Publications 2011-2015
2015
Korhonen, H. J.; Bolt, H. L.; Vicente-Gines, L., Perks, D. C.; Hodgson, D. R. W., PPN
pyrophosphate: A new reagent for the preparation of nucleoside triphosphates, Phosph. Sulfur
Silicon Related Elements 2015, 190, 758-762.
Korhonen, H. J.; Bolt, H. L.; Hodgson, D. R. W., A procedure for the preparation and isolation
of nucleoside-5 '-diphosphates, Beilstein J. Org. Chem. 2015, 11, 469-472.
Dano, M.; Elmeranta, M.; Hodgson, D. R. W., Jaakkola, J.; Korhonen, H.; Mikkola, S., Metal
ion-promoted cleavage of nucleoside diphosphosugars: a model for reactions of phosphodiester
bonds in carbohydrates. J. Biol. Inorg. Chem.2015, 20, 1299-1306.
Tähtinen, V.; Granqvist, L.; Virta, P., Synthesis of C-5, C-2 ' and C-4 '-neomycin-conjugated
triplex forming oligonucleotides and their affinity to DNA-duplexes. Bioorg. Med. Chem., 2015,
23, 4472-4480.
Granqvist, L.; Virta, P., 2´-O-[(4-CF3-triazol-1-yl)methyl]uridine – A sensitive F-19 NMR
sensor for the detection of RNA secondary structures. J. Org. Chem. 2015, 80, 7961-7970.
Taherpour, S.; Lönnberg, T., Fluorescence probing of metal-ion-mediated hybridization of
oligonucleotides, RSC Advances 2015, 5, 10837-10844.
Lehto, H. J.; Zaprudin, B.; Lehto, K. M.; Lönnberg, T.; Silén, J.; Rynö, J.; Krüger, H.;
Hilchenbach, M.; Kissel, J. Analysis of COSIMA spectra: Bayesian approach. Geosci. Instrum.
Method. Data Syst., 2015, 4, 139-148.
Lönnberg, T.; Hutchinson, M.; Rokita, S., Selective alkylation of C-rich bulge motifs in nucleic
acids by quinone methide derivative. Chem. Eur. J. 2015, 21, 13127-13136
Jadhav, S.; Käkelä, M.; Mäkilä, J.; Kiugel, M.; Liljenbäck, H.; Virta, J.; Poijärvi-Virta, P.;
Laitala-Leinonen, P.; Kytö, V.; Jalkanen,S.; Saraste, A.; Roivainen, A.; Lönnberg, H.; Virta,
P., Synthesis and in vivo PET Imaging of Hyaluronan Conjugates of Oligonucleotides,
Bioconjugate Chem., in press.
Jabgunde, A. M.; Gimenez Molina, A.; Virta, P.; Lönnberg, H., Preparation of a disulfide linked
precipitative soluble support for solution phase synthesis of trimeric oligodeoxyribonucleotide
3´-(2-chlorophenylphosphate) building blocks, Beilstein J. Org. Chem. 2015, 11, 1553-1560.
Lain, L.; Lahdenpohja, S.; Lönnberg, H.; Lönnberg, T., 2,6-Bis(1,4,7,10-tetraazacyclododecan1-ylmethyl)pyridine and its benzene analog as nonmetallic cleaving agents of RNA
phosphodiester linkages, Int. J. Mol. Sci. 2015, 16, 17798-17811; doi:10.3390/ijms160817798.
Sontakke, V.; Lönnberg, H.; Ora, M., 4-Aetylthio-2,2-dimethyl-3-oxobutyl and 4-(tertbutyldisulfanyl)-2,2-dimethyl-3-oxobutyl group as protecting groups of nucleoside 5´-
phosphoramidates derived from L-alanine methyl ester, Eur. J. Org. Chem. 2015, 5004-5012;
DOI 10.1002/ejoc.201500531.
Lain, L.; Lönnberg, H.; Lönnberg, T., Participation of an additional 4´-hydroxymethyl group in
the cleavage and isomerization of ribonucleoside 3´-phosphodiesters, Org. Biomol. Chem. 2015,
13, 4737-4742.
Lain, L.; Lönnberg, H.; Lönnberg, T.; Buffer catalyzed cleavage of uridylyl-3´,5´-uridine in
aqueous DMSO: comparison to its activated analog, 2-hydroxypropyl 4-nitrophenyl phosphate,
Org. Biomol. Chem., 2015, 13, 3484-3492.
