LABORATORY OF STRUCTURAL CHEMISTRY OF NUCLEIC ACIDS

Head:Ryszard W. Adamiak

Research Staff:
Katarzyna Pachulska-Wieczorek, Mariusz Popenda, Katarzyna J. Purzycka

Reserach Support:
Grażyna Dominiak

Ph.D. Students:
Tomasz Woźniak, Agnieszka K. Stefaniak

Keywords:
RNA chemistry, RNA structure and dynamics, RNA hydration, RNA-metal, small ligand and protein interactions; 1H, 13C, 19F NMR spectroscopy, time-resolved spectrofluorimetry, FT-IR, simulation of molecular dynamics

The Laboratory's current aim is to understand the structure, function and interactions of functionally important domains of RNA on atomic and molecular level. The idea is to combine, within the group, the synthetic and structural lines of research in the RNA field. The RNA chemical/in vitro synthesis, [13C, 15N, fluorine]- and fluorophore- labeling, including post-synthetic modifications, and RNA chemistry are dedicated to structural studies. Particular areas of interest include: retroviral RNAs (HIV-2) and their interactions with metal ions, small inhibitory molecules and recombinant proteins, studies on 2'-O-methylated RNA, structure of non-helical RNA regions (bulges, hairpins), RNA hydration and non-canonical (CG)n structures with respect to the mechanism of RNA helicity reversal. We are advancing to the RNA therapeutics (sRNAi). The major methodologies include biomolecular NMR spectroscopy, thermodynamics and optical spectroscopies. The use of 19F NMR of RNA is well advanced. Thanks to the access to in-house supercomputing and networking facilities (Poznan Supercomputing and Networking Center) simulation of molecular dynamics is intensively conducted in our Laboratory. With respect to the latter, developing new computational approaches for modeling of RNA structure and interactions leading to the prediction of properties of new RNA analogues in an aqueous solution i.e. determination of free energy changes upon the modification of the structure, small molecule bonding, water mediated hydrogen bonding and C-H...O bonding are of our interest.

Current research activities:

design and application of regioselectively modified oligoribonucleotides for 1H, 13C and 19F NMR studies of RNA structure, dynamics and interactions with metal cations, small ligands and recombinant proteins;

chemistry of nucleoside fluorophores and their introduction into oligonucleotides;

studies on the NMR structure and dynamics of RNA domains (RNA duplexes containing alternating CG base pairs, TAR RNA HIV-1) and interactions on the RNA-protein interface (13C-[C5-ribose]labelled TAR RNA and Tat-1 and Tat-2 proteins);

mechanism of "A --> Z" transition in RNA;

thermodynamics, dynamics via time-resolved spectrofluorimetry of RNA bulges, TAR RNA HIV-1;

developing new computational approaches for modelling of RNA structure and interactions leading to the prediction of the properties of new RNA analogs in aqueous solution i.e. determination of free energy changes upon the modification of the structure, determination of non-standard hydrogen bonding, water mediated hydrogen bonding and their participation in the stabilization of RNA structural domains (various regions of rRNA, retroviral RNA's) under different ionic conditions;

optimisation of different numerical methods to estimate free energy, such as free energy perturbation or methods combining molecular mechanics and continuum models for the prediction of binding affinities and stability changes of RNA;

RNA therapeutics.

BIOMOLECULAR NMR GROUP

Head: Zofia Gdaniec

Reserach Support:
Elżbieta Pasternak, Grażyna Dominiak, Anna Taubert

Ph.D. Students:
Dorota Gudanis, Magdalena Małgowska

Keywords:
NMR spectroscopy, RNA structure and dynamics, metal ion binding, RNA bulged duplexes, RNA structure calculation, virtual NMR laboratory

High-resolution NMR spectroscopy is used to probe the structure and dynamics of ribonucleic acids in solution. Of our major interest are structural studies of RNA fragments in order to understand the relationship between the sructures of these molecules and their biological functions.

