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Group: baker-group - with tag nucleic_acids [415 articles]

Recent papers posted by members of the baker-group group with tag nucleic_acids
  • Liquid Crystalline Phase Behavior of High Molecular Weight DNA: A Comparative Study of the Influence of Metal Ions of Different Size, Charge and Binding Mode
    Biomacromolecules, Vol. 9, No. 7. (14 July 2008), pp. 1860-1869.
    by Neethu Sundaresan, Cherumuttathu H Suresh, Thresia Thomas, TJ Thomas, CKS Pillai
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-07-25 12:02:47 as read
  • Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane
    Biophys. J., Vol. 82, No. 1. (1 January 2002), pp. 76-92.
    by Christian Fleck, Roland R Netz, Hans H von Grunberg
    posted to solvation pka nucleic_acids electrostatics biomembranes by sobolevnrm to the group baker-group on 2008-07-16 16:02:21 as read along with 1 person softsimu
  • Assessing the performance of implicit solvation models at a nucleic acid surface
    Physical Chemistry Chemical Physics (in press)
    by F Dong, JA Wagoner, NA Baker
    posted to solvation nucleic_acids nonpolar electrostatics by sobolevnrm to the group baker-group on 2008-07-08 12:27:15 as read
  • Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the Stability of RNA Hairpins
    J. Am. Chem. Soc., Vol. 130, No. 23. (11 June 2008), pp. 7364-7372.
    by David L Pincus, Changbong Hyeon, D Thirumalai
    posted to solvation nucleic_acids by sobolevnrm to the group baker-group on 2008-07-08 11:59:21 as read
  • Solvation Free Energies of the Nucleic Acid Bases
    J. Phys. Chem., Vol. 100, No. 20. (16 May 1996), pp. 8587-8594.
    by JL Miller, PA Kollman
    posted to solvation nucleic_acids molecular_simulation by sobolevnrm to the group baker-group on 2008-06-30 12:15:23 as read
  • Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory
    The Journal of Chemical Physics, Vol. 128, No. 18. (2008)
    by Yoshiteru Yonetani, Yutaka Maruyama, Fumio Hirata, Hidetoshi Kono
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-06-27 12:08:04 as read
  • Mono- and Trivalent Ions around DNA: A Small-Angle Scattering Study of Competition and Interactions
    Biophys. J., Vol. 95, No. 1. (1 July 2008), pp. 287-295.
    by Kurt Andresen, Xiangyun Qiu, Suzette A Pabit, Jessica S Lamb, Hye Y Park, Lisa W Kwok, Lois Pollack
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-06-16 18:15:25 as read
  • The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff
    Journal of Computational Chemistry (in press)
    by M Gruziel, P Grochowski, J Trylska
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-05-27 11:34:49 as read
  • Solvent Structure and Hammerhead Ribozyme Catalysis
    Chemistry & Biology, Vol. 15, No. 4. (21 April 2008), pp. 332-342.
    by Monika Martick, Tai-Sung Lee, Darrin M York, William G Scott
    posted to solvation nucleic_acids by sobolevnrm to the group baker-group on 2008-05-27 11:19:49 as read
  • Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations
    Biochemistry, Vol. 47, No. 19. (13 May 2008), pp. 5336-5353.
    by Richard Owczarzy, Bernardo G Moreira, Yong You, Mark A Behlke, Joseph A Walder
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-05-22 12:05:00 as read
  • Targeted Quantum Dot Conjugates for siRNA Delivery.
    Bioconjug Chem (14 July 2007)
    by Austin M Derfus, Alice A Chen, Dal-Hee H Min, Erkki Ruoslahti, Sangeeta N Bhatia
    posted to nucleic_acids nanotech drug_design ccne by sobolevnrm to the group baker-group on 2008-05-15 11:51:36 as ** along with 2 people jyuh ml115
  • Quantum dots to monitor RNAi delivery and improve gene silencing
    Nucleic Acids Research, Vol. 33, No. 22. (2005), pp. e190-e190.
    by Alice A Chen, Austin M Derfus, Salman R Khetani, Sangeeta N Bhatia
    posted to nucleic_acids imaging drug_design ccne by sobolevnrm to the group baker-group on 2008-05-15 11:46:38 as read along with 1 person ml115
  • Association of Aminoglycosidic Antibiotics with the Ribosomal A-Site Studied with Brownian Dynamics
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 549-559.