Gimenez Molina, A.; Jabgunde, A.; Virta, P.; Lönnberg, H., Assembly of short
oligoribonucleotides from commercially available building blocks on a tetrapodal soluble
support, Curr. Org. Synth. 2015, 12, 202-207; DOI: 10.2174/1570179411666141120215703
Vihakas, M.; Gómez Avila, I.; Karonen, M.; Tähtinen, P.; Sääksjärvi, I.; Salminen, J.-P.,
Phenolic compounds and their fates in tropical lepidopteran larvae: modifications in alkaline
conditions, J. Chem. Ecol. 2015, 41, 822-836.
2014
Taherpour, S.; Golubev, O.; Lönnberg, T., Metal-ion-mediated base pairing between natural
nucleobases and bidentate 3,5-dimethylpyrazolyl-substituted purine ligands, J. Org. Chem.
2014, 79, 8990–8999.
Ghidini, A.; Steunenberg, P.; Murtola, M.; Strömberg, R., Synthesis of PNA Oligoether
Conjugates, Molecules 2014, 19, 3135-3148.
Korhonen, H. J.; Conway, L. P.; Hodgson, D. R. W., Phosphate analogues in the dissection of
mechanism. Curr. Opin. Chem. Biol. 2014, 21, 63-72.
Sontakke, V.A.; Shinde,V. S.; Lönnberg, H.; Ora, M., Synthesis and stability of nucleoside
3´,5´-cyclic phosphate triesters masked with biodegradable and thermolabile phosphate
protecting groups, Eur. J. Org. Chem. 2015, 389-394; DOI: 10.1002/ejoc.201403227.
Golubev, O.; Lönnberg, T.; Lönnberg, H., Formation of mixed-ligand Pd2+ complexes between
nuceloside 5´-monophosphates and some metal-ion-binding nucleoside surrogates, Molecules
2014, 19, 16976-16986.
Mäkilä, J.; Jadhav, S.; Kiviniemi, A.; Käkelä, M.; Liljenbäck, H.; Poijärvi-Virta, P.; LaitalaLeinonen, T.; Lönnberg, H.; Roivainen, A.; Virta, P., Synthesis of multi-galactose-conjugated
2´-O-methyl oligoribonucleotides and their in vivo imaging with positron emission tomography,
Bioorg. Med. Chem. 2014, 22. 6806–6813http://dx.doi.org/10.1016/j.bmc.2014.10.034
Gimenez Molina, A.; Jabgunde, A. M.; Virta, P.; Lönnberg, H., Solution phase synthesis of
short oligoribonucleotides on a precipitative tetrapodal support, Beilstein J. Org. Chem. 2014,
10, 2279-2285.
Leisvuori, A., Lönnberg, H., Ora, M., 4-Acetylthio-2,2-dimethyl-3-oxobutyl group as an
esterase and thermolabile protecting group for oligomeric phosphodiesters, Eur. J. Org. Chem.
2014, 5816-5826.
Golubev, O.; Lönnberg, T.; Lönnberg, H., Interaction of Pd(II) complexes of 2,6-disubstituted
pyridines with nucleoside 5´-monophosphates, J. Inorg. Biochem., 2014, 139, 21–29.
Lönnberg, H., Isomerization of RNA Phosphodiester Linkages, in “Chemical Biology of Nucleic
Acids: Fundamentals and Clinical Applications”, Erdmann, V. A.; Markiewicz, W. T.,
Barciszewski, J., Eds., Springer, Berlin Heidelberg 2014, 41-56.
Granqvist, L.; Virta, P., 4'-C-[(4-Trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine as a
sensitive 19F NMR sensor for the detection of oligonucleotide secondary structures,
J.Org.Chem., 2014, 79(8), 3529-3536.
Patrikainen, P.; Niiranen, L.; Thapa, K.; Paananen, P.; Tähtinen, P.; Mäntsälä, P.; Niemi, J.;
Metsä-Ketelä, M., Structure-Based Engineering of Angucyclinone 6-Ketoreductases, Chem.
Biol. 2014, 21, 1381-1391.
