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Ryszard Kierzek

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Thermodynamics

Chemicals & Drugs

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RNA Splicing

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Jolanta Lepczyńska; Jan Milecki; Stefan Franzen; Zofia Gdaniec; Ryszard Kierzek; Krzysztof Komodziński; Bohdan Skalski
Photoaddition of 5-bromouracil to uracil in oligonucleotides leading to 5,5'-bipyrimidine-type adducts: mechanism of the photoreaction.
Agnieszka Kiliszek; Wlodzimierz J Krzyzosiak; Ryszard Kierzek; Wojciech Rypniewski
Crystallographic characterization of CCG repeats.
Walter N Moss; Salvatore F Priore; Lumbini I Dela-Moss; Elzbieta Kierzek; Ryszard Kierzek; Douglas H Turner
The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin.

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2012: Jolanta Lepczyńska; Jan Milecki; Stefan Franzen; Zofia Gdaniec; Ryszard Kierzek; Krzysztof Komodziński; Bohdan Skalski
Photoaddition of 5-bromouracil to uracil in oligonucleotides leading to 5,5'-bipyrimidine-type adducts: mechanism of the photoreaction.
The Journal of organic chemistry 2012;77(24):11362-7.
2012: Agnieszka Kiliszek; Wlodzimierz J Krzyzosiak; Ryszard Kierzek; Wojciech Rypniewski
Crystallographic characterization of CCG repeats.
Nucleic acids research 2012;40(16):8155-62.
2012: Walter N Moss; Salvatore F Priore; Lumbini I Dela-Moss; Elzbieta Kierzek; Ryszard Kierzek; Douglas H Turner
The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin.
PloS one 2012;7(6):e38323.
2011: Agata Fratczak; Ryszard Kierzek; Elzbieta Kierzek
Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes.
Biochemistry 2011;50(35):7647-65.
2011: Agnieszka Kiliszek; Wlodzimierz J Krzyzosiak; Ryszard Kierzek; Wojciech Rypniewski
Crystal structures of CGG RNA repeats with implications for fragile X-associated tremor ataxia syndrome.
Nucleic acids research 2011;39(16):7308-15.
2010: Agnieszka Kiliszek; Ryszard Kierzek; Wlodzimierz J Krzyzosiak; Wojciech Rypniewski
Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases.
Nucleic acids research 2010;38(22):8370-6.
2010: Ruiting Liang; Elzbieta Kierzek; Ryszard Kierzek; Douglas H Turner
Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain.
Biochemistry 2010;49(37):8155-68.
2010: Anna Olejnik; Zofia Gdaniec; Elzbieta Kierzek; Ryszard Kierzek
The spontaneous rearrangement of 2,4-dinitrophenyl substituent in ribonucleosides under neutral conditions.
Nucleosides, nucleotides & nucleic acids 2010;29(9):684-97.
2010: Chun Chen; Xinliang Zhao; Ryszard Kierzek; Yi-Tao Yu
A flexible RNA backbone within the polypyrimidine tract is required for U2AF65 binding and pre-mRNA splicing in vivo.
Molecular and cellular biology 2010;30(17):4108-19.
2010: Nicholas B Hammond; Blanton S Tolbert; Ryszard Kierzek; Douglas H Turner; Scott D Kennedy
RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.
Biochemistry 2010;49(27):5817-27.
2010: Nathan A Siegfried; Ryszard Kierzek; Philip C Bevilacqua
Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity.
Journal of the American Chemical Society 2010;132(15):5342-4.
2009: Marta Carlucci; Elzbieta Kierzek; Anna Olejnik; Douglas H Turner; Ryszard Kierzek
Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA.
Biochemistry 2009;48(46):10882-93.
2009: Elzbieta Kierzek; Shawn M Christensen; Thomas H Eickbush; Ryszard Kierzek; Douglas H Turner; Walter N Moss
Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.
Journal of molecular biology 2009;390(3):428-42.
2009: Agnieszka Kiliszek; Ryszard Kierzek; Wlodzimierz J Krzyzosiak; Wojciech Rypniewski
Structural insights into CUG repeats containing the 'stretched U-U wobble': implications for myotonic dystrophy.
Nucleic acids research 2009;37(12):4149-56.
2009: Elzbieta Kierzek; Anna Pasternak; Karol Pasternak; Zofia Gdaniec; Ilyas Yildirim; Douglas H Turner; Ryszard Kierzek
Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with locked nucleic acids.
Biochemistry 2009;48(20):4377-87.
2009: Agata Fratczak; Ryszard Kierzek; Elzbieta Kierzek
LNA-modified primers drastically improve hybridization to target RNA and reverse transcription.
