Molecular Collection


One of our long-standing goals is to develop new modified nucleotides as research tools for biophysics, biochemistry, molecular biology and biotechnology. Therefore, we are very happy if our ideas are found useful by others. Below you will find a summary on the compounds we published to date, together with some standard compounds commonly used as reference in biological studies. The main applications of some compounds and appropriate references are also listed below.

If you are interested in applying either of our modified compounds in your research or you deal with a scientific problem that could be solved by means of modified nucleotides, please contact us. We are open to establishing scientific collaborations.

Mononucleotide mRNA cap analogs with unmodified (oligo)phosphate moiety


These compounds are primarily used as inhibitors of cap-dependent translation and ligands for probing interactions with cap binding proteins

Synthesis&Applications:
Zuberek et al. 2004, Biochemistry 43, 5370-5379.

Applications:
Wypijewska et al. 2012, Biochemistry 51, 8003-8013
Zuberek et al. 2007, RNA 13, 691-697


m7GMP


Short description


m7GDP


Short description


m7GTP, m7Gp4, m7Gp5


Mononucleotide cap analogs with high affinity for eukaryotic translation initiation factor 4E (eIF4E). Potent inhibitors of cap dependent translation in vitro.


Zuberek et al. 2004, Biochemistry 43, 5370-5379.


Mononucleotide mRNA cap analogs with modified (oligo)phosphate moiety


These compounds are primarily used as inhibitors of cap-dependent translation and ligands for probing interactions with cap binding proteins

Synthesis&Applications:
Kowalska et al. 2009, Bioorg. Med. Chem. Lett. 19, 1921-1925
Kowalska et al. 2012, Bioorganic & Medicinal Chemistry Letters 22, 3661-3664


m7GDP


Short description


Dinucleotide mRNA cap analogs with unmodified (oligo)phosphate moiety


Useful as inhibitors of cap-dependent translation, ligands for probing interactions with cap binding proteins and reagents for the preparation of capped mRNAs by transcription in vitro

Synthesis&Applications:
Jemielity et al. 2003, RNA 9, 1108-1122

Application:
Zuberek et al. 2007, RNA 13, 691-697


Dinucleotide mRNA cap analogs with the non-bridging modifications in the (oligo)phosphate moiety


Reagent for the preparation of mRNAs with enhanced stability and translation efficiency

Synthesis&Applications:
Kowalska et al. 2008, RNA, 14, 1119-1131
Kowalska et al. 2009, ChemBioChem 10, 2469-2473
Strenkowska et al. 2010, New J. Chem. 34, 993-1007

Applications:
Grudzien-Nogalska et al. 2007, RNA, 13, 1745-1755
Zdanowicz et al. 2009, Molec. Cell 35, 881-888
Kuhn et al. 2010, Gene Therapy, 17, 961-971
Su et al. 2011. RNA 17, 978-988


m27,2'-OGpSppG (gamma-S-ARCA)


Kowalska et al. 2008, RNA, 14, 1119-1131


m27,2'-OGppSpG (beta-S-ARCA


Kowalska et al. 2008, RNA, 14, 1119-1131


m27,2'-OGpppSG (alfa-S-ARCA)


Kowalska et al. 2008, RNA, 14, 1119-1131


m27,2'-OGppSepG (beta-Se-ARCA)


Kowalska et al. 2009, ChemBioChem 10, 2469-2473


m27,2'-OGpSpppG (delta-S-tetraARCA)


Strenkowska et al. 2010, New J. Chem. 34, 993-1007


2',3'-O,O-iPr-m7GppSpG


Warminski et al. 2013, Bioorg. Med. Chem. Lett. 23, 3753-3758


Dinucleotide mRNA cap analogs with the bridging modifications in the (oligo)phosphate moiety


Ligands for probing interactions with cap binding proteins. Reagents for the preparation of capped mRNAs. Molecular tools for decapping studies.