    by Maciej Długosz, Jan M Antosiewicz, Joanna Trylska
    posted to nucleic_acids electrostatics diffusion by sobolevnrm to the group baker-group on 2008-05-12 12:08:14 as read along with 1 person and 1 group barry McCammon
  • Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method
    Chemical Physics Letters, Vol. 454, No. 4-6. (20 March 2008), pp. 391-395.
    by Donghong Min, Hongzhi Li, Guohui Li, Bernd A Berg, Marcia O Fenley, Wei Yang
    posted to statistical_mechanics nucleic_acids molecular_simulation electrostatics by sobolevnrm to the group baker-group on 2008-05-08 11:41:20 as read
  • Enhanced delivery of antisense oligonucleotides with fluorophore-conjugated PAMAM dendrimers
    Nucl. Acids Res., Vol. 28, No. 21. (1 November 2000), pp. 4225-4231.
    by Hoon Yoo, RL Juliano
    posted to nucleic_acids nanotech imaging ccne by sobolevnrm to the group baker-group on 2008-05-08 11:18:40 as read along with 1 person ml115
  • Intracellular delivery of an anionic antisense oligonucleotide via receptor-mediated endocytosis
    Nucl. Acids Res. (26 March 2008), gkn115.
    by Md R Alam, Vidula Dixit, Hyunmin Kang, Zi-Bo Li, Xiaoyaun Chen, Joann Trejo, Michael Fisher, Rudy L Juliano
    posted to nucleic_acids nanotech ccne by sobolevnrm to the group baker-group on 2008-05-08 11:18:10 as read along with 1 person ml115
  • PAMAM Dendrimers as Delivery Agents for Antisense Oligonucleotides
    Pharmaceutical Research, Vol. 16, No. 12. (1 December 1999), pp. 1799-1804.
    by Hoon Yoo, Peter Sazani, RL Juliano
    posted to nucleic_acids nanotech ccne by sobolevnrm to the group baker-group on 2008-05-08 11:17:42 as read
  • Characterization of complexes of oligonucleotides with polyamidoamine starburst dendrimers and effects on intracellular delivery
    Journal of Pharmaceutical Sciences, Vol. 86, No. 6. (1997), pp. 762-764.
    by Robert Delong, Katherine Stephenson, Todd Loftus, Michael Fisher, Suresh Alahari, Arno Nolting, RL Juliano
    posted to nucleic_acids nanotech ccne by sobolevnrm to the group baker-group on 2008-05-07 11:35:40 as read along with 1 person ml115
  • Low-Frequency Electrophoretic Actuation of Nanoscale Optoentropic Transduction Mechanisms
    Nano Lett., Vol. 7, No. 4. (11 April 2007), pp. 950-955.
    by BD Sullivan, DA Dehlinger, S Zlatanovic, SA Esener, MJ Heller
    posted to nucleic_acids nanotech imaging ccne by sobolevnrm to the group baker-group on 2008-05-07 11:19:53 as read along with 1 person ml115
  • Oligonucleotide-Modified Gold Nanoparticles for Intracellular Gene Regulation
    Science, Vol. 312, No. 5776. (19 May 2006), pp. 1027-1030.
    by Nathaniel L Rosi, David A Giljohann, Shad C Thaxton, Abigail K Lytton-Jean, Min S Han, Chad A Mirkin
    posted to nucleic_acids nanotech ccne by sobolevnrm to the group baker-group on 2008-05-07 11:18:57 as read along with 1 person ml115
  • Screening the Sequence Selectivity of DNA-Binding Molecules Using a Gold Nanoparticle-Based Colorimetric Approach
    Anal. Chem., Vol. 79, No. 18. (15 September 2007), pp. 7201-7205.
    by SJ Hurst, MS Han, AKR Lytton-Jean, CA Mirkin
    posted to nucleic_acids nanotech ccne by sobolevnrm to the group baker-group on 2008-05-07 11:18:12 as read along with 1 person ml115
  • Maximizing DNA Loading on a Range of Gold Nanoparticle Sizes
    Anal. Chem., Vol. 78, No. 24. (15 December 2006), pp. 8313-8318.
    by SJ Hurst, AKR Lytton-Jean, CA Mirkin
    posted to nucleic_acids nanotech ccne by sobolevnrm to the group baker-group on 2008-05-07 11:17:49 as read along with 1 person ml115
  • Electrostatic Free Energy Landscapes for DNA Helix Bending
    Biophys. J., Vol. 94, No. 8. (15 April 2008), pp. 3137-3149.
    by Zhi-Jie Tan, Shi-Jie Chen
    posted to statistical_mechanics nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-05-05 11:11:07 as read along with 1 person sunhwan
  • Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules
    Physical Review Letters, Vol. 100, No. 11. (2008)
    by Liang Dai, Yuguang Mu, Lars Nordenskiöld, Johan RC van der Maarel
    posted to nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-05-02 11:13:36 as read along with 1 person kkims
  • DNA and its counterions: a molecular dynamics study.
