Thermodynamics and NMR of Internal G·T Mismatches in DNA

Allawi, Hatim T., SantaLucia, John·1997·Biochemistry

Cited by (531)

Items 101–200 of 531

  1. Identification of a Novel Tandem Duplication in Exon 1 of the TNFRSF11A Gene in Two Unrelated Patients With Familial Expansile Osteolysis
    Teresa L. Johnson‐Pais, Frederick R. Singer, Henry G. Bone, Cynthia T. McMurray, Marc F. Hansen, Robin J. Leach · 2003 · Journal of Bone and Mineral Research
  2. APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure
    Colleen M. Holtz, Holly A. Sadler, Louis M. Mansky · 2013 · Nucleic Acids Research
  3. Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting.
    Ellen M Moody, J. Lecomte, P. Bevilacqua · 2005 · RNA: A publication of the RNA Society
  4. Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: Comparison of single base mismatches and base bulges
    T. Naiser, Oliver Ehler, J. Kayser, Ti-Mo Mai, Wolfgang Michel, A. Ott · 2008 · BMC Biotechnology
  5. Influence of pH, temperature and the cationic porphyrin TMPyP4 on the stability of the i-motif formed by the 5'-(C3TA2)4-3' sequence of the human telomere.
    Sergio Fernández, R. Eritja, A. Aviñó, J. Jaumot, R. Gargallo · 2011 · International Journal of Biological Macromolecules
  6. Codeword design and information encoding in DNA ensembles
    Max Garzón, Russell J. Deaton · 2004 · Natural Computing
  7. Multiple biological roles associated with the repeat (R) Region of the HIV-I RNA genome
    Ben Berkhout · 2000 · Advances in pharmacology
  8. Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition
    Vetriselvi Rangannan, Manju Bansal · 2009 · Molecular BioSystems
  9. Thermodynamics of protein folding: A statistical mechanical study of a small all-β protein
    Zhuyan Guo, Charles L. Brooks · 1997 · Biopolymers
  10. Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition
    Dipanwita Banerjee, Hisae Tateishi-Karimata, Tatsuya Ohyama, Saptarshi Ghosh, T. Endoh, Shuntaro Takahashi, N. Sugimoto · 2020 · Nucleic Acids Research
  11. PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR
    Jennifer Lu, Andrew D. Johnston, Philippe Berichon, K. Ru, D. Korbie, M. Trau · 2017 · Scientific Reports
  12. Expression of multiple catechol‐o‐methyltransferase (COMT) mRNA variants in human brain
    Elizabeth M. Tunbridge, Tracy A. Lane, Paul J. Harrison · 2007 · American Journal of Medical Genetics Part B Neuropsychiatric Genetics
  13. A thermodynamic approach to designing structure-free combinatorial DNA word sets
    Michael R. Shortreed, S. B. Chang, DongGee Hong, Maggie E. Phillips, Bridget Campion, D. Tulpan, Mirela Andronescu, A. Condon, H. Hoos, L. Smith · 2005 · Nucleic Acids Research
  14. The Main Role of Human Thymine-DNA Glycosylase Is Removal of Thymine Produced by Deamination of 5-Methylcytosine and Not Removal of Ethenocytosine*
    Mika Abu, Timothy R. Waters · 2003 · Journal of Biological Chemistry
  15. Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics.
    Richard J. Isaacs, W. Rayens, H. Spielmann · 2002 · Journal of Molecular Biology
  16. Mismatch Extension of DNA Polymerases and High-Accuracy Single Nucleotide Polymorphism Diagnostics by Gold Nanoparticle-Improved Isothermal Amplification
    Feng Chen, Yue Zhao, Chunhai Fan, Yongxi Zhao · 2015 · Analytical Chemistry
  17. GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR
    Carine Gubelmann, Alexandre Gattiker, Andreas Massouras, Korneel Hens, Fabrice P. A. David, Frederik Decouttere, Jacques Rougemont, Bart Deplancke · 2011 · Database
  18. pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.