Biochemistry 2009;48(3):514-6.
2008: Anna Pasternak; Ryszard Kierzek; Zofia Gdaniec; Maria Gdaniec
A locked derivative of 8-aza-7-deazaadenosine.
Acta crystallographica. Section C, Crystal structure communications 2008;64(Pt 8):o467-70.
2008: Elzbieta Kierzek; Ryszard Kierzek; Walter N Moss; Shawn M Christensen; Thomas H Eickbush; Douglas H Turner
Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.
Nucleic acids research 2008;36(6):1770-82.
2008: Anna Pasternak; Elzbieta Kierzek; Karol Pasternak; Agata Fratczak; Douglas H Turner; Ryszard Kierzek
The thermodynamics of 3'-terminal pyrene and guanosine for the design of isoenergetic 2'-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure.
Biochemistry 2008;47(5):1249-58.
2007: Gang Chen; Ryszard Kierzek; Ilyas Yildirim; Thomas R Krugh; Douglas H Turner; Scott D Kennedy
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.
The journal of physical chemistry. B 2007;111(24):6718-27.
2007: Anna Pasternak; Elzbieta Kierzek; Karol Pasternak; Douglas H Turner; Ryszard Kierzek
A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes.
Nucleic acids research 2007;35(12):4055-63.
2007: Rieko Yajima; David Proctor; Ryszard Kierzek; Elzbieta Kierzek; Philip C Bevilacqua
A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme.
Chemistry & biology 2007;14(1):23-30.
2006: Hairong Ma; David Proctor; Elzbieta Kierzek; Ryszard Kierzek; Philip C Bevilacqua; Martin Gruebele
Exploring the energy landscape of a small RNA hairpin.
Journal of the American Chemical Society 2006;128(5):1523-30.
2006: Elzbieta Kierzek; Ryszard Kierzek; Douglas H Turner; Irina Catrina
Facilitating RNA structure prediction with microarrays.
Biochemistry 2006;45(2):581-93.
2006: Elzbieta Kierzek; David H Mathews; Anna Pasternak; Douglas H Turner; Ryszard Kierzek
Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides.
Nucleic acids research 2006;34(13):3609-14.
2005: Magdalena Broda; Elzbieta Kierzek; Zofia Gdaniec; Tadeusz Kulinski; Ryszard Kierzek
Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure.
Biochemistry 2005;44(32):10873-82.
2005: Elzbieta Kierzek; Anna Pasternak; Karol Pasternak; David H Mathews; Douglas H Turner; Ryszard Kierzek
The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes.
Nucleic acids research 2005;33(16):5082-93.
2004: David Proctor; Hairong Ma; Elzbieta Kierzek; Ryszard Kierzek; Martin Gruebele; Philip C Bevilacqua
Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate.
Biochemistry 2004;43(44):14004-14.
2004: Elzbieta Kierzek; Ryszard Kierzek
Synthesis of oligoribonucleotides containing N6-alkyladenosine and 2-methylthio-N6-alkyladenosine.
Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 2004;Chapter 4():Unit 4.23.
2003: Elzbieta Kierzek; Ryszard Kierzek
The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines.
Nucleic acids research 2003;31(15):4472-80.
2003: Elzbieta Kierzek; Ryszard Kierzek
The synthesis of oligoribonucleotides containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines via post-synthetic modification of precursor oligomers.
Nucleic acids research 2003;31(15):4461-71.
2003: David Proctor; Elzbieta Kierzek; Ryszard Kierzek; Philip C Bevilacqua
Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine.
Journal of the American Chemical Society 2003;125(9):2390-1.
2002: Krzysztof Ziomek; Elzbieta Kierzek; Ewa Biała; Ryszard Kierzek
The influence of various modified nucleotides placed as 3'-dangling end on thermal stability of RNA duplexes.
Biophysical chemistry 2002;97(2-3):243-9.
2002: Krzysztof Ziomek; Elzbieta Kierzek; Ewa Biała; Ryszard Kierzek
The thermal stability of RNA duplexes containing modified base pairs placed at internal and terminal positions of the oligoribonucleotides.
Biophysical chemistry 2002;97(2-3):233-41.
2001: Michelle A Steiger; Ryszard Kierzek; Douglas H Turner; Eric M Phizicky
Substrate recognition by a yeast 2'-phosphotransferase involved in tRNA splicing and by its Escherichia coli homolog.
Biochemistry 2001;40(46):14098-105.
2001: Elzbieta Kierzek; Ryszard Kierzek
Influence of N6-isopentenyladenosine (i(6)A) on thermal stability of RNA duplexes.
