ribosome motor stalling forceDeepak Kumar Sinha, Upinder S. Bhalla, G. V. Shivashankar · 2004 · Applied Physics Letters
- Effective affinities in microarray dataThomas M. Heim, J. Klein Wolterink, Enrico Carlon · 2006 · Journal of Physics Condensed Matter
- Displacement and dissociation of oligonucleotides during DNA hairpin closure under strainFang-Yuan Ding, S. Cocco, Saurabh Raj, M. Manosas, T. Nguyen, M. M. Spiering, D. Bensimon, J. Allemand, V. Croquette · 2022 · bioRxiv
- An Aptamer-Based Hydrogel Sensing Platform Enabling Low Micromolar Detection of Small Molecules Using Low Sample VolumesMilana Pikula, Yingfu Li, Carlos D. M. Filipe · 2024 · ACS Applied Materials & Interfaces
- Synthesis of 2′-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAsKohei Nomura, Seongjin An, Yoshiaki Kobayashi, Jiro Kondo, Ting Shi, Hirotaka Murase, Kosuke Nakamoto, Yasuaki Kimura, Naoko Abe, Kumiko Ui‐Tei et al. · 2024 · Nucleic Acids Research
- Universal force correlations in an RNA-DNA unzipping experimentKay Jörg Wiese, Mathilde Bercy, Lena Melkonyan, Thierry Bizebard · 2020 · Physical Review Research
- Recognition and unfolding of human telomeric G-quadruplex by short peptide binding identified from the HRDC domain of BLM helicaseTaniya Sharma, Nikita Kundu, Sarvpreet Kaur, Amlan Chakraborty, Aman Kumar Mahto, Rikeshwer Prasad Dewangan, Jadala Shankaraswamy, Sarika Saxena · 2022 · RSC Advances
- DNA Template Dependent Accuracy Variation of Nucleotide Selection in TranscriptionHarriet Mellenius, Måns Ehrenberg · 2015 · PLoS ONE
- Minimal Model of Intrinsic Chirality to Study the Folding Behavior of Helical PolymersChristian R. Boehm, Eugene Michael Terentjev · 2014 · Macromolecules
- Formation of the double helix: a mutational studyMehrdad Majlessi, Michael M. Becker · 2008 · Nucleic Acids Research
- GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid DuplexesDongni Yang, Wenzhao Liu, Xiangyu Deng, Wei Xie, Hu Chen, Zhensheng Zhong, Jie Ma · 2020 · Biophysical Journal
- Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotypeIsrael Martínez-Pérez, Gong Zhang, Zoya Ignatova, Karl-Heinz Zimmermann · 2007 · BMC Bioinformatics
- Optical Antisense Tumor Targeting in Vivo with an Improved Fluorescent DNA Duplex ProbeMinmin Liang, Xinrong Liu, Dengfeng Cheng · 2009 · Bioconjugate Chemistry
- Target-Site Selection for the 10–23 DNAzymeMurray J. Cairns, Lun‐Quan Sun · 2004 · Humana Press eBooks
- General Introduction to In Situ Hybridization Protocol Using Nonradioactively Labeled Probes to Detect mRNAs on Tissue SectionsDaehoon Lee, Shan Xiong, Wen‐Cheng Xiong · 2013 · Methods in molecular biology
- Modeling background intensity in DNA microarraysKyung Myriam Kroll, G. T. Barkema, Enrico Carlon · 2008 · Physical Review E
- Perfectly Complementary Nucleic Acid EnzymesScott T. Kuhns, Gerald F. Joyce · 2003 · Journal of Molecular Evolution
- Elucidating the Role of Groove Hydration on Stability and Functions of Biased DNA Duplexes in Cell-Like Chemical EnvironmentsSaptarshi Ghosh, Shuntaro Takahashi, Tatsuya Ohyama · 2024 · Journal of the American Chemical Society
- Elimination of Off-Target Effect by Chemical Modification of 5′-End of siRNAYasuo Shiohama, Ryosuke Fujita, Maika Sonokawa · 2022 · Nucleic Acid Therapeutics
- Use of a Designed Peptide Library to Screen for Binders to a Particular DNA G-Quadruplex SequenceKeita Kobayashi, Noriko Matsui, Kenji Usui · 2011 · Journal of Nucleic Acids
