Thermodynamics and NMR of Internal G·T Mismatches in DNA

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Items 201–300 of 531

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   M. Kiviniemi, J. Nurmi, H. Turpeinen, T. Lövgren, J. Ilonen · 2003 · Clinical Biochemistry
2. Homogeneous amplification and mutation scanning of the p53 gene using fluorescent melting curves.
   Haleigh Millward, W. Samowitz, C. Wittwer, P. Bernard · 2002 · Clinical Chemistry
3. Internal transcribed spacer primer evaluation for vascular plant metabarcoding
   Andreas Kolter, B. Gemeinholzer · 2021 · Metabarcoding and Metagenomics
4. Design of allele‐specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem
   Hidenobu Yaku, T. Yukimasa, S. Nakano, N. Sugimoto, H. Oka · 2008 · Electrophoresis
5. pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA.
   Sanjaya C. Abeysirigunawardena, Christine S. Chow · 2008 · RNA: A publication of the RNA Society
6. DNA-mounted self-assembly: New approaches for genomic analysis and SNP detection
   Elena V. Bichenkova, Zhaolei Lang, Xuan Yu, Candelaria Rogert, Kenneth Thomas Douglas · 2010 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
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   P. Buček, R. Gargallo, A. Kudrev · 2010 · Analytica Chimica Acta
8. Free energy estimation of short DNA duplex hybridizations
   Dan Tulpan, Mirela Andronescu, Serge Leger · 2010 · BMC Bioinformatics
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   Jing Yang, Dandan Li, Jie Wang, Rui Zhang, Jin-Ming Li · 2022 · Critical reviews in clinical laboratory sciences
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    X. Xia, H. Liu, D. Choi, J. Noh · 2017 · Microbial Ecology
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    J. Bullard, Jennifer C. Williams, Wendy K. Acker, C. Jacobi, N. Janjić, C. McHenry · 2002 · Journal of Biological Chemistry
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    Owen J. Marshall · 2007 · Methods in molecular biology
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    A. Cumberworth, D. Frenkel, Aleks Reinhardt · 2022 · Nano letters (Print)
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    Xin Zhao, Lei Li · 2013 · Genomics, Proteomics & Bioinformatics
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    Kasper K. Karlsen, A. Pasternak, Troels Bundgaard Jensen, J. Wengel · 2012 · ChemBioChem
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    Hui-Hsien Chou · 2010 · BMC Bioinformatics
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    Vinhthuy T. Phan, M. Garzon · 2009 · Natural Computing
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    A. Fuglsang · 2003 · Gene
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    K. Pierce, L. Wangh · 2007 · Methods in Molecular Medicine
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    N. Sugimoto, Y. Okumoto, T. Ohmichi · 1999 · Journal of the Chemical Society Perkin Transactions 2
21. Chemical equilibria studies using multivariate analysis methods
    J. Jaumot, R. Eritja, R. Gargallo · 2011 · Analytical and Bioanalytical Chemistry
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    Li-Li Wang, A. Gaigalas, J. Blasic, M. Holden · 2004 · Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy
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    Xian-Bin Tian, G. Shearer · 2001 · Gene
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    Hao Tang, Michael Harte · 2021 · Genes
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    R. Kalendar, Akmaral Baidyussen, D. Serikbay, L. Zotova, G. Khassanova, M. Kuzbakova, S. Jatayev, Yin-Gang Hu, Carly Schramm, P. Anderson et al. · 2021 · Frontiers in Plant Science
26. A dual amplification strategy for DNA detection combining bio-barcode assay and metal-enhanced fluorescence modality.