    P. Buček, J. Jaumot, A. Aviñó, R. Eritja, R. Gargallo · 2009 · Chemistry
  19. Solution equilibria of the i-motif-forming region upstream of the B-cell lymphoma-2 P1 promoter.
    Nasiruddin Khan, A. Aviñó, R. Tauler, C. González, R. Eritja, R. Gargallo · 2007 · Biochimie
  20. Multiplex allele-specific target amplification based on PCR suppression.
    N. Broude, Lingang Zhang, Karen Woodward, David Englert, Charles R. Cantor · 2001 · Proceedings of the National Academy of Sciences of the United States of America
  21. In Vitro Mutagenesis Protocols
    J. Braman · 2010 · Methods in Molecular Biology
  22. DNAzyme catalytic beacon sensors that resist temperature-dependent variations
    Nandini Nagraj, Jue-Wen Liu, S. Sterling, J. Wu, Yi Lu · 2009 · Chemical Communications
  23. Position dependent mismatch discrimination on DNA microarrays – experiments and model
    T. Naiser, J. Kayser, Ti-Mo Mai, Wolfgang Michel, A. Ott · 2008 · BMC Bioinformatics
  24. Thermodynamic dependence of DNA/DNA and DNA/RNA hybridization reactions on temperature and ionic strength.
    Brian E. Lang, F. Schwarz · 2007 · Biophysical Chemistry
  25. Biophysics of DNA
    A. Vologodskii · 2015
  26. High resolution genetic diversity studies of marine Synechococcus isolates using rpoC1-based restriction fragment length polymorphism
    Martin Mühling, Nicholas J. Fuller, P. Somerfield, A. F. Post, W. Wilson, D. Scanlan, I. Joint, N. Mann · 2006
  27. DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes
    Czuee Morey, Sushmita Mookherjee, Ganesan Rajasekaran, Manju Bansal · 2011 · PLANT PHYSIOLOGY
  28. High-quality annotation of promoter regions for 913 bacterial genomes
    Vetriselvi Rangannan, M. Bansal · 2010 · Bioinform.
  29. DNA single-base mismatch study with an electrochemical enzymatic genosensor
    P. Abad-Valle, M. Fernández-Abedul, A. Costa-García · 2006 · Biosensors & bioelectronics
  30. Structural effect of the anticancer agent 6-thioguanine on duplex DNA.
    Bo-Hon Jen, C. R. de los Santos · 2003 · Nucleic Acids Research
  31. Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization.
    M. A. Reyes-López, A. Méndez-Tenorio, R. Maldonado-Rodríguez, M. Doktycz, J. Fleming, K. Beattie · 2003 · Nucleic Acids Research
  32. Targeting the G-quadruplex-forming region near the P1 promoter in the human BCL-2 gene with the cationic porphyrin TMPyP4 and with the complementary C-rich strand.
    Miquel del Toro, P. Buček, A. Aviñó, J. Jaumot, C. González, R. Eritja, R. Gargallo · 2009 · Biochimie
  33. Influencing factors of dsDNA dye (high-resolution) melting curves and improved genotype call based on thermodynamic considerations.
    E. Schütz, N. von Ahsen · 2009 · Analytical Biochemistry
  34. Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis.
    Xin Zhao, Hui-Yong Zhang, Lei Li · 2013 · Genomics
  35. The mechanism of actinomycin D-mediated inhibition of HIV-1 reverse transcription
    Rienk E. Jeeninga, Hendrik T. Huthoff, Ben Berkhout, Alexander P. Gultyaev · 1998 · Nucleic Acids Research
  36. Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes
    Norman E. Watkins, William J. Kennelly, Mike J. Tsay, Astrid Tuin, Lara Swenson, Nana Lee, Svetlana V Morosyuk, Donald A. Hicks, John SantaLucia · 2010 · Nucleic Acids Research
  37. Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization
    Xin Chen, Na Liu, Liquan Liu, Wei Chen, Na Chen, Meng Lin, Jia-Ju Xu, Xing Zhou, Hongbo Wang, Mei-Ping Zhao et al. · 2019 · Nature Communications
  38. A unified Poland-Scheraga model of oligo- and polynucleotide DNA melting: salt effects and predictive power.
    D. Jost, R. Everaers · 2009 · Biophysical Journal
  39. Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.