    Nucleic Acids Res, Vol. 32, No. 14. (2004), pp. 4269-4280.
    by P Várnai, K Zakrzewska
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-29 19:40:22 as read
  • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    Biopolymers, Vol. 56, No. 4. (2001), pp. 232-256.
    by Iii Cheatham, MA Young
    posted to solvation nucleic_acids molecular_dynamics electrostatics by sobolevnrm to the group baker-group on 2008-04-29 19:38:40 as read
  • Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry
    Nucl. Acids Res. (14 February 2008), gkn008.
    by Yao C Chen, Carmay Lim
    posted to structure protein-nucleic_acid_interactions nucleic_acids electrostatics bioinformatics by sobolevnrm to the group baker-group on 2008-04-29 11:22:51 as read along with 3 people marck kaarsinogen sunhwan
  • Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E
    Biophys. J., Vol. 84, No. 6. (1 June 2003), pp. 3564-3582.
    by Kamila Reblova, Nad'a Spackova, Richard Stefl, Kristina Csaszar, Jaroslav Koca, Neocles B Leontis, Jiri Sponer
    posted to solvation nucleic_acids by sobolevnrm to the group baker-group on 2008-04-25 16:19:18 as read
  • Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability
    Proceedings of the National Academy of Sciences, Vol. 104, No. 30. (24 July 2007), pp. 12336-12340.
    by Michael T Sykes, Michael Levitt
    posted to solvation nucleic_acids by sobolevnrm to the group baker-group on 2008-04-25 16:16:00 as read
  • Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding
    Journal of Molecular Biology, Vol. 313, No. 5. (9 November 2001), pp. 1073-1091.
    by Kristina Csaszar, Nad'a Spacková, Richard Stefl, Jirí Sponer, Neocles B Leontis
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 15:54:39 as read
  • Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator
    Journal of Molecular Biology, Vol. 282, No. 4. (2 October 1998), pp. 859-873.
    by Alexandre M Bonvin, Maria Sunnerhagen, Gottfried Otting, Wilfred F van Gunsteren
    posted to solvation protein-nucleic_acid_interactions nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 15:52:31 as read
  • RNA solvation: A molecular dynamics simulation perspective
    Biopolymers, Vol. 56, No. 4. (2000), pp. 266-274.
    by Pascal Auffinger, Eric Westhof
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 15:43:05 as read
  • A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.
    Biophys. J., Vol. 73, No. 5. (1 November 1997), pp. 2313-2336.
    by MA Young, G Ravishanker, DL Beveridge
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 15:37:20 as read
  • NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex
    Journal of Molecular Biology, Vol. 302, No. 5. (6 October 2000), pp. 1101-1117.
    by Vickie Tsui, Ishwar Radhakrishnan, Peter E Wright, David A Case
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 15:30:08 as read
  • Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes.
    J Mol Biol, Vol. 305, No. 5. (2 February 2001), pp. 1057-1072.
    by P Auffinger, E Westhof
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 15:07:46 as read along with 1 person lillekatt
  • Water and ion binding around RNA and DNA (C,G) oligomers.
    J Mol Biol, Vol. 300, No. 5. (28 July 2000), pp. 1113-1131.
    by P Auffinger, E Westhof
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 15:04:29 as read along with 2 people lillekatt ffranca
  • Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation
    Journal of Molecular Biology, Vol. 286, No. 4. (5 March 1999), pp. 1075-1095.
    by Michael Feig, Montgomery B Pettitt
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 15:00:38 as read
  • A molecular simulation picture of DNA hydration around A- and B-DNA
    Biopolymers, Vol. 48, No. 4. (1998), pp. 199-209.