    Zhenpeng Zhou, Tian Li, Hong-Duan Huang, Yang Chen, Feng Liu, C. Huang, Na Li · 2014 · Chemical Communications
27. Preferential base pairing modes of T·T mismatches
    Guoyun He, Chun-Kit Kwok, Sik L. Lam · 2011 · FEBS Letters
28. Design and analysis of mismatch probes for long oligonucleotide microarrays
    Ye Deng, Z. He, J. V. Van Nostrand, J. Zhou · 2008 · BMC Genomics
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    Yu-Huei Cheng · 2016 · IEEE/ACM Transactions on Computational Biology & Bioinformatics
30. Calculating sequence-dependent melting stability of duplex DNA oligomers and multiplex sequence analysis by graphs.
    Albert S. Benight, P. Pančoška, R. Owczarzy, Peter M. Vallone, Jaroslav Nešetřil, Peter V. Riccelli · 2001 · Methods in Enzymology
31. Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation
    Guan-Qing Liu, Tao Zhang · 2021 · International Journal of Molecular Sciences
32. A Guide to Using FASTPCR Software for PCR, In Silico PCR, and Oligonucleotide Analysis.
    R. Kalendar · 2021 · Methods in molecular biology
33. Strand displacement in DNA-based materials systems
    Bryan Baker, Gita Mahmoudabadi, V. Milam · 2013 · Soft Matter
34. Origins of sequence selectivity in homologous genetic recombination: insights from rapid kinetic probing of RecA-mediated DNA strand exchange.
    A. M. Lee, Jie Xiao, S. Singleton · 2006 · Journal of Molecular Biology
35. Oligo Design: a computer program for development of probes for oligonucleotide microarrays.
    K. Herold, A. Rasooly · 2003 · BioTechniques
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    I. Stoev, Tian-Yang Cao, A. Caciagli, Jiaming Yu, C. Ness, Ren-Bao Liu, Rini Ghosh, Thomas O'Neill, Dong-Sheng Liu, E. Eiser · 2019 · Soft Matter
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    Angela Schneider, Fabian J. Eber, Nana L Wenz, Klara Altintoprak, H. Jeske, Sabine Eiben, C. Wege · 2016 · Nanoscale
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    J. Araque, Athanasios Panagiotopoulos, M. Robert · 2011 · Journal of Chemical Physics
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    S. R. Schlesinger, Mieke Lahousse, T. O. Foster, Sung-Kun Kim · 2011 · Pharmaceuticals
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    L. Valle, Daniela Amicizia, Sabrina Bacilieri, F. Banfi, R. Riente, P. Durando, L. Sticchi, R. Gasparini, C. Esposito, G. Icardi et al. · 2006 · Journal of preventive medicine and hygiene
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    H. Allawi, Hai-Jing Li, T. Sander, A. Aslanukov, V. Lyamichev, A. Blackman, S. Elagin, Yi-Wei Tang · 2006 · Journal of Clinical Microbiology
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    Peng Wu, Naoki Sugimoto · 2000 · Nucleic Acids Research
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    Andrea L. Mast, M. D. de Arruda · 2006 · Methods in molecular biology
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    M. Fornace, Ji-Ning Huang, C. Newman, Avinash Nanjundiah, Nicholas J. Porubsky, Marshall B. Pierce, N. Pierce · 2026 · ACS Synthetic Biology
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    Zhaoxi Sun, Xiao-Hui Wang, J. Zhang, Qiao-Le He · 2019 · Physical Chemistry, Chemical Physics - PCCP
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    Xutiange Han, Erchie Wang, Yixiao Cui, Yikai Lin, Hui Chen, Ran An, Xing-Guo Liang, M. Komiyama · 2019 · Electrophoresis
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    Aron A. Shoara, Oren Reinstein, Okty Abbasi Borhani, Taylor R Martin, Sladjana Slavkovic, Zachary R. Churcher, Philip E. Johnson · 2017 · Biochimie
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    B. Allred, Magdalena Gebala, D. Herschlag · 2017 · Journal of the American Chemical Society
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    P. Licínio, J. O. Guerra · 2007 · Biophysical Journal
