Thermodynamics and NMR of Internal G·T Mismatches in DNA

Cited by (531)

Items 401–500 of 531

1. Structural features of a central mismatch in oligonucleotide hybrid duplexes visualized via Raman spectroscopy: Model system for evaluation of potential “antisense” drugs
   D. Nĕmec̆ek, Hana Vaisocherová, J. Štěpánek, P. Turpin · 2005 · Biopolymers
2. Design tools for the fabrication of a photonic crystal based on DNA junctions
   P. Sauer, Hong-Liang Cui, N. Seeman · 2003 · 2003 Third IEEE Conference on Nanotechnology, 2003. IEEE-NANO 2003.
3. Algorithm for thermodynamically based prediction of DNA/DNA cross-hybridisation
   Svetlana Torgasin, K. Zimmermann · 2010 · International Journal of Bioinformatics Research and Applications
4. Establishment of a simple prediction method for DNA melting temperature: high-resolution melting curve analysis of PCR products
   Yun-Chao Zhou, Shan Ha, Yu-Zhao Xu, X. Qin, Yi-Xin Ma, Jiang-Huan Lu, Bo Wang, Jie Cai, Zhiao Duan, Bin Cong et al. · 2025 · PLoS ONE
5. A Molecular Marker Within the NLP3-B1 Gene Is Associated with Earliness in Spring Wheat (Triticum aestivum L.)
   M. Bazhenov, Lyubov Nazarova, T. Mokhov, Olga Pukhova, Anastasia G. Chernook, A. Kocheshkova, P. Kroupin, G. Karlov, M. Divashuk · 2024 · Agronomy
6. Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration.
   Erik de Oliveira Martins, Gerald Weber · 2023 · Biophysical Chemistry
7. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters
   T. Pham, Terrel Miffin, Hong-Ying Sun, Kenneth K Sharp, Xiaoyu Wang, Mingyi Zhu, Shuichi Hoshika, Raymond J. Peterson, S. Benner, J. Kahn et al. · 2023 · bioRxiv
8. Structure- and Content-Dependent Efficiency of Cas9-Assisted DNA Cleavage in Genome-Editing Systems
   Баранова Светлана Владимировна, Polina V. Zhdanova, Alexander A. Lomzov, Vladimir V. Koval, Alexander А. Chernonosov · 2022 · International Journal of Molecular Sciences
9. PhyloPrimer: a taxon-specific oligonucleotide design platform
   G. Varliero, J. Wray, C. Malandain, Gary L. A. Barker · 2021 · PeerJ
10. Mismatch Recognition by Saccharomyces cerevisiae Msh2-Msh6: Role of Structure and Dynamics
    Yan Li, Zane Lombardo, Meera Joshi, M. Hingorani, Ishita Mukerji · 2019 · International Journal of Molecular Sciences
11. How much free energy is absorbed upon breaking DNA base pairs?: Comment on "DNA melting and energetics of the double helix" by Maxim Frank-Kamenetskii et al.
    J. SantaLucia · 2018 · Physics of Life Reviews
12. EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments
    Marek C. Milewski, Karol Kamel, A. Kurzyńska-Kokorniak, M. Chmielewski, M. Figlerowicz · 2017 · J. Comput. Biol.
13. Computational 3D Assembling Methods for DNA: A Survey
    Adriano N. Raposo, A. Gomes · 2016 · IEEE/ACM Transactions on Computational Biology & Bioinformatics
