Hänsel R, Luh LM, Corbeski I, Trantirek L, Dötsch V.In-cell NMR & EPR spectroscopy of biomacromolecules. [Submitted]
Bernatik O, Novakova K, Sri Ganji R, Červenka I, Trantirek L, Zdrahal Z, Bryja V.Functional analysis of Dishevelled3 phosphorylation identifies distinct mechanisms driven
by Casein Kinase 1ε and Fzd5. [Submitted]
Buchtova M, Vesela I, Zakrzewska M, Chaloupkova R, Cela P, Zajickova R, Trantirek L,
Martin J, Balek L, Kostas M, Otlewski J, Damborsky J, Kozubik A, Wiedlocha A, Krejci P.Instability restricts signaling of multiple fibroblast growth factors. [Submitted]
Šebera J, Trantírek L, Tanaka Y, Nencka R, Fukal J, Sychrovský V.The N-glycosidic bond activation for catalytic base excision with hOGG1 enzyme;
theoretical study of the role of lysine 249 hOGG1 residue. [Submitted]
2013
Krejci P, Kunova M, Kubikova I, Trantirek L, Kozubik A, Dvorak P.Expression
of FGF19 in Human Embryonic Stem Cells. Stem Cells. 2013 Nov; 31(11):2582-4.
Hänsel R, Löhr F, Trantirek L, Dötsch V.High-resolution insight into
G-overhang architecture. J Am Chem Soc. 2013 Feb 20; 135(7):2816-24.
Emmer J, Vavrinská A, Sychrovský V, Benda L, Kříž Z, Koča J, Boelens R,
Sklenář V, Trantírek L.Influence of the O-phosphorylation of serine, threonine
and tyrosine in proteins on the amidic 15N chemical shielding anisotropy tensors.
J Biomol NMR. 2013 Jan; 55(1):59-70.
Hänsel R, Foldynová-Trantírková S, Dötsch V, Trantírek L.Investigation of
quadruplex structure under physiological conditions using in-cell NMR. Top Curr
Chem. 2013; 330:47-65.
2012
Šebera J, Trantírek L, Tanaka Y, Sychrovský V. Pyramidalization of the
glycosidic nitrogen provides the way for efficient cleavage of the N-glycosidic
bond of 8-OxoG with the hOGG1 DNA repair protein. J Phys Chem B. 2012 Oct
18; 116(41):12535-44.
Fessl T, Adamec F, Polívka T, Foldynová-Trantírková S, Vácha F, Trantírek L.
Towards characterization of DNA structure under physiological conditions in vivo at the single-molecule
level using single-pair FRET. Nucleic Acids Res. 2012
Sep; 40(16):e121.
Sychrovský V, Sochorová Vokáčová Z, Trantírek L. Guanine bases in DNA
G-quadruplex adopt nonplanar geometries owing to solvation and base pairing. J
Phys Chem A. 2012 Apr 26; 116(16):4144-51.
2011
Fiala R, Spacková N, Foldynová-Trantírková S, Sponer J, Sklenár V, Trantírek
L. NMR cross-correlated relaxation rates reveal ion coordination sites in DNA. J
Am Chem Soc. 2011 Sep 7; 133(35):13790-3.
Hänsel R, Löhr F, Foldynová-Trantírková S, Bamberg E, Trantírek L, Dötsch V.
The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is
not the preferred folding topology under physiological conditions. Nucleic Acids
Res. 2011 Jul; 39(13):5768-75.
2010
Vokácová Z, Trantírek L, Sychrovský V. Evaluating the effects of the
nonplanarity of nucleic acid bases on NMR, IR, and vibrational circular dichroism
spectra: a density functional theory computational study. J Phys Chem A. 2010 Sep 23; 114(37):10202-8.
Foldynová-Trantírková S, Sekyrová P, Tmejová K, Brumovská E, Bernatík O,
Blankenfeldt W, Krejcí P, Kozubík A, Dolezal T, Trantírek L, Bryja V. Breast
cancer-specific mutations in CK1epsilon inhibit Wnt/beta-catenin and activate
the Wnt/Rac1/JNK and NFAT pathways to decrease cell adhesion and promote cell migration.
Breast Cancer Res. 2010; 12(3):R30.
Krejci P, Murakami S, Prochazkova J, Trantirek L, Chlebova K, Ouyang Z,
Aklian A, Smutny J, Bryja V, Kozubik A, Wilcox WR. NF449 is a novel inhibitor of
fibroblast growth factor receptor 3 (FGFR3) signaling active in chondrocytes and
multiple myeloma cells. J Biol Chem. 2010 Jul 2; 285(27):20644-53.
Kubícek K, Monnet J, Scintilla S, Kopecná J, Arnesano F, Trantírek L, Chopard
C, Natile G, Kozelka J. Unusual interstrand Pt(S,S-diaminocyclohexane)-GG
crosslink formed by rearrangement of a classical intrastrand crosslink within a
DNA duplex. Chem Asian J. 2010 Feb 1; 5(2):244-7.
2009
Hänsel R, Foldynová-Trantírková S, Löhr F, Buck J, Bongartz E, Bamberg E,
Schwalbe H, Dötsch V, Trantírek L. Evaluation of parameters critical for
observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR
spectroscopy. J Am Chem Soc. 2009 Nov 4; 131(43):15761-8.