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    Gregory L. Moore, C. Maranas · 2002 · Journal of Theoretical Biology
51. 6.03 – Thermodynamics of RNA Secondary Structure Formation
    T. Xia, D. Mathews, D. Turner · 1999 · Elsevier eBooks
52. A fast machine-learning-guided primer design pipeline for selective whole genome amplification
    Jane A. Dwivedi-Yu, Zachary J. Oppler, Matthew W. Mitchell, Yun S. Song, Dustin Brisson · 2022 · bioRxiv
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    N. Sugimoto, T. Endoh, Shuntaro Takahashi, Hisae Tateishi-Karimata · 2021 · Bulletin of the Chemical Society of Japan
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    B. Petersen, Michael S. Liu, R. Podicheti, Albert Ying-Po Yang, Chelsea A. Simpson, Chris Hemmerich, D. Rusch, J. C. van Kessel · 2021 · bioRxiv
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    S. Archer, N. Shirokikh, T. Preiss · 2015 · Current Protocols in Human Genetics
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    Miller, S., Jones, L. E., Giovannitti, K., Piper, D., Serra, M. J. · 2008 · Nucleic Acids Research
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    Shailender Nagpal, Mazen W. Karaman, M. M. Timmerman, Vincent V. Ho, B. Pike, J. Hacia · 2004 · Nucleic Acids Research
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    M. Szemes, C. Schoen · 2003 · Analytical Biochemistry
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    R. Kalendar, Timofey V. Tselykh, B. Khassenov, E. Ramanculov · 2017 · Methods in molecular biology
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    Michael D. McCann, Geoff Lim, M. Manni, Julie Estes, Kelly A Klapec, G. Frattini, Robert J. Knarr, Jessica L. Gratton, Martin J. Serra · 2011 · RNA: A publication of the RNA Society
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    Nathan Oken Hodas, D. Aalberts · 2004 · Nucleic Acids Research
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    P. Bernard, A. Reiser, G. Pritham · 2001
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    I. Garanina, G. Fisunov, V. Govorun · 2018 · Frontiers in Microbiology
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    Amalia Ávila Figueroa, S. Delaney · 2010 · Journal of Biological Chemistry
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    J. A. Rose, R. Deaton · 2000 · International Workshop on DNA-Based Computers
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    Hong Bo Fan, Jocelyn Y. Kishi, Ryan Nicholas Delgado, Jiyoun Jeong, Sinem K. Saka, Hanquan Su, Constance L. Cepko, Peng Yin · 2023 · Nature Methods
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    Georg Mohr, Sean Yoon-Seo Kang, S. Park, Yidan Qin, Jacob K. Grohman, Jun Yao, J. Stamos, A. Lambowitz · 2018 · Journal of Molecular Biology
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    Felix Francis, M. Dumas, R. Wisser · 2017 · Scientific Reports
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    Ping-Fang Liu, Jacob A. Theruvathu, Agus Darwanto, V. Lao, T. Pascal, W. Goddard, L. Sowers · 2008 · Journal of Biological Chemistry
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    A. Kameda, Masahito Yamamoto, H. Uejima, M. Hagiya, K. Sakamoto, A. Ohuchi · 2005 · Natural Computing
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    Shin-Hee Kim, H. An, K. Field, Cheng-I Wei, J. B. Velazquez, B. Ben-Gigirey, M. Morrissey, R. J. Price, T. Pitta · 2003 · Journal of Food Protection
72. ssDNA templated assembly of oligonucleotides and bivalent naphthalene guests
    Pim G. A. Janssen, Niels J. M. Brankaert, Xavier Vila, A. Schenning · 2010
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    S. Chavali, A. Mahajan, Rubina Tabassum, S. Maiti, D. Bharadwaj · 2005 · Bioinform.