- In situ Hybridization of Embryos with Antisense RNA ProbesGina Broitman-Maduro, Morris Maduro · 2011 · Methods in cell biology
- Overview of Methods in RNA Nanotechnology: Synthesis, Purification, and Characterization of RNA NanoparticlesFarzin Haque, Peixuan Guo · 2015 · Methods in molecular biology
- Structural Flexibility and the Thermodynamics of Helix Exchange Constrain Attenuation and Allosteric Activation of Hammerhead Ribozyme TRAPsVanvimon Saksmerprome, Donald H. Burke · 2003 · Biochemistry
- Thermodynamics of RNA Secondary Structure FormationTianbing Xia, David H. Mathews, Douglas H. Turner · 1999 · Elsevier eBooks
- Chromatin structure and context-dependent sequence features control prime editing efficiencyKim, Somang, Yuan, Jimmy B., Woods, Wendy S., Newton, Destry A., Perez-Pinera, Pablo, Song, Jun S. · 2023 · Frontiers in Genetics
- Homoduplex to i-motif structural switch exhibited by a cytosine rich strand of the MYH7 heavy chain β gene promoter at physiological pHAnju Singh, Shrikant Kukreti · 2018 · RSC Advances
- siRNAs target sites selection of ezrin and the influence of RNA interference on ezrin expression and biological characters of osteosarcoma cellsXifu Shang, YaoFei Wang, Qichun Zhao, Kerong Wu, Li Xu, XiaoFeng Ji, Rui He, Wenzhi Zhang · 2012 · Molecular and Cellular Biochemistry
- Microfludic Device for Creating Ionic Strength Gradients over DNA Microarrays for Efficient DNA Melting Studies and Assay DevelopmentJesper Petersen, Lena Poulsen, Henrik Birgens · 2009 · PLoS ONE
- Long-Range Cooperativity Due to C5-Propynylation of Oligopyrimidines Enhances Specific Recognition by Uridine of ribo-Adenosine over ribo-GuanosineThomas W. Barnes, Douglas H. Turner · 2001 · Journal of the American Chemical Society
- Strategy for designing specific antisense oligonucleotide sequencesMasato Mitsuhashi · 1997 · Journal of Gastroenterology
- High Temperature, Isothermal Growth Promotes Close Packing and Thermal Stability in DNA-Engineered Colloidal CrystalsHeather A. Calcaterra, Nikhil S. Chellam, Byeongdu Lee, George Chappell Schatz, Chad Alexander Mirkin · 2024 · ACS Nano
- The thermodynamic patterns of eukaryotic genes suggest a mechanism for intron–exon recognitionMarina Nedelcheva‐Veleva, Mihail Sarov, Ivan Yanakiev, Eva Mihailovska, Miroslav Penchev Ivanov, Greta Panova, Stoyno Stoynov · 2013 · Nature Communications
- Recognition of a Flipped Base in a Hairpinloop DNA by a Small PeptideJunji Kawakami, Shinji Okabe, Yoshiatsu Tanabe · 2008 · Nucleosides Nucleotides & Nucleic Acids
- One‐pot synthesis and characterization CdTe:Zn2+ quantum dots and its molecular interaction with calf thymus DNACheng‐Zhang Yang, Linyi Li, Xiaohan Wang · 2017 · Journal of Molecular Recognition
- Uniqueness, Advantages, Challenges, Solutions, and Perspectives in Therapeutics Applying RNA NanotechnologyPeixuan Guo, Farzin Haque, Brent J. Hallahan, Randall D. Reif, Hui Li, Shaoying Wang · 2013 · CRC Press eBooks
- Selection and antitumor activity of anti-Bcl-2 DNAzymesXinhui Yang, Zhi Li, Lu Zhang · 2016 · Biochemical and Biophysical Research Communications
- Specific Inhibition of Interleukin-10 Production in Murine Macrophage-like Cells by Phosphorothioate Antisense OligonucleotidesHidetoshi Arima, Mamiko Takahashi, Yukihiko Aramaki · 1998 · Antisense and Nucleic Acid Drug Development