14. NP-Sticky: a web server for optimizing DNA ligation with non-palindromic sticky ends.
    Daphne T. W. Ng, Casim A. Sarkar · 2014 · Journal of Molecular Biology
15. An information security-based literature survey and classification framework of data storage in DNA
    Shipra Jain, Himanshu Chaudhary, V. Bhatnagar · 2013 · Int. J. Netw. Virtual Organisations
16. Flexible and efficient genome tiling design with penalized uniqueness score
    Yang Du, E. Muráni, S. Ponsuksili, K. Wimmers · 2012 · BMC Bioinformatics
17. Solution structure and stability of the DNA undecamer duplexes containing oxanine mismatch
    S. Pack, Hirohisa Morimoto, K. Makino, K. Tajima, K. Kanaori · 2011 · Nucleic Acids Research
18. Thin membrane transducer detectiing DNA hybridization on chip
    Jun-kyu Choi, M. Cha, Junghoon Lee · 2009 · Italian National Conference on Sensors
19. Controlling nanoparticle aggregation in colloidal microwave absorbers via interface chemistry
    B. Larsen, Michael A. Haag, M. H. Stowell, D. Walther, A. Pisano, C. Stoldt · 2007 · SPIE Smart Structures and Materials + Nondestructive Evaluation and Health Monitoring
20. Nearest-Neighbor Thermodynamics of DNA Sequences with Single Bulge Loo
    Fumiaki Tanaka, A. Kameda, Masahito Yamamoto, A. Ohuchi · 2003 · DNA
21. Single Cell Diagnostics
    A. Thornhill · 2007 · Methods in Molecular Medicine™
22. Stability of non-canonical nucleic acid structure as a potential modulator of cell fate
    Shuntaro Takahashi, Hisae Tateishi-Karimata, Naoki Sugimoto · 2026 · Nucleic Acids Research
23. Multiplexed, universal probe-based rare variant detection with USE-PCR
    John Alvarado, Lucien Jacky, Dominic Yurk, Aaron Aguiar, Paul Belitz, Jerrod J. Schwartz · 2025 · Scientific Reports
24. Effect of Internal and Bulge Loops on the Thermal Stability of Small DNA Duplexes
    E. Stellwagen, P. Barnard, N. Stellwagen · 2024 · Journal of Physical Chemistry B
25. A duplexed high-throughput mass spectrometry assay for bifunctional POLB polymerase and lyase activity.
    Z. A. Gurard-Levin, Brian J McMillan, D. Whittington, Brian Doyon, M. Scholle, Jacques Ermolieff, Madhavi Bandi, Mu-Sen Liu, Alvaro J. Amor, W. Mallender · 2024 · SLAS technology
26. Exploring Artificial Nucleic Acid Mimicking Peptide Nanofibers
    Simone I. S. Hendrikse, Nevena Todorova, Hamid Soleimaninejad, P. Charchar, M. Sani, Karrar Al Taief, Jonathan F. Berengut, S. Wickham, S. Gras, A. Fahrenbach et al. · 2023 · Chemistry of Materials
27. Beneficial and Detrimental Effects of Nonspecific Binding During DNA Hybridization
    Tam T. M. Phan, T. Phan, J. Schmit · 2022 · bioRxiv
28. Pulsed‐Field Gel Electrophoresis and the Molecular Epidemiology of Foodborne Pathogens
    Mohana Ray, D. Schwartz · 2014
29. Calculation of nucleation free energy for duplex oligomers in the context of nearest neighbor models.
    João Carlos de Oliveira Guerra · 2013 · Biopolymers
30. Oligonucleotide optimization for DNA synthesis
    T. Louw, S. Whitney, Joel R. Termaat, E. Pienaar, H. Viljoen · 2011
31. Heterology tolerance and recognition of mismatched base pairs by human Rad51 protein
    Yu‐Cheng Tsai, Yuzhen Wang, Damian E. Urena, Sandip Kumar, Junghuei Chen · 2011 · DNA repair
32. Preliminary dielectric measurement and analysis protocol for determining the melting temperature and binding energy of short sequences of DNA in solution
    W. Spillman, R. Asmatulu, C. Jullian, B. Geist, R. Claus, J. Robertson · 2008 · Biotechnology Journal
33. Raman spectroscopic study of G—A mismatches
    Y. Liao, Yaoqing Meng, Hao-Dong Lei, Ying Wang · 2007
34. A base‐pairing model of duplex formation. I. Watson–Crick pairing geometries
    J. Bashford, Peter D. Jarvis · 2005 · Biopolymers
35. Studies on the Extension of Sequence-independence and the Enhancement of DNA Triplex Formation
    Ming-Tsai Wei, A. Walter, A. Gabriélian, H. Schütz, E. Birch-Hirschfeld, Shwu-Bin Lin, Wei-Chen Lin, H. Fritzsche, Lou S. Kan · 2005
36. Raman study of potential "antisense" drugs: nonamer oligonucleotide duplexes with a central mismatch as a model system for the binding selectivity evaluation.