Synthesis&Applications:
Kalek et al. 2006, Bioorganic and Medicinal Chemistry 14, 3223-3230
Rydzik et al. 2009, Org. Biomol. Chem. 7, 4763-4776
Rydzik et al. 2012, Bioorganic and Medicinal Chemistry 20, 1699-1710

Applications:
Grudzien et al. 2006, Journal of Biological Chemistry 281, 1857-186
Deshmukh et al. 2008, Molec. Cell 29, 324-336
Banerjee et al. 2009, RNA 15, 1554-1564
Su et al. 2011. RNA 17, 978-988


Derivatisable nucleotides


Dinucleotide mRNA cap analog bearing a derivatizable group within the second nucleobase for labelling and immobilization.

Synthesis&Applications:
Szczepaniak et al. 2012, RNA, 18, 1421-1432
Jemielity et al. 2012, Organic& Biomolecular Chemistry 10, 8570-8574


m72'-NH2GpppG


Tool for mRNA labeling

Jemielity et al. 2012, Organic& Biomolecular Chemistry 10, 8570-8574



Biotinylated cap analogue for labelling mRNA

Jemielity et al. 2012, Organic& Biomolecular Chemistry 10, 8570-8574


Labelled nucleotides



Ant-m7GpppG



Mant-m7GpppG



Ant-m72OGpppG



Mant-m7GpCH2ppG



Mant-m7GppCH2pG



Modified NDPs, NTPs and Np4


Phosphate-modified nucleotides. Synthetic bulding blocks. Various biochemical applications.

Synthesis:
Kalek et al. 2005, Tetrahedron Letters 46, 2417-2421
Kowalska et al. 2007, Tetrahedron Lett. 48, 5475-5479
Strenkowska et al. 2012, Organic Letters 14, 4782-4785

Applications:
Guranowski et al. 2006, FEBS Journal 273, 829-838
Tölle et al. 2008, Circulation Research 108, 1100 - 1108
Guranowski et al. 2010, New J. Chem. 34, 888-893


AppSep



AppBH3p



AppSp



AppSe



GppSe



GppSep



GppBH3p



GppSp



Nucleoside phosphosulphates


Key biochemical intermediates and their analogs, useful in molecular probing as a nucleotide analogs as well as in biotechnology.

Synthesis:
Kowalska et al. 2012, Bioorganic & Medicinal Chemistry Letters 22, 3661-3664

Applications:
Guranowski et al. 2010, FEBS Lett. 584, 93-98
Guranowski et al. 2010, New J. Chem. 34, 888-893


APS



cPAPS



GPS



CPS



UPS



m7GPS



Affinity resins


Tools for affinity chromatography. Purification and identification of cap-related proteins.

Szczepaniak et al. 2012, RNA, 18, 1421-1432


m7GpCH2pp-Speharose


Enzymatically resistant analog of m7GTP-Sepharose.

Szczepaniak et al. 2012, RNA, 18, 1421-1432


m7GpppA-HMDA-Sepharose


A dinucleotide cap analog (m7GpppA) with hexamethylenediamine (HMDA) linker immobilized on Sepharose.

Szczepaniak et al. 2012, RNA, 18, 1421-1432


m7GpCH2ppA-HMDA-Sepharose


Enzymatically resistant analog of m7GpppA with hexamethylenediamine (HMDA) linker immobilized on Sepharose.

Suitable for purfication of pyrophosphates hydrolyzing beta/gamma pyrophosphate bond (e.g. DcpS).

Szczepaniak et al. 2012, RNA, 18, 1421-1432


Nucleotide sugars


Natural nucleotide sugars and their analogs - key intermediates in sugar methabolism, oligosugar and glycoprotein biosynthesis. Potential tools for investigating the tlycotransferases mechanisms. Potential glycotransferases inhibitors.

Dabrowski-Tumanski, P., Kowalska, J. and Jemielity, J. (2013), Efficient and Rapid Synthesis of Nucleoside Diphosphate Sugars from Nucleoside Phosphorimidazolides. Eur. J. Org. Chem., 2013: 2147–2154.


ADP-1-Glc



GDP-1-Glc



UDP-1-Glc



UDP-1-Gal



GDP-1-L-Fuc



ADP-5-Rib



ADP-6-Glc



GDP-6-Glc



UDP-6-Glc