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2002
Brunel C, Marquet R, Romby P, Ehresmann C
RNA loop-loop interactions as dynamic functional motifs Journal Article
In: Biochimie, vol. 84, no. 9, pp. 925-944, 2002, ISBN: 12458085, (0300-9084 Journal Article Review Review Literature).
Abstract | Links | BibTeX | Tags: Animals Base Pairing Base Sequence Dimerization HIV-1/genetics Human Kinetics Molecular Sequence Data *Nucleic Acid Conformation RNA/genetics/*metabolism Support, MARQUET, Non-U.S. Gov't Thermodynamics, ROMBY, Unité ARN
@article{,
title = {RNA loop-loop interactions as dynamic functional motifs},
author = {C Brunel and R Marquet and P Romby and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12458085},
isbn = {12458085},
year = {2002},
date = {2002-01-01},
journal = {Biochimie},
volume = {84},
number = {9},
pages = {925-944},
abstract = {RNA loop-loop interactions are frequently used to trigger initial recognition between two RNA molecules. In this review, we present selected well-documented cases that illustrate the diversity of biological processes using RNA loop-loop recognition properties. The first one is related to natural antisense RNAs that play a variety of regulatory functions in bacteria and their extra-chromosomal elements. The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome. The third one concerns RNA interactions involving double-loop interactions. These are used by the bicoid mRNA to form dimers, a property that appears to be important for mRNA localization in drosophila embryo, and by bacteriophage phi29 pRNA which forms hexamers that participate in the translocation of the DNA genome through the portal vertex of the capsid. Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme. (2) The initial recognition is favored by particular conformations of the loops enabling a proper presentation of nucleotides (generally a restricted number) that initiate the recognition process. (3) The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints. RNA structures have evolved either to "freeze" the initial complex, or to convert it into a more stable one, which involves propagation of intermolecular interactions along topologically feasible pathways. Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.},
note = {0300-9084
Journal Article
Review
Review Literature},
keywords = {Animals Base Pairing Base Sequence Dimerization HIV-1/genetics Human Kinetics Molecular Sequence Data *Nucleic Acid Conformation RNA/genetics/*metabolism Support, MARQUET, Non-U.S. Gov't Thermodynamics, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNA loop-loop interactions are frequently used to trigger initial recognition between two RNA molecules. In this review, we present selected well-documented cases that illustrate the diversity of biological processes using RNA loop-loop recognition properties. The first one is related to natural antisense RNAs that play a variety of regulatory functions in bacteria and their extra-chromosomal elements. The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome. The third one concerns RNA interactions involving double-loop interactions. These are used by the bicoid mRNA to form dimers, a property that appears to be important for mRNA localization in drosophila embryo, and by bacteriophage phi29 pRNA which forms hexamers that participate in the translocation of the DNA genome through the portal vertex of the capsid. Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme. (2) The initial recognition is favored by particular conformations of the loops enabling a proper presentation of nucleotides (generally a restricted number) that initiate the recognition process. (3) The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints. RNA structures have evolved either to "freeze" the initial complex, or to convert it into a more stable one, which involves propagation of intermolecular interactions along topologically feasible pathways. Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.
2000
Ennifar E, Nikulin A, Tishchenko S, Serganov A, Nevskaya N, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P
The crystal structure of UUCG tetraloop Journal Article
In: J Mol Biol, vol. 304, no. 1, pp. 35-42, 2000, ISBN: 11071808, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: 16S/*chemistry/genetics/*metabolism Ribosomal Proteins/chemistry/*metabolism Solvents Support, Base Sequence Crystallography, Biomolecular *Nucleic Acid Conformation RNA Stability RNA, ENNIFAR, Molecular Molecular Sequence Data Motion Nuclear Magnetic Resonance, Non-U.S. Gov't Thermodynamics, Ribosomal, Unité ARN, X-Ray Hydrogen Bonding Models
@article{,
title = {The crystal structure of UUCG tetraloop},
author = {E Ennifar and A Nikulin and S Tishchenko and A Serganov and N Nevskaya and M Garber and B Ehresmann and C Ehresmann and S Nikonov and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11071808},
isbn = {11071808},
year = {2000},
date = {2000-01-01},
journal = {J Mol Biol},
volume = {304},
number = {1},
pages = {35-42},