    D. Nĕmec̆ek, J. Štěpánek, P. Turpin, I. Rosenberg · 2004 · Biopolymers
37. DNA dimer correlations reflect in vivo conditions and discriminate among nearest-neighbor base pair free energy parameter measures
    P. Miramontes, G. Cocho · 2003
38. Molecular Dynamics and Mechanics Calculations on a DNA Duplex with A+C, G-T and T-C Mispairs
    Sukesh R. Bhaumik, K. Chary · 2002 · Journal of Biomolecular Structure and Dynamics
39. Differential amplifying RT-PCR: a novel RT-PCR method to differentiate mRNA from its DNA lacking intron.
    C. Joo, Heuiran Lee, Eunok Kim, Boyoung Lee, Young-Keol Cho, Y. Kim · 2002 · Journal of Virological Methods
40. Effects of 5‐[S‐(2,4‐dinitrophenyl)‐thio]‐2′‐deoxyuridine analog incorporation on the structure and stability of DNA hybrids: implications for the design of nucleic acid probes
    E. Yuriev, Daniel Scott, M. Hanna · 1999 · Journal of Molecular Recognition
41. How kinetically accessible is an RNA target for hybridization with an antisense oligo? A lesson from an RNA target which is as small as a 20mer
    Nitin K. Puri, J. Chattopadhyaya · 1999
42. A Guide to Using STITCHER for Overlapping Assembly PCR Applications.
    Damien M. O'Halloran · 2017 · Methods in molecular biology
43. DNA detection by cascade enzymatic signal amplification.
    B. Zou, Yin-Jiao Ma, Guo-Hua Zhou · 2013 · Methods in molecular biology
44. MultiPLX: automatic grouping and evaluation of PCR primers.
    L. Kaplinski, M. Remm · 2007 · Methods in molecular biology
45. Invader assay for RNA quantitation.
    Marilyn C. Olson, T. Takova, Luanne Chehak, Michelle Curtis, Sarah M. Olson, R. Kwiatkowski · 2004 · Methods in molecular biology
46. Sea spiders of the Salish Sea: Comparative morphology and molecular phylogenetic analysis of seven coastal species (Arthropoda, Pycnogonida)
    Cormac Toler-Scott, Eunji Park, Heather Gordon, B. Leander · 2026 · Organisms Diversity & Evolution
47. Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting
    Or Szekely, Yeongjoon Lee, A. Rangadurai, S. Guseva, Joshua Cooksey, Edgar M. Faison, Nikita Zalenski, Qi Zhang, Zu-Cai Suo, Hashim M. Al-Hashimi · 2026 · Nature Communications
48. Effects of N–1-Mer Impurities in Antisense Oligonucleotides on the Target RNA Suppression
    Tomoka Akita, Elisa Tomita-Sudo, Renshin Sano, Nae Sakimoto, Shigenori Iwai, Hirokazu Nankai, Satoshi Obika, Takao Inoue, J. Kawakami · 2026 · Nucleic Acid Therapeutics
49. ThermoPlex: an automated design tool for target-specific multiplex PCR primers based on DNA thermodynamics
    Altair Agmata, Kevin L. Labrador, J. D. Palermo, Ma. Josefa R. Pante · 2024 · bioRxiv