Current research activities:

conformational studies of bulged RNA duplexes;

molecular modelling studies of RNA;

application of heteronuclear NMR spectroscopy to study RNA-metal ions interaction;

Virtual NMR Laboratory. A pilot project in collaboration with Poznań Supercomputing and Networking Center.

BIOMOLECULAR MODELING GROUP

Head: Tadeusz Kuliński

Research Staff:
Katarzyna Kulińska, Joanna Sarzyńska

Reserach Support:
Bartłomiej Gramowski

Keywords:
RNA structure and dynamics, structure-function relationship, hydration and metal ion binding,small ligand and protein interactions, RNA structural motifs, RNA structure prediction, RNA folding, molecular recognition, Molecular Dynamics simulations, Free energy calculations, Forcefield development, modified nucleosides, Rational drug design, RNA therapeutics.

Of our major interest are structural studies of RNA fragments in order to understand the relationship between the structures of these molecules and their biological functions. We are using different computational approaches for modeling of RNA structure and interactions, determination of non-standard hydrogen bonding, water mediated hydrogen bonding and their participation in the stabilization of RNA structural domains (various regions of ribosomal RNA, retroviral RNA's) under different ionic conditions. We are working on the optimization of different numerical methods to estimate free energy, such as free energy perturbation or methods combining molecular mechanics and continuum models for the prediction of binding affinities and stability changes of RNA, for the prediction of the properties of new RNA analogs in aqueous solution i.e. determination of free energy changes upon the modification of the structure.

Current research activities:

Structure-function relationship, functionally important RNA structural motifs;

RNA structure formation;

role of monovalent and divalent cations;

Role of modified nucleosides in structure and function of RNA;

Regulation of gene expression by small RNAs;

Molecular modeling of RNA, computer methods for the prediction of nucleic acids structure and biomolecular interactions;

Molecular Dynamics simulations of RNA and proteins;

Molecular Dynamics force fields development;

Thermodynamics, free energy calculation, free energy perturbation;

Molecular recognition;

RNA therapeutics.

SELECTED PUBLICATIONS

K. Kulińska, T. Kuliński, A. Lyubartsev, A. Laaksonen, R. W. Adamiak
Spatial distribution functions as a tool in the analysis of ribonucleic acids hydration – Molecular Dynamics studies.
Comp. Chem. 24, 451-457 (2000).

Y. Ke, H. Sierzputowska-Gracz, Z. Gdaniec, E. C. Theil
Internal loop/bulge and hairpin loop of the iron-responsive element of ferritin mRNA contribute to maximal iron regulatory protein 2 binding and translational regulation in the iso-iron-responsive element/iso-iron regulatory protein family.
Biochemistry 39, 6235-6242 (2000).

G. Wenska, B. Skalski, Z. Gdaniec, R. W. Adamiak, J. Matulic-Adamic, L. Beigelman
Photophysical and photochemical properties of C-linked ribosides of pyridin-2-one.
J. Photochem. Photobiol. A-Chem. 133, 169-176 (2000).

J. Sarzynska, T. Kulinski, L. Nilsson
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
Biophys. J. 79, 1213-27 (2000).

J. W. Stuart, Z. Gdaniec, R. Guenther, M. Marszałek, E. Sochacka, A. Małkiewicz, P. F. Agris
Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A.
Biochemistry 39, 13396-13404 (2000).

U. Kaukinen, L. Bielecki, S. Mikkola, R. W. Adamiak, H. Lonnberg
The cleavage of phosphodiester bonds within small RNA bulges in the presence and absence of metal ion catalysts.
J. Chem. Soc. Perkin Trans. 2, 1024-1031 (2001).

D. A. Adamiak, W. R. Rypniewski, J. Milecki, R. W. Adamiak
The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)2 duplex shows dehydrated RNA with 2 methyl-2,4-pentanediol in the minor groove.
Nucleic Acids Res. 29, 4144-4153 (2001).

