Tetraloop-like Geometries Could Form the Basis of the Catalytic
Activity of the Most Ancient Ribooligonucleotides

J 2015

Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides

STADLBAUER, Petr, Jiří ŠPONER, Giovanna COSTANZO, Ernesto DI MAURO, Samanta PINO et. al.

Basic information

Original name

Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides

Authors

STADLBAUER, Petr (203 Czech Republic), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution), Giovanna COSTANZO (380 Italy), Ernesto DI MAURO (380 Italy), Samanta PINO (380 Italy) and Judit ŠPONEROVÁ (348 Hungary, belonging to the institution)

Edition

Chemistry - A European Journal, WEINHEIM, WILEY-VCH, 2015, 0947-6539

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.771

RIV identification code

RIV/00216224:14740/15:00082899

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1002/chem.201406140

UT WoS

000350116200001

Keywords in English

catalysis; molecular dynamics; oligonucleotides; ribozymes; RNA

Abstract

V originále

The origin of the catalytic activity of ancient oligonucleotides is a largely unexplored field of contemporary science. In the current work we use molecular dynamics simulations to investigate the plausibility of tetraloop-like overhang geometries to initiate transphosphorylation reactions that lead to ligation and terminal cleavage in simple, Watson-Crick (WC) complementary oligoC/oligoG sequences observed experimentally. We show a series of examples of known tetraloop architectures, which can be adopted by the unpaired overhangs of short oligonucleotide sequences for a sufficiently long time to enable chemical reactions that lead to simple ribozyme-like catalytic activity. Thus, our computations demonstrate that the role of non-WC interactions at the emergence of the most ancient catalytic oligonucleotides could be more significant than ever believed.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

STADLBAUER, Petr, Jiří ŠPONER, Giovanna COSTANZO, Ernesto DI MAURO, Samanta PINO and Judit ŠPONEROVÁ. Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides. Chemistry - A European Journal. WEINHEIM: WILEY-VCH, 2015, vol. 21, No 9, p. 3596-3604. ISSN 0947-6539. Available from: https://dx.doi.org/10.1002/chem.201406140.

@article{1299594,
   author = {Stadlbauer, Petr and Šponer, Jiří and Costanzo, Giovanna and Di Mauro, Ernesto and Pino, Samanta and Šponerová, Judit},
   article_location = {WEINHEIM},
   article_number = {9},
   doi = {http://dx.doi.org/10.1002/chem.201406140},
   keywords = {catalysis; molecular dynamics; oligonucleotides; ribozymes; RNA},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides},
   url = {http://onlinelibrary.wiley.com/doi/10.1002/chem.201406140/epdf},
   volume = {21},
   year = {2015}
}

TY  - JOUR
ID  - 1299594
AU  - Stadlbauer, Petr - Šponer, Jiří - Costanzo, Giovanna - Di Mauro, Ernesto - Pino, Samanta - Šponerová, Judit
PY  - 2015
TI  - Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides
JF  - Chemistry - A European Journal
VL  - 21
IS  - 9
SP  - 3596-3604
EP  - 3596-3604
PB  - WILEY-VCH
SN  - 09476539
KW  - catalysis
KW  - molecular dynamics
KW  - oligonucleotides
KW  - ribozymes
KW  - RNA
UR  - http://onlinelibrary.wiley.com/doi/10.1002/chem.201406140/epdf
L2  - http://onlinelibrary.wiley.com/doi/10.1002/chem.201406140/epdf
N2  - The origin of the catalytic activity of ancient oligonucleotides is a largely unexplored field of contemporary science. In the current work we use molecular dynamics simulations to investigate the plausibility of tetraloop-like overhang geometries to initiate transphosphorylation reactions that lead to ligation and terminal cleavage in simple, Watson-Crick (WC) complementary oligoC/oligoG sequences observed experimentally. We show a series of examples of known tetraloop architectures, which can be adopted by the unpaired overhangs of short oligonucleotide sequences for a sufficiently long time to enable chemical reactions that lead to simple ribozyme-like catalytic activity. Thus, our computations demonstrate that the role of non-WC interactions at the emergence of the most ancient catalytic oligonucleotides could be more significant than ever believed.
ER  -

STADLBAUER, Petr, Jiří ŠPONER, Giovanna COSTANZO, Ernesto DI MAURO, Samanta PINO and Judit ŠPONEROVÁ. Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides. \textit{Chemistry - A European Journal}. WEINHEIM: WILEY-VCH, 2015, vol.~21, No~9, p.~3596-3604. ISSN~0947-6539. Available from: https://dx.doi.org/10.1002/chem.201406140.

Detailed Information on Publication Record