50. An Approach to Identifying Single-Nucleotide Mutations Using Noncovalent Associates of Gold Nanoparticles with Fluorescently Labeled Oligonucleotides
    A. Epanchintseva, E. A. Gorbunova, M. D. Nekrasov, Julia E. Poletaeva, I. Pyshnaya · 2024 · International Journal of Molecular Sciences
51. Final Scientific and Technical Report
    2026
52. DNA-Coated Microspheres with Base Mismatches for Stepwise Programmed Assembly
    In-Seong Jo, J. Oh, M. Soula, Manhee Lee, David J. Pine, Étienne Ducrot, Gi-Ra Yi · 2024 · Chemistry of Materials
53. STR genotyping by real-time PCR using QueSTR probes
    S. Škevin, O. Tytgat, Maarten Fauvart, Liesl De Keyzer, D. Deforce, F. van Nieuwerburgh · 2023 · Sensors and actuators. B, Chemical
54. Thermodynamic Parameters Contributions of Single Internal Mismatches In RNA/DNA Hybrid Duplexes
    Tongjun Xiang, Huibao Feng, Xin-Hui Xing, Chong Zhang · 2022 · bioRxiv
55. Needles in Haystacks: Understanding the Success of Selective Pairing of Nucleic Acids
    Carlos A. Plata, S. Marni, S. Suweis, T. Bellini, E. Paraboschi · 2022 · International Journal of Molecular Sciences
56. Improving the accuracy of the nearest neighbor model of DNA melting: Comment on "DNA melting and energetics of the double helix" by Alexander Vologodskii and Maxim D. Frank-Kamenetskii.
    R. Wartell · 2018 · Physics of Life Reviews
57. Analytical consideration of the selectivity of oligonucleotide hybridization
    Marsel R Kabilov, D. Pyshnyĭ · 2011
58. Synthesis of oligodeoxynucleotides incorporating 2-N-carbamoylguanine and evaluation of the hybridization properties.
    Takeshi Sasami, Yoko Odawara, A. Ohkubo, M. Sekine, K. Seio · 2009 · Bioorganic & Medicinal Chemistry
59. Computer aided DNA sequence design
    Udo Feldkamp · 2005
60. Investigating the Thermodynamic Stability of DNA Four-Way Junctions Using Fluorescent Nucleoside Analogues
    Rachel E. Savage · 2017
61. Thermodynamics of Denaturation Transition of DNA Duplex Oligomers in the Context of Nearest Neighbor Models: A Short Review☆
    João Carlos de Oliveira Guerra · 2015
62. Low-concentration initiator primers improve the amplification of gene targets with high sequence variability.
    K. Pierce, L. Wangh · 2015 · Methods in molecular biology
63. PRIMEGENSw3: a web-based tool for high-throughput primer and probe design.
    Garima Kushwaha, G. Srivastava, Dong Xu · 2015 · Methods in molecular biology
64. Technical considerations in quantitating gene expression.
    R. Shimkets · 2004 · Methods in molecular biology
65. Dual‐Stage Mismatch Interrogation (DMI) for High‐Fidelity G–T Discrimination by a DNA Nanodevice
    Christina Patra, Daria P. Kisareva, A. Eldeeb, D. Kolpashchikov · 2026 · ChemistrySelect