2013
Kungurtsev, V.; Virta, P.; Lönnberg, H., Synthesis of short oligodeoxyribonucleotides by
phosphotriester chemistry on a precitative tetrapodal support, Eur. J. Org. Chem., 2013, 78867890.
Kungurtsev, V.; Laakkonen, J.; Gimenez Molina, A.; Virta, P., Solution-phase synthesis of short
oligo-2'-deoxyribonucleotides by using clustered nucleosides as a soluble support, Eur. J. Org.
Chem., 2013, 6687-6693.
Lain, L.; Lönnberg, H.; Lönnberg, T., Intramolecular participation of amino groups in the
cleavage and isomerization of ribonucleoside 3'-phosphodiesters: the role of stabilization of the
phosphorane intermediate, Chem. Eur. J., 2013,19,12424-12434.
Golubev, O.; Lönnberg, T.; Lönnberg, H., Metal-ion-binding analogs of ribonucleosides:
preparation and formation of ternary Pd2+ and Hg2+ complexes with natural pyrimidine
nucleosides, Helv. Chim. Acta, 2013, 96, 1658-1669.
Kiuru, E.; Lönnberg, H.; Ora, M., 2-Acetyloxymethyl-4-acetylthio-2-ethoxycarbonyl-3-oxobutyl
group: a thermolabile protecting group for phosphodiesters, Helv. Chim. Acta, 2013, 96, 19972008.
Kiuru, E.; Ahmed, Z.; Lönnberg, H.; Beigelman, L.; Ora, M., 2,2-Disubstituted 4-acylthio-3oxobutyl groups as esterase- and thermo-labile protecting groups of phosphodiesters, J. Org.
Chem. 2013, 78, 950-959.
Niittymäki, T.; Burakova, E.; Laitinen, E.; Leisvuori, A.; Virta, P.; Lönnberg, H., Zn2+
Complexes of 3,5-bis[(1,5,9-triazacyclododecane-3-yl)oxymethyl]phenyl conjugates of
oligonucleotides as artificial RNases: the effect of oligonucleotide conjugation on uridine
selectivity of the cleaving agent, Helv. Chim. Acta 2013, 96, 31-43.
Taherpour, S.; Lönnberg, H.; Lönnberg, T., 2,6-Bis(functionalized) purines as metal-ion-binding
surrogate nucleobases that enhance hybridization with unmodified 2´-O-methyl
oligoribonucleotides, Org. Biomol. Chem. 2013, 11, 991-1000.
Lönnberg, H. Solid-supported synthesis of glycoconjugates, in “Advances in Organic
Synthesis”, Vol. 5, Atta-ur-Rahman, Ed., Bentham Science Publishers, Sharjah 2013, pp. 3-50.
Mikkola, S., Hydrolysis and isomerization of sugar phosphates and carbohydrate
phosphodiesters. Curr. Org. Chem. 2013, 17, 1525-1544.
Korhonen, H.; Williams, N. H.; Mikkola, S., β(LG) values in mechanistic studies on the
transesterification of RNA models and their application in a metal ion complex promoted
transesterification, J. Phys. Org. Chem. 2013, 26,182-186.
Korhonen, H.; Koivusalo, T.; Toivola, S.; Mikkola, S., There is no universal mechanism for the
cleavage of RNA model compounds in the presence of metal ion catalysts, Org. Biomol. Chem.
2013, 11, 8324-8339
Kiviniemi, A.; Murtola, M.; Ingman, P.; Virta, P., Synthesis of fluorine-labeled peptide nucleic
acid building blocks as sensors for the 19F NMR spectroscopic detection of different hybridization
modes, J. Org. Chem. 2013, 78, 5153–5159.
Neuvonen, K.; Neuvonen, H.; Koch, A.; Kleinpeter, E., Nature of the steric omega(S), E-R and
E-S ' substituent constants. Comparison with the aid of NBO and STERIC analysis. Comput.
Theor. Chem. 2013, 1015, 34-43.
Ora, M.; Martikainen, K.; Lautkoski, K., Hydrolytic reactions of cyclic bis(3 '-5 ')diadenylic acid
(c-di-AMP), J. Phys. Org. Chem. 2013, 26, 218-225.