Biophysical chemistry 2001;91(2):135-40.
2001: X Chen; Ryszard Kierzek; Douglas H Turner
Stability and structure of RNA duplexes containing isoguanosine and isocytidine.
Journal of the American Chemical Society 2001;123(7):1267-74.
2001: Elzbieta Kierzek; E Biała; Ryszard Kierzek
Elements of thermodynamics in RNA evolution.
Acta biochimica Polonica 2001;48(2):485-93.
2001: Magdalena Alejska; M Broda; Ryszard Kierzek; A Kurzyńska-Kokorniak; Magdalena Figlerowicz
How RNA viruses exchange their genetic material.
Acta biochimica Polonica 2001;48(2):391-407.
2001: Ryszard Kierzek
Nonenzymatic cleavage of oligoribonucleotides.
Methods in enzymology 2001;341():657-75.
2000: X Chen; JA McDowell; Ryszard Kierzek; Thomas R Krugh; Douglas H Turner
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).
Biochemistry 2000;39(30):8970-82.
2000: A Bibillo; Magdalena Figlerowicz; Krzysztof Ziomek; Ryszard Kierzek
The nonenzymatic hydrolysis of oligoribonucleotides. VII. Structural elements affecting hydrolysis.
Nucleosides, nucleotides & nucleic acids 2000;19(5-6):977-94.
2000: Ryszard Kierzek; Michelle A Steiger; Sherry L Spinelli; Douglas H Turner; Eric M Phizicky
The chemical synthesis of oligoribonucleotides with selectively placed 2'-O-phosphates.
Nucleosides, nucleotides & nucleic acids 2000;19(5-6):917-33.
1999: SM Testa; Matthew D Disney; Douglas H Turner; Ryszard Kierzek
Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: implications for antisense design and targeting a group I intron.
Biochemistry 1999;38(50):16655-62.
1999: Ryszard Kierzek; Mark E Burkard; Douglas H Turner
Thermodynamics of single mismatches in RNA duplexes.
Biochemistry 1999;38(43):14214-23.
1999: A Bibillo; Magdalena Figlerowicz; Ryszard Kierzek
The non-enzymatic hydrolysis of oligoribonucleotides VI. The role of biogenic polyamines.
Nucleic acids research 1999;27(19):3931-7.
1999: Mark E Burkard; Ryszard Kierzek; Douglas H Turner
Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs.
Journal of molecular biology 1999;290(5):967-82.
1999: Sherry L Spinelli; Ryszard Kierzek; Douglas H Turner; Eric M Phizicky
Transient ADP-ribosylation of a 2'-phosphate implicated in its removal from ligated tRNA during splicing in yeast.
The Journal of biological chemistry 1999;274(5):2637-44.
1999: Krzysztof Ziomek; Ryszard Kierzek
[The secondary structural motifs of RNA].
Postepy biochemii 1999;45(2):80-7.
1999: Krzysztof Ziomek; Ryszard Kierzek
[Predicting the secondary structures of the ribonucleic acids (RNA)].
Postepy biochemii 1999;45(2):74-80.
1999: A Bibiłło; Krzysztof Ziomek; Magdalena Figlerowicz; Ryszard Kierzek
Nonenzymatic hydrolysis of oligoribonucleotides. V. The elements affecting the process of self-hydrolysis.
Acta biochimica Polonica 1999;46(1):145-53.
1998: T Xia; John SantaLucia; Mark E Burkard; Ryszard Kierzek; Susan J Schroeder; X Jiao; Christopher Cox; Douglas H Turner
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.
Biochemistry 1998;37(42):14719-35.
1997: L A Profenno; Ryszard Kierzek; SM Testa; Douglas H Turner
Guanosine binds to the Tetrahymena ribozyme in more than one step, and its 2'-OH and the nonbridging pro-Sp phosphoryl oxygen at the cleavage site are required for productive docking.
Biochemistry 1997;36(41):12477-85.
1993: Gloria M Culver; S M McCraith; M Zillmann; Ryszard Kierzek; N Michaud; R D LaReau; Douglas H Turner; Eric M Phizicky
An NAD derivative produced during transfer RNA splicing: ADP-ribose 1"-2" cyclic phosphate.
Science (New York, N.Y.) 1993;261(5118):206-8.
1993: S Moran; Ryszard Kierzek; Douglas H Turner
Binding of guanosine and 3' splice site analogues to a group I ribozyme: interactions with functional groups of guanosine and with additional nucleotides.
Biochemistry 1993;32(19):5247-56.
1992: P C Bevilacqua; Ryszard Kierzek; K A Johnson; Douglas H Turner
Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods.
