Peter Podbevšek
Ph.D.
peter.podbevsek@ki.si
(01) 47-60-240
I have spent more than 15 years researching the structure of nucleic acids. Starting with my B.Sc. degree in biochemistry at the Faculty of chemistry and chemical technology, University of Ljubljana in 2009 I have focused on non-canonical DNA structures, especially four-stranded G-quadruplexes. I spent several months as a Marie Curie fellow at the University of southern Denmark, Odense working with short viral RNA hairpins. In the following years I was enrolled in the “Young researcher” programme at the NMR Centre at the National institute of chemistry in Ljubljana under the supervision of prof. Janez Plavec. In the year 2011 I received my Ph.D. degree in biochemistry and molecular biology at the Faculty of medicine, University of Ljubljana. The topic of my Ph.D. thesis was the influence of chemical modifications and cations on 3D structures of oligonucleotides. As a postdoc I spent two years at the International School for Advances Studies, SISSA in Trieste, Italy. My postdoc project supervised by Prof. Stefano Gustincich was dealing with structural characterization of long noncoding RNAs. My work continues to revolve around DNA and RNA and is currently focused on oxidative damage of guanine. While nuclear magnetic resonance is my primary research method I like to implement other modern analytical methods in our lab. I have co-authored 20 research papers and am involved in training of students on all levels. As a co-organizer of the annual symposium series “ANNA - Advances in non-canonical nucleic acids” I make sure that our collaborators from Europe, Asia and USA get a glimpse of Slovenia.
Current research interests:
• Structure and dynamics of non-canonical DNA folds derived from the human genome
• The influence of oxidative and nitrative stress on DNA structures
• Structure-function relationship of non-coding RNAs
SELECTED PUBLICATIONS
1
P. Podbevsek and J. Plavec
KRAS promoter oligonucleotide with decoy activity dimerizes into a unique topology consisting of two G-quadruplex units
Nucleic Acids Res. 2016, 44(2), 917-925.
Web access at Oxford Journals.
2
P. Podbevsek, C.R. Allerson, B. Balkrishen and J. Plavec
Solution-state structure of a fully alternately 2'-F/2'-OMe modified 42-nt dimeric siRNA construct
Nucleic Acids Res., 2010, 38 (20), 7298-7307.
Web access at Oxford Journals
3
S. Bielskutė, J. Plavec and P. Podbevsek
Impact of Oxidative Lesions on the Human Telomeric G-quadruplex
J. Amer. Chem. Soc. 2019, 141 (6), 2594-2603.
Web access at ACS Publications
LIST OF PUBLICATIONS
2023
22
K. Peterková, M. Stitch, R. Boota, P. A. Scattergood, P. I. P. Elliott, P. Podbevšek, J. Plavec and S. J. Quinn
G-Quadruplex Binding of a NIR Emitting Osmium Polypyridyl Probe Revealed by Solution NMR and Time-Resolved Infrared Studies
Chem. Eur. J. 2023, 29 (11), e202203250.
Web access at Wiley Online Library
2022
21
S Aleksič, P. Podbevšek and J. Plavec
8-Oxoguanine forms quartets with a large central cavity
Biochemistry 2022, 61 (21), 2390-2397.
Web access at ACS publications
2021
20
H. Jahns, R. Degaonkar, P. Podbevsek, S. Gupta, A. Bisbe, K. Aluri, J. Szeto, P. Kumar, S. LeBlanc, T. Racie, C. R. Brown, A. Castoreno, D. C. Guenther, V. Jadhav, M. A. Maier, J. Plavec, M. Egli, M. Manoharan and I. Zlatev
Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing
Nucleic Acids Res. 2021, 49 (18), 10250-10264.
Web access at Oxford Journals
19
E. Balanikas, L. Martinez-Fernandez, R. Improta, P. Podbevšek, G. Baldacchino, and D. Markovitsi
The Structural Duality of Nucleobases in Guanine Quadruplexes Controls Their Low-Energy Photoionization
J. Phys. Chem. Lett. 2021, 12 (34), 8309–8313.
Web access at ACS Publications
18
K. Peterková, I. Durník, R. Marek, J. Plavec and P. Podbevšek
c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry
Nucleic Acids Res. 2021, 49 (15), 8947-8960.
Web access at Oxford Journals
17
S. Satpathi, T. Endoh, P. Podbevšek, J. Plavec and N. Sugimoto
Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity
Nucleic Acids Res. 2021, 49 (15), 2346-2356.
Web access at Oxford Journals
This paper is highlighted as a cover image of the issue
16
S. Bielskutė, J. Plavec and P. Podbevšek
Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter
Nucleic Acids Res. 2021, 49 (4), 2346-2356.