T. Kuliński, £. Bielecki, R. W. Adamiak
Structure and dynamics of adenosine loops in RNA bulge duplexes as revealed by linked application of molecular dynamics.
Nucleic Acids Research Supplement 1, 139-140 (2001).

G. Wenska, K. Taras-Go¶lińska, K. Lamparska-Kupsik, B. Skalski, M. Gdaniec, Z. Gdaniec
Photochemical transformations of 5-halogeno-4-thiouridines.
J. Chem. Soc. Perkin Trans. 1, 53-57 (2002).

L. Bielecki, M. Popenda, R.W. Adamiak
The molecular dynamics thermocycler. A new approach to sample conformational space, as exemplified by the RNA hairpin.
Nucleic Acids Res. Supplement 2, 57-58 (2002).

T. Kuliński, K. Kulińska
Molecular Dynamics of RNA structural motif. Temperature enhanced sampling of the conformational space.
Comp. Meth. Sci. Tech. 1, 43-52 (2002).

M. Olejniczak, Z. Gdaniec, A. Fischer, T. Grabarkiewicz, £. Bielecki, R. W. Adamiak
The bulge region of HIV-1 TAR RNA binds metal ions in solution.
Nucleic Acids Res. 30, 4241-4249 (2002).

T. Kulinski, M. Olejniczak, H. Huthoff, L. Bielecki, K. Pachulska-Wieczorek, D. Atze, B. Berkhout, R. W. Adamiak
The apical loop of the HIV-1 TAR RNA hairpin is stabilized by cross-loop base pair.
J. Biol. Chem. 278, 38892-38901 (2003).

M. Cie¶lak, J. Szymański, R. W. Adamiak, C. S. Cierniewski
Structural rearrangements of the „10-23” DNAzyme to beta 3 integrin subunit mRNA induced by cations and their relations to the catalytic activity.
J. Biol. Chem. 279, 47987-47996 (2003).

S. Hajdasz, Z.Gdaniec, L. Latanowicz
Application of the „model-free approach” to study the internal dynamics of biological molecules.
Mol. Phys. Rep. 37, 80-87 (2003).

J. Sarzynska, L. Nilsson, T. Kulinski
Effects of base substitutions in an RNA hairpin from Molecular Dynamics and Free Energy simulations.
Biophys. J. 85, 3445 (2003).

P. Auffinger, £. Bielecki, E. Westhof
The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations.
Chem. Biol. 10, 551-561 (2003).

J. Sarzynska, K. Kulińska, T. Kuliński
Parametrization of 2-aminopurine and purine in CHARMM force field.
Comp. Meth. Sci. Tech. 9, 127-135 (2003).

A. Timoszyk, Z. Gdaniec, L. Latanowicz
The effect of polysialic acid on molecular dynamics of model membranes studied by 31P NMR spectroscopy.
Solid State Nucl. Mag. Res. 25, 142-145 (2004).

P. Auffinger, £. Bielecki, E. Westhof
Symmetric K+ and Mg2+ ion binding sites in the 5S rRNA loop E motif inferred from molecular dynamics simulations.
J. Mol. Biol. 335, 555-571 (2004).

Auffinger, £. Bielecki, E. Westhof
Anion binding to nucleic acids.
Structure 12, 379-388 (2004).

R. W. Adamiak, J. Blażewicz, P. Formanowicz, Z. Gdaniec, M. Kasprzak, I. Król, M. Popenda, M. Szachniuk
An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes.
J. Comput. Biol. 11, 167-183 (2004).

M. Popenda, J. Milecki, R. W. Adamiak
High salt solution structure of a left-handed RNA double helix.
Nucleic Acids Res. 32, 4044-4054 (2004).

J. Sarzynska, T. Kuliński
Dynamics and Stability of GCAA Tetraloops with 2-Aminopurine and Purine Substitutions.
J. Biomol. Struct. Dynam. 22, 425-440 (2005).