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M. Popenda, E. Biała, J. Milecki and R. W. Adamiak, Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions, Nucleic Acids Res., 25 (22), 4589-4598 (1997). [pdf]

D. A. Adamiak, J. Milecki, M. Popenda, R. W. Adamiak, Z. Dauter and W. R. Rypniewski, Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 Å resolution. Hydration pattern of the 2'-O-methylated RNA, Nucleic Acids Res., 25 (22), 4599-4607 (1997). [pdf]

A. Burdzy, B. Skalski, S. Paszyc, Z. Gdaniec and R. W. Adamiak, Photosensitized Preparation of Fluorescent Luminarosine and Analogues, Nucleosides & Nucleotides, 17, 143-151 (1998).

A. Burdzy, B. Skalski, S. Paszyc, M. Popenda, R. W. Adamiak, Acid promoted transformations of fluorescent luminarosine and its 2'-modified analogs, Acta Biochim. Pol., 45 (4), 941-948 (1998). [Medline]

Z. Gdaniec, H. Sierzputowska-Gracz, E. C. Theil, Iron Regulatory Element (IRE) and Internal loop/bulge Structure for Ferritin mRNA Studied by Co(III)hexammine binding, molecular modeling and NMR Spectroscopy, Biochemistry, 37, 1505-1512 (1998). [pdf]

W. T. Markiewicz, A. Niewczyk, Z. Gdaniec, D. A. Adamiak, Z. Dauter, W. Rypniewski, M. Chmielewski, Studies on Synthesis and strucutre of O-b-D-Ribofuranosyl(1"-2') Ribonucleosides and Oligonucleotides, Nucleosides & Nucleotides, 17, 411-442 (1998).

Ł. Bielecki, T. Kuliński and R. W. Adamiak, Structure and dynamics of adenosine loops in RNA bulge duplexes. RNA hydration at the bulge site, NATO series, RNA Biochemistry and Biotechnology (Eds. J. Barciszewski & B.F.C. Clark).pp 73-87 (1999).

E. C. Theil, Y. Ke, Z. Gdaniec, H. Sierzputowska-Gracz, The IRE model for families of RNA structures. Selective recognition by binding proteins (IRPs), NMR spectroscopy and probing with metal coordination complexes, RNA Biochemistry and Biotechnology (eds. J.Barciszewski & B.F.C. Clark) NATO ASI Series, Kluwer Academic Publishers, 241-247 (1999).

A. Fischer, Z. Gdaniec, M. Olejniczak, Ł. Bielecki R. W. Adamiak, Does 29-mer RNA hairpin of the HIV-1 TAR RNA sequence bind magnesium? 19F-NMR and modelling studies, Nucleic Acids Symp. Series, 42, 117-118 (1999).

J. Milecki, E. Zamaratski, T. V. Maltseva, A. Földesi, R. W. Adamiak and J. Chattopadhyaya, The First Example of Sequence-specific Non-uniformly 13C5 labelled RNA: Synthesis of the 29mer HIV-1 TAR RNA with 13C Relaxation Window, Tetrahedron, 55, 6603-6622 (1999).

E. Wyszko, J.-P. Fuerste, M. Barciszewska, M. Szymański, R. W. Adamiak, V. A. Erdmann and J. Barciszewski, Preparation of HIV TAR RNA with RNA scissors, J. Biochem., 126, 326-332 (1999).

T. Kuliński, Ł. Bielecki, M. Olejniczak, I. Zagórowska and R. W. Adamiak, Structure and dynamics of the apical loop region of 29-mer hairpin of the TAR RNA HIV-1 sequence, Collection Symposium Series, Vol. 2, pp 191-196, (1999).

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

Ł. Bielecki, B. Skalski, I. Zagórowska, R. E. Verrall and R. W. Adamiak, Fluorescent a-anomeric 1,N(6)etheno-deoxyadenosine in DNA duplexes. The a-edA / dG pair, Nucleosides, Nucleotides & Nucleic Acids, 19, 1735-1750 (2000).

J. Jankowska, M. Wenska, M. Popenda, J. Stawiński, A. Kraszewski, A new, efficient entry to nucleoside 2',3'-O,O-cyklophosphorothioates, Tetrahedron Letters., 41, 2227-2229 (2000). [pdf]

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). [pdf]

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. W. Stuart, Z. Gdaniec, R. Guenther, M. Marszalek, E. Sochacka, A. Malkiewicz, 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). [pdf]

U. Kaukinen, Ł. Bielecki, S. Mikkola, R. W. Adamiak and 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).

K. Kulińska, T. Kuliński, A. Lyubartsev, A. Laaksonen and R. W. Adamiak, Structure and dynamics of the water shell in the (CG)n duplexes in a view of stabilization of 2'-O-methylated RNA, J. Biomol. Struct. Dynam., 18, 6, 936, (2001).