abstract = {All large structured RNAs contain hairpin motifs made of a stem closed by several looped nucleotides. The most frequent loop motif is the UUCG one. This motif belongs to the tetraloop family and has the peculiarity of being highly thermodynamically stable. Here, we report the first crystal structure of two UUCG tetraloops embedded in a larger RNA-protein complex solved at 2.8 A resolution. The two loops present in the asymmetric unit are in a different crystal packing environment but, nevertheless, have an identical conformation. The observed structure is globally close to that obtained in solution by nuclear magnetic resonance. However, subtle differences point to a more detailed picture of the role played by 2'-hydroxyl groups in stabilising this tetraloop.},
note = {0022-2836
Journal Article},
keywords = {16S/*chemistry/genetics/*metabolism Ribosomal Proteins/chemistry/*metabolism Solvents Support, Base Sequence Crystallography, Biomolecular *Nucleic Acid Conformation RNA Stability RNA, ENNIFAR, Molecular Molecular Sequence Data Motion Nuclear Magnetic Resonance, Non-U.S. Gov't Thermodynamics, Ribosomal, Unité ARN, X-Ray Hydrogen Bonding Models},
pubstate = {published},
tppubtype = {article}
}
All large structured RNAs contain hairpin motifs made of a stem closed by several looped nucleotides. The most frequent loop motif is the UUCG one. This motif belongs to the tetraloop family and has the peculiarity of being highly thermodynamically stable. Here, we report the first crystal structure of two UUCG tetraloops embedded in a larger RNA-protein complex solved at 2.8 A resolution. The two loops present in the asymmetric unit are in a different crystal packing environment but, nevertheless, have an identical conformation. The observed structure is globally close to that obtained in solution by nuclear magnetic resonance. However, subtle differences point to a more detailed picture of the role played by 2'-hydroxyl groups in stabilising this tetraloop.
1994
Marquet R, Paillart J C, Skripkin E, Ehresmann C, Ehresmann B
Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site Journal Article
In: Nucleic Acids Res, vol. 22, no. 2, pp. 145-151, 1994, ISBN: 8121797, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Cations HIV-1/*genetics Kinetics Macromolecular Systems Magnesium Models, Chemical Models, Genetic Molecular Sequence Data RNA Splicing RNA, MARQUET, Non-U.S. Gov't Thermodynamics, PAILLART, Unité ARN, Viral/*chemistry Support
@article{,
title = {Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site},
author = {R Marquet and J C Paillart and E Skripkin and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8121797},
isbn = {8121797},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {2},
pages = {145-151},
abstract = {The retroviral genome consists of two homologous RNA molecules associated close to their 5' ends. We studied the spontaneous dimerization of four HIV-1 RNA fragments (RNAs 1-707, 1-615, 311-612, and 311-415) containing the previously defined dimerization domain, and a RNA fragment (RNA 1-311) corresponding to the upstream sequences. Significant dimerization of all RNAs is observed on agarose gels when magnesium is included in the electrophoresis buffer. In contrast to dimerization of RNAs 311-612 and 311-415, dimerization of RNAs 1-707, 1-615 and 1-311 strongly depends on the size of the monovalent cation present in the incubation buffer. Also, dimerization of RNAs 1-707, 1-615, and 1-311 is 10 times faster than that of RNAs 311-612 and 311-415. The dimers formed by the latter RNAs are substantially more stable than that of RNA 1-615, while RNA 1-311 dimer is 5-7 degrees C less stable than RNA 1-615 dimer. These results indicate that dimerization of HIV-1 genomic RNA involves elements located upstream of the splice donor site (position 305), i.e. outside of the previously defined dimerization domain.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Cations HIV-1/*genetics Kinetics Macromolecular Systems Magnesium Models, Chemical Models, Genetic Molecular Sequence Data RNA Splicing RNA, MARQUET, Non-U.S. Gov't Thermodynamics, PAILLART, Unité ARN, Viral/*chemistry Support},
pubstate = {published},
tppubtype = {article}
}
The retroviral genome consists of two homologous RNA molecules associated close to their 5' ends. We studied the spontaneous dimerization of four HIV-1 RNA fragments (RNAs 1-707, 1-615, 311-612, and 311-415) containing the previously defined dimerization domain, and a RNA fragment (RNA 1-311) corresponding to the upstream sequences. Significant dimerization of all RNAs is observed on agarose gels when magnesium is included in the electrophoresis buffer. In contrast to dimerization of RNAs 311-612 and 311-415, dimerization of RNAs 1-707, 1-615 and 1-311 strongly depends on the size of the monovalent cation present in the incubation buffer. Also, dimerization of RNAs 1-707, 1-615, and 1-311 is 10 times faster than that of RNAs 311-612 and 311-415. The dimers formed by the latter RNAs are substantially more stable than that of RNA 1-615, while RNA 1-311 dimer is 5-7 degrees C less stable than RNA 1-615 dimer. These results indicate that dimerization of HIV-1 genomic RNA involves elements located upstream of the splice donor site (position 305), i.e. outside of the previously defined dimerization domain.