2012
Kiviniemi, A.; Mäkelä, J.; Mäkilä, J.; Saanijoki, T.; Liljenback, H.; Poijärvi-Virta, P.; Lönnberg,
H.; Laitala-Leinonen, T.; Roivainen, A.; Virta, P. Solid-Supported NOTA and DOTA Chelators
Useful for the Synthesis of 3’-Radiometalated Oligonucleotides. Bioconjugate Chem. 2012, 23,
1981-1988.
Viola, J. R.; Strömberg, R.; Simonson, O. E.; Andaloussi, S. E. L.; Smith, C. I. E.; Murtola, M.,
Diaminopropionic acid lipopeptides: Characterization studies of polyplexesaimed at pDNA
delivery, Bioorg. Med. Chem. Lett. 2012, 22, 5635–5638.
Gimenez Molina, A.; Kungurtsev, V.; Virta, P.; Lönnberg, H., Acetylated and methylated βcyclodextrins as viable soluble supports for the synthesis of short 2’-oligodeoxyribo-nucleotides
in solution, Molecules 2012, 17, 12102-12120.
Karskela, M.; von Usedom, M.; Virta, P.; Lönnberg, H., Synthesis of biotinylated multipodal
glycoclusters on a solid support, Eur. J. Org. Chem. 2012, 6594-6605.
Korhonen, H.; Mikkola, S.; Williams, N.H., The mechanism of cleavage and isomerization of
RNA promoted by an efficient dinuclear Zn2+ complex, Chem Eur J. 2012, 18, 659-670.
Leisvuori, A.; Ahmed, Z.; Ora, M.; Beigelman, L.; Blatt, L.; Lönnberg, H., Synthesis of 3´,5´cyclic phosphate and thiophosphate esters of 2´-C-methylribonucleosides, Helv. Chim. Acta 2012,
95, 1512-1520.
Leisvuori, A.; Ahmed, Z.; Ora, M.; Blatt, L.; Beigelman, L.; Lönnberg, H. 5´,5´-Phosphodiesters
and esterase labile triesters of 2´-C-methylribonucleosides, ARKIVOC, 2012 (V), 226-243.
Lönnberg, T., Can phosphate-branched RNA persist under physiological conditions?
ChemBioChem 2012, 13, 2690-2700.
Kiuru, E., Ora, M., Beigelman, L., Blatt, L. and Lönnberg, H., Synthesis and Enzymatic
Deprotection of Fully Protected 2-5A Trimers: Towards a Pro-drug Strategy for Short 2´,5´Oligoadenylates, Chem. Biodivers. 2012, 9, 669-688
Lönnberg, T. A.; Helkearo, M.; Jancsó, A.; Gajda, T., Mimics of small ribozymes utilizing a
supramolecular scaffold, Dalton Trans. 2012, 41, 3328-3338.
Lönnberg, T.; Luomala, M., Intracomplex general acid/base catalyzed cleavage of RNA
phosphodiester bonds: the leaving group effect, Org. Biomol. Chem. 2012, 10, 6785-6791.
Lönnberg, T.; Kero, K-M. Impact of steric constraints on the product distribution of phosphatebranched oligonucleotide models of the large ribozymes, Org. Biomol. Chem. 2012, 10, 569-574.
Neuvonen, K.; Neuvonen, H.; Koch, A.; Kleinpeter, E., Taft equation in the light of NBO
computations. Introduction of a novel polar computational substituent constant scale σq* for alkyl
groups, Comput. Theor. Chem. 2012, 981, 52-58.
Ora, M.; Lönnberg, T.; Lönnberg, H., Thio effects as a tool for mechanistic studies of the cleavage
of RNA phosphodiester bonds: the chemical basis, in ”From Nucleic Acids Sequences to
Molecular Medicine”, Erdmann, V. A.; Barciszewski, J., Eds., Springer, Berlin 2012, Chapter 3,
pp. 48-65.
Taherpour, S.; Lönnberg, T., Metal ion chelates as surrogates of nucleobases for the recognition
of nucleic acid sequences: The Pd2+ complex of 2,6-bis(3,5-dimethylpyrazol-1-yl)purine
riboside., J. Nucleic Acids 2012, 196845.
Tähtinen, P.; Oja, T.; Dreiack, N.; Mäntsälä, P.; Niemi, J.; Metsä-Ketelä, M.; Klika, K. D.,
Epimers vs. inverse epimers: the C-1 configuration in alnumycin A1, RSC Advances 2012, 2,
5098-5100.