    Fang Dong, H. Allawi, Todd A. Anderson, Bruce N. Neri, V. Lyamichev · 2001 · Nucleic Acids Research
  40. Pitfalls during in silico prediction of primer specificity for eDNA surveillance
    Ken Y. K. So, J. Fong, Ivan P. Y. Lam, D. Dudgeon · 2020 · Ecosphere
  41. HIV-1 nucleocapsid protein binds to the viral DNA initiation sequences and chaperones their kissing interactions.
    C. Égelé, E. Schaub, N. Ramalanjaona, É. Piémont, D. Ficheux, B. Roques, J. Darlix, Y. Mély · 2004 · Journal of Molecular Biology
  42. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.
    Shuntaro Takahashi, N. Sugimoto · 2020 · Chemical Society Reviews
  43. PrimerPooler: automated primer pooling to prepare library for targeted sequencing
    Silas S. Brown, Yun-Wen Chen, Ming Wang, A. Clipson, Eguzkine Ochoa, M. Du · 2017 · Biology Methods and Protocols
  44. MELTING, a flexible platform to predict the melting temperatures of nucleic acids
    M. Dumousseau, Nicolas Rodriguez, N. Juty, N. Le Novère · 2012 · BMC Bioinformatics
  45. A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences
    F. Miura, C. Uematsu, Y. Sakaki, Takashi Ito · 2005 · Bioinform.
  46. Oligonucleotide Probes for RNA‐Targeted Fluorescence In Situ Hybridization
    Adam P. Silverman, Eric T. Kool · 2006 · Advances in clinical chemistry
  47. Virtual PCR
    M. Lexa, J. Horak, Bretislav Brzobohaty · 2001 · Bioinform.
  48. Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data
    Jason P. Ross, S. V. van Dijk, M. Phang, M. Skilton, P. Molloy, Y. Oytam · 2022 · Clinical Epigenetics
  49. Recognition of Damaged DNA: Structure and Dynamic Markers
    Markus W. Germann, Christopher N. Johnson, Alexander M. Spring · 2010 · Medicinal Research Reviews
  50. Recognition of T*G mismatched base pairs in DNA by stacked imidazole-containing polyamides: surface plasmon resonance and circular dichroism studies.
    E. Lacy, Kari K. Cox, W. Wilson, Moses Lee · 2002 · Nucleic Acids Research
  51. Forces maintaining the DNA double helix and its complexes with transcription factors.
    P. Privalov, C. Crane-Robinson · 2018 · Progress in Biophysics and Molecular Biology
  52. Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy
    Venkata Rajesh Yella, Aditya Arun Kumar, Manju Bansal · 2018 · Scientific Reports
  53. swga: a primer design toolkit for selective whole genome amplification
    E. Clarke, Sesh A. Sundararaman, S. Seifert, F. Bushman, B. Hahn, Dustin Brisson · 2017 · Bioinform.
  54. Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation
    Alexander A. Lomzov, Yury N. Vorobjev, Dmitrii V. Pyshnyi · 2015 · The Journal of Physical Chemistry B
  55. Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)
    Sandra C. Koch, Jochen Kuper, Karola L. Gasteiger, Nina Simon, Ralf Strasser, David Eisen, Simon Geiger, Sabine Schneider, Caroline Kisker, Thomas Carell · 2015 · Proceedings of the National Academy of Sciences
  56. Computational and experimental analysis of DNA shuffling
    N. Maheshri, D. Schaffer · 2003 · Proceedings of the National Academy of Sciences of the United States of America
  57. Selective recognition of pyrimidine–pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators
    Matthias Bahr, V. Gabélica, A. Granzhan, M. Teulade-Fichou, E. Weinhold · 2008 · Nucleic Acids Research