    by Michael Feig, Montgomery B Pettitt
    posted to solvation nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2008-04-25 14:56:37 as read
  • Recent advances in the study of nucleic acid flexibility by molecular dynamics
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Modesto Orozco, Agnes Noy, Alberto Pérez
    posted to molecular_simulation nucleic_acids by sobolevnrm to the group baker-group on 2008-04-15 11:50:15 as read along with 2 people mazo onufriev
  • Dynamics of Recognition between tRNA and Elongation Factor Tu
    Journal of Molecular Biology, Vol. 377, No. 5. (11 April 2008), pp. 1382-1405.
    by John Eargle, Alexis A Black, Anurag Sethi, Leonardo G Trabuco, Zaida Luthey-Schulten
    posted to allostery electrostatics nucleic_acids protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-03-25 11:14:58 as read
  • Nanoparticulate delivery of suicide DNA to murine prostate and prostate tumors
    The Prostate, Vol. 67, No. 8. (2007), pp. 855-862.
    by Weidan Peng, Daniel G Anderson, Yunhua Bao, Robert F Padera, Robert Langer, Janet A Sawicki
    posted to cancer ccne drug_design nanotech nucleic_acids by sobolevnrm to the group baker-group on 2008-03-12 11:22:23 as read along with 1 person ml115
  • Interplay of ion binding and attraction in DNA condensed by multivalent cations
    Nucl. Acids Res., Vol. 36, No. 2. (2 February 2008), pp. 501-510.
    by Brian A Todd, Donald C Rau
    posted to electrostatics nucleic_acids solvation by sobolevnrm to the group baker-group on 2008-02-29 12:40:04 as read along with 1 person and 1 group skoch3 Koch_Lab
  • Structure and Dynamics of Poly(T) Single-Strand DNA: Implications toward CPD Formation
    J. Phys. Chem. B, Vol. 111, No. 51. (27 December 2007), pp. 14398-14404.
    by AT Johnson, O Wiest
    posted to molecular_dynamics molecular_simulation nucleic_acids by sobolevnrm to the group baker-group on 2008-02-01 12:50:34 as read
  • Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin
    J. Am. Chem. Soc., Vol. 130, No. 3. (23 January 2008), pp. 815-817.
    by AE Garcia, D Paschek
    posted to molecular_dynamics molecular_simulation nucleic_acids by sobolevnrm to the group baker-group on 2008-01-30 12:42:58 as read
  • Visualizing spatially correlated dynamics that directs RNA conformational transitions
    Nature, Vol. 450, No. 7173., pp. 1263-1267.
    by Qi Zhang, Andrew C Stelzer, Charles K Fisher, Hashim M Al-Hashimi
    posted to molecular_dynamics nmr nucleic_acids by sobolevnrm to the group baker-group on 2008-01-29 12:25:39 as read along with 7 people and 2 groups simone nigham cactus niallhaslam joseph_x_zhou kintoki kluck HIV_DR Soft Matter
  • Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Ninad V Prabhu, Manoranjan Panda, Qingyi Yang, Kim A Sharp
    posted to electrostatics nucleic_acids solvation by sobolevnrm to the group baker-group on 2008-01-21 12:55:09 as read along with 3 people dimka RamuAnandakrishnan onufriev
  • Interplay of ion binding and attraction in DNA condensed by multivalent cations
    Nucleic Acids Research (in press)
    by BA Todd, DC Rau
    posted to electrostatics nucleic_acids by sobolevnrm to the group baker-group on 2008-01-03 12:21:47 as read
  • Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin
    Nucl. Acids Res., Vol. 35, No. 20. (29 November 2007), pp. 6995-7002.
    by Zhuoyun Zhuang, Luc Jaeger, Joan-Emma Shea
    posted to molecular_simulation nucleic_acids protein_folding by sobolevnrm to the group baker-group on 2008-01-02 12:32:22 as read
  • Dynamics of B-DNA on the Microsecond Time Scale
    J. Am. Chem. Soc., Vol. 129, No. 47. (28 November 2007), pp. 14739-14745.
    by A Perez, FJ Luque, M Orozco
    posted to electrostatics molecular_simulation nucleic_acids solvation by sobolevnrm to the group baker-group on 2007-12-17 13:00:05 as read
  • Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids
    J. Am. Chem. Soc., Vol. 129, No. 48. (5 December 2007), pp. 14981-14988.
    by Y Bai, M Greenfeld, KJ Travers, VB Chu, J Lipfert, S Doniach, D Herschlag
    posted to electrostatics nucleic_acids solvation by sobolevnrm to the group baker-group on 2007-12-14 13:05:08 as read
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