74. Secondary Structure Design of Multi-state DNA Machines Based on Sequential Structure Transitions
    H. Uejima, M. Hagiya · 2003 · DNA
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    D. Cullinan, F. Johnson, C. R. de los Santos · 2000 · Journal of Molecular Biology
76. Thermodynamic and structural characterization of 2'-nitrogen-modified RNA duplexes.
    John W. Pham, I. Radhakrishnan, E. Sontheimer · 2004 · Nucleic Acids Research
77. Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex
    A. Altun, Miquel Garcia-Ratés, F. Neese, G. Bistoni · 2021 · Chemical Science
78. Nearest-neighbour transition-state analysis for nucleic acid kinetics
    N. Rejali, Felix Ye, Aisha M Zuiter, Caroline C Keller, C. Wittwer · 2021 · Nucleic Acids Research
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    U. Jakobsen, S. Vogel · 2016 · Organic and biomolecular chemistry
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    G. Tamulaitis, M. Zaremba, R. Szczepanowski, M. Bochtler, V. Šikšnys · 2008 · Nucleic Acids Research
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    James Brown, T. Brown, K. Fox · 2003 · Biochemical Journal
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    A. Cumberworth, Aleks Reinhardt · 2025 · Chemical Society Reviews
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    D. Taylor, Samuel R Davidson, Lu-Lu Qian · 2021 · Journal of the American Chemical Society
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    Y. Jakubek, D. Cutler · 2012 · BMC Genomics
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    K. Loo, L. Griffiths, S. Gan · 2012 · BMC Medical Genetics
86. Design of an optimal allele-specific oligonucleotide probe for the efficient discrimination of a thermodynamically stable (G x T) mismatch.
    Fausto Lucarelli, G. Marrazza, M. Mascini · 2007 · Analytica Chimica Acta
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    Andreas E. Müller, R. Atkinson, Robert B. Sandoval, R. Jorgensen · 2007 · Plant Cell Reports
88. DNA Sequencing by Hybridization Using Semi-Degenerate Bases
    F. Preparata, J. Oliver · 2004 · J. Comput. Biol.
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    J. G. Rudolph, S. White, Cara L. Sokolsky, D. Bozak, C. Mazzanti, Robert Lipsky, D. Goldman · 2002 · Genetic Testing
90. Structural factors determining DNA length limitations in conformation‐sensitive mutation detection methods
    P. Kozłowski, W. Krzyzosiak · 2005 · Electrophoresis
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    Gustavo Sganzerla Martinez, Sharmilee Sarkar, Aditya Kumar, Ernesto Pérez-Rueda, Scheila de Avila e Silva · 2021 · MicrobiologyOpen
92. Dynamics changes of CRISPR-Cas9 systems induced by high fidelity mutations.
    Liang-Zhen Zheng, Jia-Hai Shi, Y. Mu · 2018 · Physical Chemistry, Chemical Physics - PCCP
93. Molecular switching behavior in isosteric DNA base pairs.
    A. K. Jissy, Sukanya Konar, A. Datta · 2013 · ChemPhysChem
94. Considering the oligonucleotide secondary structures in thermodynamic and kinetic analysis of DNA duplex formation
    A. A. Lomzov, D. Pyshnyi · 2012
95. NMR assessment of the global shape of a non‐labelled DNA dodecamer containing a tandem of GT mismatches
    F. Álvarez-Salgado, H. Desvaux, Y. Boulard · 2006 · Magnetic resonance in chemistry : MRC
96. Thermodynamic parameters for calculating the stability of complexes of bridged oligonucleotides
    A. A. Lomzov, I. Pyshnaya, E. M. Ivanova, D. Pyshnyĭ · 2006 · Doklady Biochemistry and Biophysics
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    J. Kawakami, Kazuhiko Tsujita, N. Sugimoto · 2005 · Analytical Sciences
98. Evaluation of the phosphorescent palladium(II)-coproporphyrin labels in separation-free hybridization assays.
    M. Burke, P. J. O'Sullivan, Aleksi E. Soini, H. Berney, D. Papkovsky · 2003 · Analytical Biochemistry
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    N. Kihal, P. Nguyen, Ali Nazemi, Andrea A. Greschner, M. Gauthier, Steve Bourgault · 2024 · Aggregate
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