- Mechanism of oligonucleotide hybridization with the 3′-terminal region of the yeast tRNAPheVladislav Petyuk, Richard Giegé, Valentin V. Vlassov, Зенкова Марина Аркадьевна · 2000 · Molecular Biology
- Universal Force Correlations in an RNA-DNA Unzipping ExperimentKay Jörg Wiese, Lena Melkonyan, Thierry Bizebard · 2019 · HAL
- DNA rehybridization drives product release from Cas9 ribonucleoprotein to enable multiple-turnover cleavageJuan Pan, Megumu Yamada Mabuchi, G. Brett Robb · 2023 · Nucleic Acids Research
- Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of DrosophilaXianhong Zhang, Shao-Bo Liang, Zhengyi Yi et al. · 2024 · Nucleic Acids Research
- Predictability of environment-dependent formation of G-quadruplex DNAs in human mitochondriaLutan Liu, Shuntaro Takahashi, Sarptarshi Ghosh · 2025 · Communications Chemistry
- Using double-stranded DNA probes to promote specificity in target captureBryan A. Baker, Gita Mahmoudabadi, Valeria Tohver Milam · 2012 · Colloids and Surfaces B Biointerfaces
- A computational approach to identify efficient RNA cleaving 10–23 DNAzymesAngela C. Pine, Greg Nicholas Brooke, Antonio De Marco · 2023 · NAR Genomics and Bioinformatics
- Advances in Antisense Oligo Technology for Sustainable Crop ProtectionVishal Patil, Sumit Jangra, Amalendu Ghosh · 2024 · Critical Reviews in Plant Sciences
- Production of Digoxigenin‐Labeled Riboprobes for In Situ Hybridization ExperimentsKristen S. Barratt, Ruth M. Arkell · 2020 · Current Protocols in Mouse Biology
- Global assessment of cross-hybridization for oligonucleotide arrays.Cavan Reilly, Arvind Raghavan, Paul R. Bohjanen · 2006 · PubMed
- Watson–Crick hydrogen bonding of unlocked nucleic acidsNiels Langkjær, Jesper Wengel, Anna Pasternak · 2015 · Bioorganic & Medicinal Chemistry Letters
- Mismatch and G-Stack Modulated Probe Signals on SNP MicroarraysHans Binder, Mario Fasold, Torsten Glomb · 2009 · PLoS ONE
- Limited Use of Cationic Liposomes as Tools to Enhance the Antiherpetic Activities of Oligonucleotides in Vero Cells Infected with Herpes Simplex Virus Type 1Yôko Shôji, Miki Norimatsu, Jingoro Shimada, YUTAKA MIZUSHIMA · 1998 · Antisense and Nucleic Acid Drug Development
- Selection of Chemical Modifications in the siRNA Seed Region That Repress Off-Target EffectYoshiaki Kobayashi, Kengo Miyamoto, Misako Aida, Kumiko Ui‐Tei · 2021 · Methods in molecular biology
- In situ HybridizationChung‐Jui Tsai, Scott A. Harding · 2013 · Methods in cell biology
- Study of the Mechanism of Interaction of Oligonucleotides with the 3′-Terminal Region of tRNAPhe by Computer ModelingYu. N. Vorobjev · 2005 · Molecular Biology
- Invasion of Strongly Binding Oligonucleotides into tRNA StructureVladislav Petyuk, Roman N. Serikov, Vladimir Tolstikov · 2000 · Nucleosides Nucleotides & Nucleic Acids
- Nucleic Acid Hybrids, Formation and Structure ofJames G. Wetmur · 2006 · Encyclopedia of Molecular Cell Biology and Molecular Medicine
- Single-Stranded DNA Recognition of a 24-mer Peptide Derived from RecA ProteinShu‐ichi Nakano, Naoki Sugimoto · 1998 · Bulletin of the Chemical Society of Japan
- Structural basis of Cas12a R-loop propagation on pathway to DNA cleavageIsabel Strohkendl, Catherine Moy, Alexander-Hoi Nguyen, Rick Russell, David Ward Taylor · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Metal Ion-Directed Specific DNA Structures and Their FunctionsToshihiro Ihara, Yusuke Kitamura, Yousuke Katsuda · 2022 · Life
