List of publications

19- Oberstrass F.C., Lee A., Stefl R., Janis M., Chanfreau G. and Allain F.H.-T. (2006)
"Shape-specific recognition in the structure of the Vts1p SAM domain with RNA"
Nat. Struc. Mol. Biol., 13, 160-167
Abstract, Full text

18- Stefl R., Xu M., Skrisovska L., Emeson R.B. and Allain F.H.-T.
"Structure and specific RNA-binding of ADAR2 double-stranded RNA-binding motifs" (2006)
Structure, 14, 345-355
Abstract, Full text

17- Stefl R. and Allain F.H.-T. (2005)
"A novel RNA pentaloop fold involved in targeting ADAR2"
RNA, 11, 592-597
Abstract, Full text

16- Stefl R., Skrisovska L., Xu M., Emeson R.B. and Allain F.H.-T. (2005)
Resonance assignment of the double-stranded RNA-binding domains of adenosine deaminase acting of RNA 2 (ADAR2)
J. Biomol. NMR, 31, 71-72
Abstract, Full text

15- Stefl R., Skrisovska L. and Allain, F.H.-T. (2005)
"RNA sequence- and shape-dependant recognition by proteins in the ribonucleoprotein particle"
EMBO Reports, 6, 33-8
Abstract, Full text

14- Fadrna E., Spackova N., Stefl R., Koca J., Cheatham T.E. 3rd and Sponer J. (2004)
"Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations"
Biophys J., 87(1), 227-42
Abstract, Full text

13- Stefl R., Wu H., Ravindranathan S., Sklenar V. and Feigon J. (2004)
"DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum"
Proc Natl Acad Sci U S A., 101(5):1177-82
Abstract, Full text

12- Stefl R., Cheatham T.E. 3rd, Spackova N., Fadrna E., Berger I., Koca J. and Sponer J. (2003)
"Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates"
Biophys J., 85(3), 1787-804
Abstract, Full text

11- Reblova K., Spackova N., Stefl R., Csaszar K., Koca J., Leontis N.B. and Sponer J. (2003)
"Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E"
Biophys J., 84(6), 3564-82
Abstract, Full text

10- Padrta P., Stefl R., Kralik L., Zidek L. and Sklenar V. (2002)
"Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings"
J. Biomol. NMR., 24(1), 1-14
Abstract, Full text

9- Trantirek L., Stefl R., Masse J.E., Feigon J. and Sklenar V. (2002)
"Determination of the glycosidic torsion angles in uniformly 13C-labeled nucleic acids from vicinal coupling constants 3J(C2)/4-H1' and 3J(C6)/8-H1'"
J. Biomol. NMR., 23(1):1-12
Abstract, Full text

8- Csaszar K., Spackova N., Stefl R., Sponer J. and Leontis N.B. (2001)
"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"
J. Mol. Biol., 313, 1073-1091
Abstract, Full text

7- Zidek L., Stefl R and Sklenar V. (2001)
"NMR methodology for the study of nucleic acids"
Curr. Opin. Struct. Biol., 11, 275-281
Abstract, Full text

6- Stefl R., Trantirek L., Vorlickova M., Koca J., Sklenar V. and Kypr J. (2001)
"A-like Guanine-Guanine Stacking in the Aqueous DNA Duplex of d(GGGGCCCC)"
J. Mol. Biol., 307, 513-524
Abstract, Full text

5- Stefl R., Spackova N., Berger I., Koca J. and Sponer J. (2001)
"Molecular Dynamics of DNA Quadruplex Molecules Containing Inosine, 6-Thioguanine and 6-Thiopurine"
Biophys. J., 80, 455-468
Abstract, Full text

4- Trantirek L., Urbasek M., Stefl R., Feigon J. and Sklenar V. (2000)
A method for direct determination of helical parameters in nucleic acids using residual dipolar couplings.
J. Am. Chem. Soc., 122, 10454-10455
No abstract, Full text

3- Stefl R. and Koca J. (2000)
"Unrestrained molecular dynamics simulations of [d(AT)5]2 duplex in aqueous solution: Hydration and binding of sodium ions in the minor groove"
J. Am. Chem. Soc., 122, 5025-5033
Abstract, Full text

2- Trantirek L., Stefl R., Vorlickova M., Koca J., Sklenar V. and Kypr J. (2000)
"An A-type double helix of DNA having B-type puckering of the deoxyribose rings"
J. Mol. Biol., 297, 907-922
Abstract, Full text

1- Stefl R., Fadrna E. and Koca J. (1999)
"Differences in conformational behavior of ATA and TAT sequences in single strand DNA trimers"
J. Biomol. Struct. Dyn., 16, 1087-1095
Abstract