Vihakas, M.; Tähtinen, P.; Ossipov, V.; Salminen, J.-P., Flavonoid Metabolites in the Hemolymph
of European Pine Sawfly (Neodiprion sertifer) Larvae, J. Chem. Ecology 2012, 38, 538-546.
Oja, T.; Tähtinen, P.; Dreiack, N.; Mäntsälä, P.; Niemi, J.; Metsä-Ketelä, M.; Klika, K. D.,
Alnumycins A2 and A3, new inverse-epimeric pairs stereoisomeric to alnumycin A1,
Tetrahedron: Asymm. 2012, 23, 670-682.
Klika, K. D.; Tähtinen, P.; Mäntsälä, P.; Niemi, J.; Metsä-Ketelä, M., The potential of VCD to
resolve the epimer vs. inverse epimer quandary, Comp. Theor. Chem. 2012, 992, 156-163
2011
Huttunen, R.; Shweta, M. E.; Lahderanta, M.; Virta, P.; Hänninen, P.; Härmä, H., Single-label
time-resolved luminescence assay for estrogen receptor–ligand binding. Anal. Biochem., 2011,
415, 27-31.
Aiba, Y.; Lönnberg, T.; Komiyama, M., Manipulation of single-stranded DNA by using an
artificial site-selected DNA cutter composed of Cerium(IV)/EDTA and phosphonateoligonucleotide conjugates, Chem. Asian. J. 2011, 6, 2407-2411.
Karskela, T.; Klika, K. D.; Lönnberg, H., Synthesis of 7-substituted 3-β-D-ribofuranosyl-3Himidazo[2,1-i]purines, Collec. Czech. Chem. Commun., 2011, 76, 1043–1054.
Kiuru, E.; Ora, M.; Beigelman, L.; Blatt, L.; Lönnberg, H., Synthesis and enzymatic deprotection
of
biodegradably
protected
dinucleoside-2´,5´-monophosphates:
3-acetyloxy-2,2bis(ethoxycarbonyl)propyl phosphoesters of 3´-O-acyloxymethyladenylyl-2´,5´-adenosines.
Chem. Biodiversity, 2011, 8, 266-286.
Kiviniemi, A.; Virta, P., Synthesis of aminoglycoside-3’-conjugates of 2’-O-methyl
oligoribonucleotides and their invasion to a 19F labeled HIV-1 TAR model, Bioconjugate Chem.
2011, 22, 1559-1566.
Kiviniemi, A.; Virta, P.; Drenichev, M.S.; Mikhailov, S. N.; Lönnberg, H., Solid-supported 2´-Oglycoconjugation of oligonucleotides by azidation and click reactions, Bioconjugate Chem., 2011,
22, 1249-1255.
Laine, M.; Aromaa, M.; Virta, P.; Lönnberg, T.; Poijärvi-Virta, P.; Lönnberg, H. The Zn2+
complex of 1,4,7,10-tetraazacyclododecane as an artificial nucleobase, Nucleosides Nucleotides
& Nucleic Acids, 2011, 30, 609-618.
Lönnberg, H., Nonenzymatic and metal-ion-dependent RNA cleavage, and RNase models, in
“Ribonucleases”, Nucleic Acids and Molecular Biology 26, Nicholson, A. W., Ed., Springer,
Berlin 2011, pp 343-366
Lönnberg, H., Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic
insight, Org. Biomol. Chem. 2011, 9, 1687-1703.
Lönnberg, T., Understanding catalysis of phosphate-transfer reactions by the large
ribozymes. Chem. Eur. J. 2011, 17, 7140-7153.
Neuvonen, K.; Neuvonen, H.; Koch, A.; Kleinpeter, E., NBO analysis of polar and steric effect
using the axial-equatorial equilibrium of cyclohexyl acetates as a probe. Comput. Theor. 2011,
964, 234-242.
Ora, M.; Mäntyvaara, A.; Lönnberg, H., 3-Acetyloxy-2-cyano-2-(alkylaminocarbamoyl)propyl
groups as biodegradable protecting groups of nucleoside 5´-monophosphates, Molecules 2011, 16,
552-566.
Ora, M., Hanski, A., Stepwise Mechanism of Hydroxide Ion Catalyzed Cyclization of Uridine 3'Thiophosphates. Helv. Chim. Acta, 2011, 94, 1563-1574.