Web access at Oxford Journals
2020
15
M. Kovacic, P. Podbevsek, H. Tateishi-Karimata, S. Takahashi, N. Sugimoto and J. Plavec
Thrombin binding aptamer G-quadruplex stabilized by pyrene-modified nucleotides
Nucleic Acids Res. 2020, 48 (7), 3975-3986.
Web access at Oxford Journals
2019
14
S. Bielskutė, J. Plavec and P. Podbevsek
Impact of Oxidative Lesions on the Human Telomeric G-quadruplex
J. Amer. Chem. Soc. 2019, 141 (6), 2594-2603.
Web access at ACS Publications
2018
13
S. Takahashi, K. T. Kim, P. Podbevsek, J. Plavec, B. H. Kim and N. Sugimoto
Recovery of the formation and function of oxidized G-quadruplexes by pyrene-modified guanine-tract
J. Am. Chem Soc. 2018, 140 (17), 5774-5783.
Web access at ACS Publications
12
P. Podbevsek, F. Fasolo, C. Bon, L. Cimatti, S. Reisser, P. Carninci, G. Bussi, S. Zucchelli, J. Plavec and S. Gustincich
Structural determinants of the SINEB2 element embedded in the long non-coding RNA activator of translation AS Uchl1
Sci. Rep. 2018, 8, article number: 3189.
Web access at nature.com
2017
11
H. Tateishi-Karimata, T. Ohyama, T. Muraoka, P. Podbevsek, A. M. Wawro, S. Tanaka, S. Nakano, K, Kinbara, J. Plavec and N. Sugimoto
Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH–π interactions
Nucleic Acids Res. 2017, 45(12), 7021-7030.
Web access at Oxford Journals
10
T. Fujii, P. Podbevsek, J. Plavec and N. Sugimoto
Effects of metal ions and molecular crowding on G-quadruplex topology
J. Inorg. Biochem., 2017, 166, 190-198.
Web access at ScienceDirect
2016
9
P. Podbevsek and J. Plavec
KRAS promoter oligonucleotide with decoy activity dimerizes into a unique topology consisting of two G-quadruplex units
Nucleic Acids Res. 2016, 44(2), 917-925.
Web access at Oxford Journals.
2014
8
S. Medic, P. Podbevsek and J. Plavec
Solution Structure of a Prion Protein Aptamer Analogue
Croat. Chem. Acta 2014, 87 (4), 321–325.
Web access at CCA
2013
7
S. P. Sau, A. S. Madsen, P. Podbevsek, N. K. Andersen, T. S. Kumar, S. Andersen, R. L. Rathje, B. A. Anderson, D. C. Guenther, S. Karmakar, P. Kumar, J. Plavec, J. Wengel and P. J. Hrdlicka
Identification and Characterization of Second-Generation Invader Locked Nucleic Acids (LNAs) for Mixed-Sequence Recognition of Double-Stranded DNA
J. Org. Chem. 2013, 78 (19), 9560-9570.
Web access at ACS publications
6
J. Stanek, P. Podbevsek, W. Kozminski, J. Plavec and M. Cevec
4D Non-uniformly sampled C,C-NOESY experiment for sequential assignment of 13C,15N-labeled RNAs
J. Biomol. NMR 2013, 57 (1), 1-9.
Web access at Spriger
2011
5
J. Zavasnik, P. Podbevsek and J. Plavec
Observation of water molecules within the bimolecular d(G3CT4G3C)2 G-quadruplex
Biochemistry 2011, 50 (19), 4155-4161.
Web access at ACS Publications
2010
4
P. Podbevsek, C.R. Allerson, B. Balkrishen and J. Plavec
Solution-state structure of a fully alternately 2'-F/2'-OMe modified 42-nt dimeric siRNA construct
Nucleic Acids Res., 2010, 38 (20), 7298-7307.
Web access at Oxford Journals
2008
3
P. Podbevsek, P. Sket and J. Plavec
Stacking and Not Solely Topology of T3 Loops Controls Rigidity and Ammonium Ion Movement within d(G4T3G4)2 G-Quadruplex
J. Am. Chem. Soc. 2008, 130 (43), 14287-14293.
2007
2
P. Podbevsek, P. Sket and J. Plavec
NMR study of ammonium ion binding to d[G3T4G4]2 and d[G4(T4G4)3] G-quadruplexes
Nucl. Nucl. and Nucl. Acids 2007, 26 (10), 1547-1551.
1
P. Podbevsek, N. V. Hud and J. Plavec
NMR Evaluation of Ammonium Ion Movement within a Unimolecular G-quadruplex in Solution
Nucleic Acids Res. 2007, 35 (8), 2554-2563.