These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

164 related articles for article (PubMed ID: 22722325)

  • 1. Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes.
    Morgado CA; Svozil D; Turner DH; Šponer J
    Phys Chem Chem Phys; 2012 Sep; 14(36):12580-91. PubMed ID: 22722325
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?
    Svozil D; Hobza P; Sponer J
    J Phys Chem B; 2010 Jan; 114(2):1191-203. PubMed ID: 20000584
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.
    Chen G; Kierzek R; Yildirim I; Krugh TR; Turner DH; Kennedy SD
    J Phys Chem B; 2007 Jun; 111(24):6718-27. PubMed ID: 17411085
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.
    Deb I; Popenda Ł; Sarzyńska J; Małgowska M; Lahiri A; Gdaniec Z; Kierzek R
    Sci Rep; 2019 Nov; 9(1):16278. PubMed ID: 31700156
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations.
    Mládek A; Sharma P; Mitra A; Bhattacharyya D; Sponer J; Sponer JE
    J Phys Chem B; 2009 Feb; 113(6):1743-55. PubMed ID: 19152254
    [TBL] [Abstract][Full Text] [Related]  

  • 6. How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations.
    Negi I; Kathuria P; Sharma P; Wetmore SD
    Phys Chem Chem Phys; 2017 Jun; 19(25):16365-16374. PubMed ID: 28657627
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair.
    Chawla M; Autiero I; Oliva R; Cavallo L
    Phys Chem Chem Phys; 2018 Jan; 20(5):3699-3709. PubMed ID: 29345270
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs.
    Burkard ME; Kierzek R; Turner DH
    J Mol Biol; 1999 Jul; 290(5):967-82. PubMed ID: 10438596
    [TBL] [Abstract][Full Text] [Related]  

  • 9. NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs.
    Tolbert BS; Kennedy SD; Schroeder SJ; Krugh TR; Turner DH
    Biochemistry; 2007 Feb; 46(6):1511-22. PubMed ID: 17279616
    [TBL] [Abstract][Full Text] [Related]  

  • 10. The detailed structure of tandem G.A mismatched base-pair motifs in RNA duplexes is context dependent.
    Heus HA; Wijmenga SS; Hoppe H; Hilbers CW
    J Mol Biol; 1997 Aug; 271(1):147-58. PubMed ID: 9300061
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Investigating the Effect of Chemical Modifications on the Ribose Sugar Conformation, Watson-Crick Base Pairing, and Intrastrand Stacking Interactions: A Theoretical Approach.
    Das G; Harikrishna S; Gore KR
    J Phys Chem B; 2024 Sep; 128(35):8313-8331. PubMed ID: 39172066
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.
    Pan Y; Priyakumar UD; MacKerell AD
    Biochemistry; 2005 Feb; 44(5):1433-43. PubMed ID: 15683228
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view.
    Sponer JE; Réblova K; Mokdad A; Sychrovský V; Leszczynski J; Sponer J
    J Phys Chem B; 2007 Aug; 111(30):9153-64. PubMed ID: 17602515
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Formation of sheared G:A base pairs in an RNA duplex modelled after ribozymes, as revealed by NMR.
    Katahira M; Kanagawa M; Sato H; Uesugi S; Fujii S; Kohno T; Maeda T
    Nucleic Acids Res; 1994 Jul; 22(14):2752-9. PubMed ID: 7519767
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.
    Yildirim I; Stern HA; Sponer J; Spackova N; Turner DH
    J Chem Theory Comput; 2009 Aug; 5(8):2088-2100. PubMed ID: 20090924
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment.
    Brown RF; Andrews CT; Elcock AH
    J Chem Theory Comput; 2015 May; 11(5):2315-28. PubMed ID: 26574427
    [TBL] [Abstract][Full Text] [Related]  

  • 17. The 5-Me of thyminyl (T) interaction with the neighboring nucleobases dictate the relative stability of isosequential DNA-RNA hybrid duplexes.
    Chatterjee S; Pathmasiri W; Chattopadhyaya J
    Org Biomol Chem; 2005 Nov; 3(21):3911-5. PubMed ID: 16240008
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).
    Chen X; McDowell JA; Kierzek R; Krugh TR; Turner DH
    Biochemistry; 2000 Aug; 39(30):8970-82. PubMed ID: 10913310
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Thermodynamic stability and solution conformation of tandem G.A mismatches in RNA and RNA.DNA hybrid duplexes.
    Ebel S; Brown T; Lane AN
    Eur J Biochem; 1994 Mar; 220(3):703-15. PubMed ID: 8143725
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations.
    Reha D; Hocek M; Hobza P
    Chemistry; 2006 Apr; 12(13):3587-95. PubMed ID: 16502452
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.