D. A. Adamiak, W. R. Rypniewski, J. Milecki and R. W. Adamiak, The 1.19 Å 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(20), 4144-4153 (2001). [pdf]

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

M. Olejniczak, Z. Gdaniec, A. Fischer, T. Grabarkiewicz, Ł. Bielecki and R. W. Adamiak, The bulge region of HIV-1 TAR RNA binds metal ions in solution, Nucleic Acids Res., 30 (19) 4241-4249 (2002). [pdf]

Ł. Bielecki, M. Popenda and R. W. Adamiak, The molecular dynamics thermocycler. A new approach to sample conformational space, as exemplified by the RNA hairpin, Nucleic Acids Research Supplement No. 2, 57-58 (2002). [Medline]

T. Kuliński, M. Olejniczak, H. Huthoff, Ł. Bielecki, K. Pachulska-Wieczorek, A. T. Das, B. Berkhout and R. W. Adamiak, The Apical Loop of the HIV-1 TAR RNA Hairpin Is Stabilized by a Cross-loop Base Pair, J. Biol. Chem., 278 (40), 38892-38901 (2003). [pdf]

M. Cieslak, J. Szymanski, R. W. Adamiak and C. S. Cierniewski, Structural Rearrangements of the 10-23 DNAzyme to b3 Integrin Subunit mRNA Induced by Cations and Their Relations to the Catalytic Activity, J. Biol. Chem., 278 (48), 47987-47996 (2003). [pdf]

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

R. W. Adamiak, J. Błażewicz, P. Formanowicz, Z. Gdaniec, M. Kasprzak, M. Popenda and M. Szachniuk, An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes, J. Comput. Biol., 11 (1), 167-183 (2004). [Medline]

B. Golankiewicz, P. Januszczyk, J. Zeidler, M. Popenda, An efficient route to novel 4,5-di- and 2,4,5-tri substituted imidazoles from imidazo[1,5-a]-1,3,5-triazine (5,8-diaza-7,9-dideazapurine) derivates, Nucleosides, Nucleotides & Nucleic Acids, 23, 127-136 (2004). [Medline]

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., 25, 142-145 (2004). [pdf]

M. Popenda, J. Milecki and R. W. Adamiak, High salt solution structure of a left-handed RNA double helix, Nucleic Acids Res., 32 (13), 4044-4054 (2004). [pdf]

Z. Gdaniec, Spektroskopia NMR w badaniach strukturalnych kwasów nukleinowych. Część I, Wiadomości Chemiczne, 59, 47-65 (2005).

M. Plevnik, Z. Gdaniec, J. Plavec, Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex, Nucleic Acids Res., 33, 1749-1759 (2005). [Medline]

M. Broda, E. Kierzek, Z. Gdaniec, T. Kuliński, R. Kierzek, Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure, Biochemistry, 44, 10873-10882 (2005). [Medline]

V. Balevicius, Z. Gdaniec, H. Fuess, NMR probing of structural peculiarities in ionic solutions close to critical point, J. Chem. Phys., 123, art. no. 224503 (2005). [Medline]

D. Ciesiołka, M. Muzquiz, C. Burbano, P. Altares, M. M. Pedrosa, W. Wysocki, W. Folkman, M. Popenda and K. Gulewicz, An Effect of Various Nitrogen Forms Used as Fertilizer on Lupinus albus L. Yield and Protein, Alkaloids and a-Galactosides Content, J. Agronomy & Crop Science, 191, 458-463 (2005).

K. Pachulska-Wieczorek, K. J. Purzycka and R. W. Adamiak, New, extended hairpin form of the TAR-2 RNA domains points to the structural polymorphism at the 5' end of the HIV-2 leader RNA, Nucleic Acids Res., 34, 2984-2997 (2006). [pdf] [pdf]

G. Framski, Z. Gdaniec, M. Gdaniec, J. Boryski, A reinvestigated mechanism of ribosylation of adenine under silylating conditions, Tetrahedron, 62, 10123-10129 (2006).

M. Popenda, Ł. Bielecki and R. W. Adamiak, High-throughput method for the prediction of low-resolution, three-dimensional RNA structures, Nucleic Acids Symposium Series, 50, 67-68 (2006). [Medline]

M. Giel-Pietraszuk, Z. Gdaniec, T. Brukwicki, J. Barciszewski, Molecular mechanism of high pressure action on lupanine, J. Mol. Struct., 826, 120-125 (2007).

M. Popenda, M. Błażewicz, M. Szachniuk and R. W. Adamiak, RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures, Nucleic Acids Res., doi: 10.1093/nar/gkm786 (2007); 36 (Database issue) D 386-391 (2008). [pdf]

Ł. Popenda, R.W. Adamiak, Z. Gdaniec, Bulged Adenosine Influence on the RNA Duplex Conformation in Solution, Biochemistry, 47(18), 5059-5067 (2008). [Medline]

K. J. Purzycka and R. W. Adamiak, The HIV-2 TAR RNA domain as a potential source of viral-encoded miRNA. A reconnaissance study, Nucleic Acids Symposium Series, 52, 511-512 (2008). [pdf]

W. Rypniewski, D.A. Adamiak, J. Milecki and R.W. Adamiak, Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex, RNA, 14(9), 1845-1851 (2008). [Pdf]

Ł. Popenda, Ł. Bielecki, Z. Gdaniec, R.W. Adamiak, Structure and dynamics of adenosine bulged RNA duplex reveals formation of the dinucleotide platform in the C:G-A triple, Arkivoc, 3, 130-144 (2009). [pdf]

D. A. Adamiak, J. Milecki, R. W. Adamiak and W. Rypniewski The hydration and unusual hydrogen bonding in the crystal structure of an RNA duplex containing alternating CG base pairs, New J. Chem., 2010, DOI: 10.1039/B9NJ00601J [link]

M. Popenda, M. Szachniuk, M. Blazewicz, S. Wasik, E.K. Burke, J. Blazewicz, R.W. Adamiak. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures., BMC Bioinformatics, 2010, 11:231 (published online on May 6, 2010, doi:10.1186/1471-2105-11-231)

Katarzyna J. Purzycka, Katarzyna Pachulska-Wieczorek and Ryszard W. Adamiak, The in vitro loose dimer structure and rearrangements of the HIV-2 leader RNA, Nucleic Acids Res. 39, 7234-7248 (2011), doi:10.1093/nar/gkr385)