Mapping the universe of RNA tetraloop folds

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Mapping the universe of RNA tetraloop folds. / Bottaro, Sandro; Lindorff-Larsen, Kresten.

In: Biophysical Journal, Vol. 113, No. 2, 25.07.2017, p. 257-267.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Bottaro, S & Lindorff-Larsen, K 2017, 'Mapping the universe of RNA tetraloop folds', Biophysical Journal, vol. 113, no. 2, pp. 257-267. https://doi.org/10.1016/j.bpj.2017.06.011

APA

Bottaro, S., & Lindorff-Larsen, K. (2017). Mapping the universe of RNA tetraloop folds. Biophysical Journal, 113(2), 257-267. https://doi.org/10.1016/j.bpj.2017.06.011

Vancouver

Bottaro S, Lindorff-Larsen K. Mapping the universe of RNA tetraloop folds. Biophysical Journal. 2017 Jul 25;113(2):257-267. https://doi.org/10.1016/j.bpj.2017.06.011

Author

Bottaro, Sandro ; Lindorff-Larsen, Kresten. / Mapping the universe of RNA tetraloop folds. In: Biophysical Journal. 2017 ; Vol. 113, No. 2. pp. 257-267.

Bibtex

@article{8ec3d7e4a878421d802ed4331278055d,
title = "Mapping the universe of RNA tetraloop folds",
abstract = "We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold.",
author = "Sandro Bottaro and Kresten Lindorff-Larsen",
year = "2017",
month = jul,
day = "25",
doi = "10.1016/j.bpj.2017.06.011",
language = "English",
volume = "113",
pages = "257--267",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Cell Press",
number = "2",

}

RIS

TY - JOUR

T1 - Mapping the universe of RNA tetraloop folds

AU - Bottaro, Sandro

AU - Lindorff-Larsen, Kresten

PY - 2017/7/25

Y1 - 2017/7/25

N2 - We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold.

AB - We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold.

UR - http://www.scopus.com/inward/record.url?scp=85021398961&partnerID=8YFLogxK

U2 - 10.1016/j.bpj.2017.06.011

DO - 10.1016/j.bpj.2017.06.011

M3 - Journal article

C2 - 28673616

AN - SCOPUS:85021398961

VL - 113

SP - 257

EP - 267

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 2

ER -

ID: 181388252