Science (New York, N.Y.) 1992;258(5086):1355-8.
1992: Ryszard Kierzek
Nonenzymatic hydrolysis of oligoribonucleotides.
Nucleic acids research 1992;20(19):5079-84.
1992: Ryszard Kierzek
Hydrolysis of oligoribonucleotides: influence of sequence and length.
Nucleic acids research 1992;20(19):5073-7.
1992: Ryszard Kierzek; L He; Douglas H Turner
Association of 2'-5' oligoribonucleotides.
Nucleic acids research 1992;20(7):1685-90.
1992: John SantaLucia; Ryszard Kierzek; Douglas H Turner
Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin.
Science (New York, N.Y.) 1992;256(5054):217-9.
1991: L He; Ryszard Kierzek; John SantaLucia; A E Walter; Douglas H Turner
Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text].
Biochemistry 1991;30(46):11124-32.
1991: John SantaLucia; Ryszard Kierzek; Douglas H Turner
Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs.
Biochemistry 1991;30(33):8242-51.
1991: A E Peritz; Ryszard Kierzek; N Sugimoto; Douglas H Turner
Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops.
Biochemistry 1991;30(26):6428-36.
1990: John SantaLucia; Ryszard Kierzek; Douglas H Turner
Effects of GA mismatches on the structure and thermodynamics of RNA internal loops.
Biochemistry 1990;29(37):8813-9.
1990: J D Reilly; S K Freeman; R F Melhem; Ryszard Kierzek; M H Caruthers; M Edmonds; T W Munns
Antibodies specific for branched ribonucleic acids.
Analytical biochemistry 1990;185(1):125-30.
1990: C E Longfellow; Ryszard Kierzek; Douglas H Turner
Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides.
Biochemistry 1990;29(1):278-85.
1989: A P Williams; C E Longfellow; Susan M Freier; Ryszard Kierzek; Douglas H Turner
Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC.
Biochemistry 1989;28(10):4283-91.
1989: N Sugimoto; M Tomka; Ryszard Kierzek; P C Bevilacqua; Douglas H Turner
Effects of substrate structure on the kinetics of circle opening reactions of the self-splicing intervening sequence from Tetrahymena thermophila: evidence for substrate and Mg2+ binding interactions.
Nucleic acids research 1989;17(1):355-71.
1988: N Sugimoto; Ryszard Kierzek; Douglas H Turner
Kinetics for reaction of a circularized intervening sequence with CU, UCU, CUCU, and CUCUCU: mechanistic implications from the dependence on temperature and on oligomer and Mg2+ concentrations.
Biochemistry 1988;27(17):6384-92.
1987: N Sugimoto; Ryszard Kierzek; Douglas H Turner
Sequence dependence for the energetics of terminal mismatches in ribooligonucleotides.
Biochemistry 1987;26(14):4559-62.
1987: N Sugimoto; Ryszard Kierzek; Douglas H Turner
Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid.
Biochemistry 1987;26(14):4554-8.
1987: Douglas H Turner; N Sugimoto; J A Jaeger; C E Longfellow; Susan M Freier; Ryszard Kierzek
Improved parameters for prediction of RNA structure.
Cold Spring Harbor symposia on quantitative biology 1987;52():123-33.
1986: Ryszard Kierzek; M H Caruthers; C E Longfellow; D Swinton; Douglas H Turner; Susan M Freier
Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability.
Biochemistry 1986;25(24):7840-6.
1986: Susan M Freier; Ryszard Kierzek; J A Jaeger; N Sugimoto; M H Caruthers; T Neilson; Douglas H Turner
Improved free-energy parameters for predictions of RNA duplex stability.
Proceedings of the National Academy of Sciences of the United States of America 1986;83(24):9373-7.
1986: N Sugimoto; Ryszard Kierzek; S M Freier; D H Turner
Energetics of internal GU mismatches in ribooligonucleotide helixes.
Biochemistry 1986;25(19):5755-9.
1986: Ryszard Kierzek; D W Kopp; M Edmonds; M H Caruthers
Chemical synthesis of branched RNA.
Nucleic acids research 1986;14(12):4751-64.
1986: Susan M Freier; N Sugimoto; A Sinclair; D Alkema; T Neilson; Ryszard Kierzek; M H Caruthers; Douglas H Turner
Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids.
Biochemistry 1986;25(11):3214-9.
1986: Susan M Freier; Ryszard Kierzek; M H Caruthers; T Neilson; Douglas H Turner
Free energy contributions of G.U and other terminal mismatches to helix stability.
Biochemistry 1986;25(11):3209-13.