Sychrovsky V, Foldynova-Trantirkova S, Spackova N, Robeyns K, Van Meervelt
L, Blankenfeldt W, Vokacova Z, Sponer J, Trantirek L. Revisiting the planarity
of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is
modulated by orientation of glycosidic torsion. Nucleic Acids Res. 2009 Nov; 37(21):7321-31.
Foldynová-Trantirková S, Matulová J, Dötsch V, Löhr F, Cirstea I, Alexandov
K, Breitling R, Lukes J, Trantírek L. A cost-effective amino-acid-type selective
isotope labeling of proteins expressed in Leishmania tarentolae. J Biomol Struct
Dyn. 2009 Jun; 26(6):755-61.
2008
Brumovská E, Sychrovský V, Vokácová Z, Sponer J, Schneider B, Trantírek L.
Effect of local sugar and base geometry on 13C and 15N magnetic shielding
anisotropy in DNA nucleosides. J Biomol NMR. 2008 Nov; 42(3):209-23.
Zíková A, Kopecná J, Schumacher MA, Stuart K, Trantírek L, Lukes J. Structure
and function of the native and recombinant mitochondrial MRP1/MRP2 complex from Trypanosoma brucei.
Int J Parasitol. 2008 Jul; 38(8-9):901-12.
2007
Trantírek L, Caha E, Kaderávek P, Fiala R. NMR (13)C-relaxation study of base
and sugar dynamics in GCAA RNA hairpin tetraloop. J Biomol Struct Dyn. 2007
Dec; 25(3):243-52.
2006
Schumacher MA, Karamooz E, Zíková A, Trantírek L, Lukes J. Crystal structures of T. brucei MRP1/MRP2
guide-RNA binding complex reveal RNA matchmaking mechanism. Cell. 2006 Aug 25; 126(4):701-11.
Richards RJ, Wu H, Trantirek L, O'Connor CM, Collins K, Feigon J. Structural
study of elements of Tetrahymena telomerase RNA stem-loop IV domain important for function. RNA. 2006 Aug; 12(8):1475-85.
Sychrovský V, Sponer J, Trantírek L, Schneider B. Indirect NMR spin-spin
coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for
structure determination of nucleic acids. J Am Chem Soc. 2006 May
31; 128(21):6823-8.
2005 and older
Sychrovský V, Müller N, Schneider B, Smrecki V, Spirko V, Sponer J, Trantírek
L. Sugar pucker modulates the cross-correlated relaxation rates across the
glycosidic bond in DNA. J Am Chem Soc. 2005 Oct 26; 127(42):14663-7.
Johansson C, Finger LD, Trantirek L, Mueller TD, Kim S, Laird-Offringa IA,
Feigon J. Solution structure of the complex formed by the two N-terminal
RNA-binding domains of nucleolin and a pre-rRNA target. J Mol Biol. 2004 Apr
2; 337(4):799-816.
Finger LD, Trantirek L, Johansson C, Feigon J. Solution structures of
stem-loop RNAs that bind to the two N-terminal RNA-binding domains of nucleolin.
Nucleic Acids Res. 2003 Nov 15; 31(22):6461-72.
Theimer CA, Finger LD, Trantirek L, Feigon J. Mutations linked to
dyskeratosis congenita cause changes in the structural equilibrium in telomerase
RNA. Proc Natl Acad Sci U S A. 2003 Jan 21; 100(2):449-54.
Trantírek L, Stefl R, Masse JE, Feigon J, Sklenár V. 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. 2002 May; 23(1):1-12.
Stefl R, Trantírek L, Vorlícková M, Koca J, Sklenár V, Kypr J. A-like
guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC).
J Mol Biol. 2001 Mar 23; 307(2):513-24.
Trantírek L, Hynková K, Nagata Y, Murzin A, Ansorgová A, Sklenár V, Damborský J.
Reaction mechanism and stereochemistry of gamma-hexachlorocyclohexane dehydrochlorinase LinA.
J Biol Chem. 2001 Mar 16; 276(11):7734-40.
Damborský J, Damborská M, Stípek S, Jesenská A, Trantírek L, Sklenár V.
Effect of the carbon source on assessment of degrading bacteria with the
spread-plating technique during in situ bioremediation. Folia Microbiol (Praha).
2000; 45(1):35-40.
Trantírek L, Stefl R, Vorlícková M, Koca J, Sklenár V, Kypr J. An A-type
double helix of DNA having B-type puckering of the deoxyribose rings. J Mol Biol.
2000 Apr 7; 297(4):907-22.
Trantirek L, Urbasek M, Stefl R, Feigon J, Sklenar V. A method for direct
determination of helical parameters in nucleic acids using residual dipolar couplings.
J. Am. Chem. Soc., 2000, 122, 10454-10455
Books/Book chapters/Popularization
Dötsch V, Trantírek L. DNA folding in “crowded” conditions. Chemical & engineering news. 2011, 89(32):6.
Schöfberger W, Sychrovský V, Trantírek L. Quantum Chemical Calculations of NMR Parameters.
Computational studies of RNA and DNA ,2006, ISBN 978-1-4020-4851-7.