  58. Unified description of poly- and oligonucleotide DNA melting: nearest-neighbor, Poland-Sheraga, and lattice models.
    R. Everaers, Sanjay Kumar, C. Simm · 2007 · Physical review. E, Statistical, nonlinear, and soft matter physics
  59. Nearest neighbor parameters for Watson–Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides
    E. Kierzek, D. Mathews, A. Ciesielska, D. Turner, R. Kierzek · 2006 · Nucleic Acids Research
  60. Characterization of Non-crosshybridizing DNA Oligonucleotides Manufactured in vitro
    Junghuei Chen, R. Deaton, M. Garzon, Jin Woo Kim, D. Wood, Hong Bi, Dylan Carpenter, Yu-Zhen Wang · 2004 · Natural Computing
  61. 2 – Thermodynamics of RNA Secondary Structure Formation
    T. Xia, D. Mathews, D. Turner · 2001 · RNA
  62. Biological and nanotechnological applications using interactions between ionic liquids and nucleic acids
    Hisae Tateishi-Karimata, N. Sugimoto · 2018 · Biophysical Reviews
  63. Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine–thymine mismatch
    M. Jourdan, A. Granzhan, Régis Guillot, P. Dumy, M. Teulade-Fichou · 2012 · Nucleic Acids Research
  64. Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability
    Vetriselvi Rangannan, M. Bansal · 2007 · Journal of Biosciences
  65. Thermodynamic properties of DNA sequences: characteristic values for the human genome
    Ryan T. Koehler, N. Peyret · 2005 · Bioinform.
  66. Design of a DNA chip for detection of unknown genetically modified organisms (GMOs)
    Håvard Nesvold, A. B. Kristoffersen, A. Holst-Jensen, K. G. Berdal · 2005 · Bioinform.
  67. Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays
    Robert P. Balog, Y Emi Ponce de Souza, Hue M Tang, Gina M DeMasellis, Boning Gao, Adrian Avila, Desmond J Gaban, David Mittelman, John Dorrance Minna, Kevin J Luebke et al. · 2002 · Analytical Biochemistry
  68. In-silico Design of DNA Oligonucleotides: Challenges and Approaches
    M. Hendling, I. Barišić · 2019 · Computational and Structural Biotechnology Journal
  69. MultiPLX: automatic grouping and evaluation of PCR primers
    L. Kaplinski, R. Andreson, T. Puurand, M. Remm · 2005 · Bioinform.
  70. DNA base bulge vs unmatched end formation in probe-based diagnostic insertion/deletion genotyping: genotyping the UGT1A1 (TA)(n) polymorphism by real-time fluorescence PCR.
    N. von Ahsen, M. Oellerich, E. Schütz · 2000 · Clinical Chemistry
  71. The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application.
    Mohamad Zulkeflee Sabri, Azzmer Azzar Abdul Hamid, Sharifah Mariam Sayed Hitam, Mohd. Zulkhairi Abdul Rahim · 2020 · Biophysical Chemistry
  72. Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage
    S. Archer, N. Shirokikh, T. Preiss · 2014 · BMC Genomics
  73. The efficiency of damage recognition and excision correlate with duplex destabilization induced by acetylaminofluorene adducts in human nucleotide excision repair
    J. Yeo, A. Khoo, Adebanke F. Fagbemi, O. Schärer · 2012 · Chemical Research in Toxicology
  74. DNA interaction with flavone and hydroxyflavones
    Joana Vitorino, M. Sottomayor · 2010
  75. Thermodynamic prediction of RNA-DNA duplex-forming regions in the human genome.
    J. Huppert · 2008 · Molecular Biosystems
  76. An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification
    A. Pozhitkov, D. Tautz · 2002 · BMC Bioinformatics
  77. Impact of Sugar Pucker on Base Pair and Mispair Stability
    Adides A. Williams, Agus Darwanto, Jacob A. Theruvathu, Artur Burdzy, Jonathan W. Neidigh, Lawrence C. Sowers · 2009 · Biochemistry
  78. Pre-melting dynamics of DNA and its relation to specific functions
    Boian Alexandrov, N. Voulgarakis, K. Rasmussen, A. Usheva, A. Bishop · 2009 · Journal of Physics: Condensed Matter
  79. Characterization of synthetic oligonucleotides containing biologically important modified bases by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
    Zheng-Fang Cui, Jacob A. Theruvathu, Alvin Farrel, Artur Burdzy, L. Sowers · 2008 · Analytical Biochemistry