66. Structural and Thermodynamic Insights for Enhanced SNP Detection Using N-Benzimidazole Oligonucleotides.
    V. Golyshev, F. V. Morozova, A. A. Berdugin, Evgenia A. Kozyreva, E. E. Baranovskaya, I. Yushin, A. Lomzov · 2025 · Journal of Physical Chemistry B
67. Synergistic Effects of Autologous Plasma and Agarose Fillers in Treating Acne, Atrophic, and Hypertrophic Scars: A Case Series
    Marwa Zein AlAbidden, J. Vandeputte · 2025 · Aesthetic Surgery Journal Open Forum
68. Kullback–Leibler divergence potential for non-ergodic replication dynamics: an information-theoretic second law
    Tatsuaki Tsuruyama · 2025 · Journal of Statistical Mechanics: Theory and Experiment
69. TrueProbes: Quantitative Single-Molecule RNA-FISH Probe Design Improves RNA Detection
    Jason J. Hughes, Benjamin K. Kesler, John E. Adams, Blythe G. Hospelhorn, G. Neuert · 2025 · bioRxiv
70. Polymorphic potential of SRF binding site of c-Fos gene promoter: in vitro study
    Barbora Profantová, V. Římal, V. Profant, O. Socha, Ivan Barvík, Helena Štěpánková, Josef Štěpánek · 2024 · RSC Advances
71. A sensitive batch detection of banana bunchy top virus using SYBR® Green real-time PCR
    J. Mendoza, F. D. Dela Cueva, Jen Daine L. Nocum, A. Manohar, R. Gardoce, Grace C. Lachica, D. Lantican · 2024 · VirusDisease
72. Blocking uncertain mispriming errors of PCR
    Takumi Takahashi, Hiroyuki Aoyanagi, Simone Pigolotti, Shoichi Toyabe · 2024 · bioRxiv
73. ANNaMo: Coarse-grained modelling for folding and assembly of RNA and DNA systems
    F. Guerra, E. Poppleton, P. vSulc, L. Rovigatti · 2023
74. DNA oligomer binding in competition exhibits cooperativity
    Mina Mohammadi-Kambs, A. Ott · 2019 · New Journal of Physics
75. Nueva reacción en cadena de la polimerasa múltiple para el diagnóstico específico de especies implicadas en la candidiasis humana
    Liliana García, Liany Johanna Luna, T. Velasco, B. Guerra · 2017 · Biomédica
76. Thrombin detection in murine plasma using engineered fluorescence resonance energy transfer aptadimers
    A. Trapaidze, M. Brut, S. Mazères, D. Estève, A. Gué, A. Bancaud · 2015
77. Biopuce à aptamères : application à la détection de petites molécules par imagerie de résonnance plasmonique de surface
    F. Melaine · 2014
78. Bias toward a 1:1 ratio in primer-introduced restriction analysis PCR: mechanism and minimization.
    S. Denden, H. Abaidi, M. Hamdaoui, J. Ben Chibani, A. Khelil · 2014 · Genetics and Molecular Research
79. polDNAmelt: Local Melting Within Polymeric DNA—An Improved Method and Its Applications
    Sankar Basu, Dhananjay Bhattacharyya · 2013
80. Designing DNA Barcodes Orthogonal in Melting Temperature by Simulated Annealing Optimization
    Abdülkadir Elmas, Guido H. Jajamovich, Xiaodong Wang, Michael S. Samoilov · 2013 · Nucleic Acid Therapeutics
81. Thermodynamics of Microarray Hybridization
    R. Malutan, P. G. Vilda · 2012
82. Degenerate primer design system for gene biodiversity study using dynamic pattern matching
    Weeris Treeratanajaru, Supawin Watcharamul, R. Lipikorn · 2012 · 2012 7th International Symposium on Health Informatics and Bioinformatics
83. Structural and thermodynamic analysis of the conformational states of self-complementary hexanucleotides 5′-d(GCATGC) and 5′-d(GCTAGC) in Aqueous Solution
    V. Kostyukov, O. V. Rogova, V. Pakhomov, M. Evstigneev · 2007
84. Sum rules for free energy and frequency distribution of DNA dinucleotides