- Hybridization of antisense oligonucleotides with yeast tRNAPhe: factors determining the efficiency of interactionRoman N. Serikov, Vladislav Petyuk, Valentin V. Vlassov · 2002 · Russian Chemical Bulletin
- Atomistic to continuum model for studying mechanical properties of RNA nanotubesShyam R. Badu, Sanjay Prabhakar, Roderick Melnik, Sundeep Singh · 2020 · Computer Methods in Biomechanics & Biomedical Engineering
- Complex dependence of CRISPR-Cas9 binding strength on guide RNA spacer lengthsAset Khakimzhan, David Garenne, Benjamin I. Tickman, Jason T. Fontana, James M. Carothers, Vincent Noireaux · 2021 · Physical Biology
- Algorithms for Probe Selection and DNA Microarray DesignSven Rahmann, Knut Reinert · 2004
- Central Dogma for a Molecular Design Based on DNA: DNB (Databasing/Designable Nanobio) → ENB (Engineering Nanobio) → FNB (Functional Nanobio)Shu‐ichi Nakano, Naoki Sugimoto · 2005 · Chemistry Letters
- A neural network for predicting the stability of RNA/DNA hybrid duplexesLixin Ma, Changmei Cheng, Xiaohong Liu, Yufen Zhao, Anlin Wang, Piet A. Herdewijn · 2004 · Chemometrics and Intelligent Laboratory Systems
- The application of oligonucleotide hybridization model for PCR and microarray optimizationLauris Kaplinski · 2013 · DSpace repository (University of Tartu)
- Nucleic Acid–Metal Ion InteractionsSergei A. Kazakov, Sidney M. Hecht · 2005 · Wiley eBooks
- Folding molecular origami from ribosomal RNAAnastasia Shapiro, Noah Joseph, Nadav Mellul, Almogit Abu-Horowitz, Boaz Mizrahi, Ido Bachelet · 2024 · Journal of Nanobiotechnology
- Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA–RNA HybridsAshkan Fakharzadeh, Jing Qu, Feng Pan, Celeste Sagui, Christopher Roland · 2023 · The Journal of Physical Chemistry B
- Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-culturesJohn D. Hill, Eleftherios Terry Papoutsakis · 2024 · mSystems
- Synthesis of DNA‐Boron Cluster Composites and Assembly into Functional Nanoparticles with Dual, Anti‐EGFR, and Anti‐c‐MYC Oncogene Silencing ActivityKatarzyna Bednarska, Katarzyna Ebenryter‐Olbińska, Gabriela Gajek, Krzysztof Śmiałkowski, Justyna Suwara, Lidia Fiedorowicz, Zbigniew Jan Lesnikowski · 2024 · Chemistry - A European Journal
- Quantitative Effects of the Loop Region on Topology, Thermodynamics, and Cation Binding of DNA G-quadruplexesMinori Nakata, Naoki Kosaka, Keiko Kawauchi, Daisuke Miyoshi · 2024 · ACS Omega
- RNA Nanostructures in Physiological Solutions: Multiscale Modeling and ApplicationsShyam R. Badu, Roderick Melnik, Sanjay Prabhakar · 2015 · Springer proceedings in physics
- Using Planar Phi29 pRNA Three-Way Junction to Control Size and Shape of RNA Nanoparticles for Biodistribution Profiling in MiceFarzin Haque, Congcong Xu, Daniel L. Jasinski · 2017 · Methods in molecular biology
- Investigation of the Melting Behavior of DNA Three-Way Junctions in the Closed and Open StatesCarolyn E. Carr, Luis A. Marky · 2017 · Biophysical Journal
- Transient Circular Dichroism Measurement of the Excited Triplet State of Pristine Hexahelicene in Solution at Room TemperatureMakoto Kuronuma, Takehito Sato, Yasuyuki Araki · 2019 · Chemistry Letters
- Reciprocal Self‐Assembly of Peptide–DNA Conjugates into a Programmable Sub‐10‐nm Supramolecular DeoxyribonucleoproteinMahnseok Kye, Yong‐beom Lim · 2016 · Angewandte Chemie
- Computational Identification of Antisense Oligonucleotides That Rapidly Hybridize to RNAJian‐Ying Wang, Karl Drlica · 2004 · Oligonucleotides