  80. Altered dynamics of DNA bases adjacent to a mismatch: a cue for mismatch recognition by MutS.
    Nabanita Nag, B. Rao, G. Krishnamoorthy · 2007 · Journal of Molecular Biology
  81. Stability of complementary and mismatched DNA duplexes: Comparison and contrast in gas versus solution phases
    S. Pan, Xuejun Sun, Jeehiun K. Lee · 2006
  82. Validation of the nearest-neighbor model for Watson–Crick self-complementary DNA duplexes in molecular crowding condition
    Saptarshi Ghosh, Shuntaro Takahashi, Tamaki Endoh, Hisae Tateishi‐Karimata, Soumitra Hazra, Naoki Sugimoto · 2019 · Nucleic Acids Research
  83. What drives the binding of minor groove-directed ligands to DNA hairpins?
    J. Lah, I. Drobnak, M. Dolinar, G. Vesnaver · 2007 · Nucleic Acids Research
  84. Effect of 6-thioguanine on the stability of duplex DNA
    Bo-Hon Jen, C. R. de los Santos · 2005 · Nucleic Acids Research
  85. Design and test of noncrosshybridizing oligonucleotide building blocks for DNA computers and nanostructures
    R. Deaton, Jin-Woo Kim, Junghuei Chen · 2003 · Applied Physics Letters
  86. DNA-duplex linker for AFM-SELEX of DNA aptamer against human serum albumin.
    Musashi Takenaka, Y. Okumura, Tomokazu Amino, Y. Miyachi, C. Ogino, A. Kondo · 2017 · Bioorganic & Medicinal Chemistry Letters
  87. Assessing long-distance RNA sequence connectivity via RNA-templated DNA–DNA ligation
    Christian K. Roy, Sara Olson, Brenton R. Graveley, Phillip D. Zamore, Melissa J. Moore · 2015 · eLife
  88. Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions.
    M. Horne, Daniel J. Fish, A. S. Benight · 2006 · Biophysical Journal
  89. Detection of cystic fibrosis alleles from single cells using molecular beacons and a novel method of asymmetric real-time PCR.
    K. Pierce, J. Rice, J. Sanchez, L. Wangh · 2003 · Molecular human reproduction
  90. Predicting the success of primer extension genotyping assays using statistical modeling.
    A. Yuryev, Jianping Huang, M. Pohl, R. Patch, F. Watson, Peter A Bell, M. Donaldson, M. Phillips, M. Boyce-Jacino · 2002 · Nucleic Acids Research
  91. A DNA computing readout operation based on structure-specific cleavage
    Li-Man Wang, Jeff G. Hall, Man-Chun Lu, Qinghua Liu, L. Smith · 2001 · Nature Biotechnology
  92. Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches
    L. M. Oliveira, A. Long, T. Brown, K. Fox, G. Weber · 2020 · Chemical Science
  93. PrimerROC: accurate condition-independent dimer prediction using ROC analysis
    Andrew D. Johnston, Jennifer Lu, K. Ru, D. Korbie, M. Trau · 2019 · Scientific Reports
  94. Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures
    G. Weber · 2015 · Bioinform.
  95. Canonical nucleosides can be utilized by T4 DNA ligase as universal template bases at ligation junctions.
    Rashada C. Alexander, Ashley K. Johnson, Jeffrey Thorpe, Travis Gevedon, S. Testa · 2003 · Nucleic Acids Research
  96. Algorithms for predicting the secondary structure of pairs and combinatorial sets of nucleic acid strands
    Mirela Andronescu · 2003
  97. Monte Carlo applications to thermal and chemical denaturation experiments of nucleic acids and proteins.
    D.Jeremy Williams, Kathleen B. Hall · 2000 · Methods in Enzymology
  98. 8-Oxo-7,8-dihydro-2′-deoxyguanosine and other lesions along the coding strand of the exon 5 of the tumour suppressor gene P53 in a breast cancer case-control study
    B. Brancato, A. Munnia, F. Cellai, E. Ceni, T. Mello, S. Bianchi, S. Catarzi, G. Risso, A. Galli, M. Peluso · 2016 · DNA Research
  99. Prediction of melting temperatures in fluorescencein situhybridization (FISH) procedures using thermodynamic models
    Sílvia Fontenete, Nuno Guimarães, Jesper Wengel, Nuno F. Azevedo · 2015 · Critical Reviews in Biotechnology
  100. Examination of the premelting transition of DNA A-tracts using a fluorescent adenosine analogue.
    Katherine E. Augustyn, K. Wojtuszewski, M. Hawkins, J. Knutson, Ishita Mukerji · 2006 · Biochemistry