    L. Frappat, A. Sciarrino · 2003
85. The Effect of the Bulge Loop upon the Hybridization Process in DNA Computing
    Fumiaki Tanaka, A. Kameda, Masahito Yamamoto, A. Ohuchi · 2003 · International Conference on Evolvable Systems
86. Graph-based methods for the design of DNA computations
    Svetlana Torgasin · 2012
87. Browser-based design of loop-mediated isothermal amplification (LAMP) primer sets with template repeat masking and bisulphite support
    Ruslan Kalendar · 2026 · Frontiers in Bioinformatics
88. De novo design of functional RNAs through higher-order interactions
    Tongwei Yuan, Dong Wang, Xin-long Chen, Hanlin Tao, Chen-Chen Zheng Zheng, Xiaocong Zhao, Ya-Lan Tan, Xinghua Zhang, Zhi-Jie Tan · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
89. Development of a test system for detection of the rabies virus genome using real-time PCR with an endogenous control: Theoretical design and optimization
    S. A. Chupin, E. Chernyshova, E. A. Chufarova · 2026 · Veterinary Science Today
90. Deep Learning Predicts Dissimilar DNA-DNA Binding and Engineers Hyperconnected Networks
    Karishma Matange, Gunavaran Brihadiswaran, Kyle J. Tomek, Kevin Volkel, D. Townsend, James M. Tuck, Albert J. Keung · 2026 · Nature Communications
91. The maintenance and emergence of diversity promotes open-ended evolution in a pre-cellular system
    Maria Kalambokidis, Nahui Olin Medina-Chávez, Joleen Khey, Michael Travisano · 2026 · npj Complexity
92. Scarless one-tube genome assembly via computationally optimized uracil-DNA glycosylase reactions
    Rachel Carson, Patricia M. Needham, Pedro Fernandez Mendoza, S. Nugen · 2026 · RSC Chemical Biology
93. Dual-calibration RT-qPCR reveals distinct dnaK1/2/3 and groEL1/2 expression dynamics under heat and acid stress in the sinefungin producer Streptomyces incarnatus
    Xiao-Hui Zhao, M. Kubo, Haruka Yamagata, Yu Nakashima, T. Hasunuma, T. Kanao, Takashi Tamura · 2026 · Scientific Reports
94. DNA melting: Intra-base-pair dynamics and a vector generalization of the Peyrard-Bishop-Dauxois model.
    N. Theodorakopoulos · 2026 · Physical Review E
95. Dynamic multiplex PCR: A pioneering approach to rapid, cost-effective, and high-quality microsatellite fragment analysis
    Türker Bodur, Meryem Cansu Yeşiltaş, Bahar Eldemir · 2026 · Ankara Üniversitesi Veteriner Fakültesi Dergisi
96. Strand Displacement Increases the Fidelity of DNA Polymerases
    Anna V. Yudkina, Alexander O. Yakovlev, Denis A. Rychkov, Victor M. Golyshev, Dmitry O. Zharkov · 2026 · Biochemistry
97. A Novel MiRNA Detection System Combining TWJ-SDA, Multistep L-TEAM, and CRISPR-Cas3
    Riko Miyazaki, Kazuki Aibara, Haruhi Isse, Fumiya Kashiwai, Masashi Takahashi, A. Onodera, Yuji Tsunekawa, Yuko Yamauchi, K. Yoshimi, T. Mashimo et al. · 2025 · bioRxiv
98. Possibilities and Limits of DNA-Enabled Programmable 2D Self-Assembly
    Nicholas Tjahjono, Evgeni S. Penev, Boris I. Yakobson · 2025 · ACS Applied Materials & Interfaces
99. CRISPR-Cas9 trans-cleavage is hindered by a closed R-loop, an elongated spacer, and an inactive HNH domain
    Roser Montagud-Martínez, Raúl Ruiz, Sara Baldanta, Rubén Delicado-Mateo, Guillermo Rodrigo · 2025 · bioRxiv
100. “Exploring the denaturations in cancer and non-cancer DNA molecules by optical absorption, thermal, and electric measurements: A case study”
     Owais I. Mir, U. Gupta, I. Qasim, A. Pandith, F. Mir · 2024 · Nano TransMed