Publications
1997
Eckardt S, Romby P, Sczakiel G
Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1 Article de journal
Dans: Biochemistry, vol. 36, no. 42, p. 12711-12721, 1997, ISBN: 9335527, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anti-HIV Agents/*chemistry/pharmacology Base Sequence Cells, Antisense/*chemistry/*pharmacology RNA, Calf Thymus Ribonuclease T1 Software Support, Cultured Electrophoresis, Genetic, Insertional Mutagenesis, Non-U.S. Gov't Thermodynamics Transcription, Polyacrylamide Gel HIV-1/*drug effects/genetics Human Kinetics Molecular Sequence Data Mutagenesis, ROMBY, Site-Directed *Nucleic Acid Conformation Oligodeoxyribonucleotides Oligoribonucleotides/*chemistry/pharmacology RNA, Unité ARN, Viral/*chemistry/drug effects Ribonuclease H
@article{,
title = {Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1},
author = {S Eckardt and P Romby and G Sczakiel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9335527},
isbn = {9335527},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {42},
pages = {12711-12721},
abstract = {Antisense RNA-mediated regulation in bacterial systems is related to the kinetics of RNA-RNA annealing in vitro. Here, we investigated the secondary structure of alphaY69, an effective HIV-directed antisense RNA in human cells. Purified RNA preparations contain a single conformer. The global structure was identified by a cleavage experiment under native conditions using a short complementary oligonucleotide and RNase H. Structural analyses indicate a three-domain structure of alphaY69 consisting of two stem-loop elements connected by a seven-nucleotide single-stranded hinge region. Kinetic data suggest that the formation of base pairs between a CGC triplet of alphaY69 and its target RNA is essential for fast annealing. The complementary sequence stretch of the target folds into a high-energy secondary structure. The relationship between modifications in structural elements of alphaY69 and the annealing kinetics suggested that rate-limiting steps of the annealing involve a single site of alphaY69 and do not involve its 5' or 3'-end. Further, the data indicate that both initial base-specific interactions and duplex formation are dependent on the CGC triplet of the central region of alphaY69. This mechanism represents a specific and efficient way of RNA-RNA annealing that is initiated by the interaction of unstructured RNA regions.},
note = {0006-2960
Journal Article},
keywords = {Anti-HIV Agents/*chemistry/pharmacology Base Sequence Cells, Antisense/*chemistry/*pharmacology RNA, Calf Thymus Ribonuclease T1 Software Support, Cultured Electrophoresis, Genetic, Insertional Mutagenesis, Non-U.S. Gov't Thermodynamics Transcription, Polyacrylamide Gel HIV-1/*drug effects/genetics Human Kinetics Molecular Sequence Data Mutagenesis, ROMBY, Site-Directed *Nucleic Acid Conformation Oligodeoxyribonucleotides Oligoribonucleotides/*chemistry/pharmacology RNA, Unité ARN, Viral/*chemistry/drug effects Ribonuclease H},
pubstate = {published},
tppubtype = {article}
}
1996
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 11, p. 5572-5577, 1996, ISBN: 8643617, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support
@article{,
title = {A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA},
author = {J C Paillart and E Skripkin and B Ehresmann and C Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8643617},
isbn = {8643617},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {11},
pages = {5572-5577},
abstract = {RNA-RNA interactions govern a number of biological processes. Several RNAs, including natural sense and antisense RNAs, interact by means of a two-step mechanism: recognition is mediated by a loop-loop complex, which is then stabilized by formation of an extended intermolecular duplex. It was proposed that the same mechanism holds for dimerization of the genomic RNA of human immunodeficiency virus type 1 (HIV-1), an event thought to control crucial steps of HIV-1 replication. However, whereas interaction between the partially self-complementary loop of the dimerization initiation site (DIS) of each monomer is well established, formation of the extended duplex remained speculative. Here we first show that in vitro dimerization of HIV-1 RNA is a specific process, not resulting from simple annealing of denatured molecules. Next we used mutants of the DIS to test the formation of the extended duplex. Four pairs of transcomplementary mutants were designed in such a way that all pairs can form the loop-loop "kissing" complex, but only two of them can potentially form the extended duplex. All pairs of mutants form heterodimers whose thermal stability, dissociation constant, and dynamics were analyzed. Taken together, our results indicate that, in contrast with the interactions between natural sense and antisense RNAs, no extended duplex is formed during dimerization of HIV-1 RNA. We also showed that 55-mer sense RNAs containing the DIS are able to interfere with the preformed HIV-1 RNA dimer.},
note = {0027-8424
Journal Article},
keywords = {Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 11, p. 5572-5577, 1996, ISBN: 8643617, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support
@article{,
title = {A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA},
author = {J C Paillart and E Skripkin and B Ehresmann and C Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8643617},
isbn = {8643617},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {11},
pages = {5572-5577},
abstract = {RNA-RNA interactions govern a number of biological processes. Several RNAs, including natural sense and antisense RNAs, interact by means of a two-step mechanism: recognition is mediated by a loop-loop complex, which is then stabilized by formation of an extended intermolecular duplex. It was proposed that the same mechanism holds for dimerization of the genomic RNA of human immunodeficiency virus type 1 (HIV-1), an event thought to control crucial steps of HIV-1 replication. However, whereas interaction between the partially self-complementary loop of the dimerization initiation site (DIS) of each monomer is well established, formation of the extended duplex remained speculative. Here we first show that in vitro dimerization of HIV-1 RNA is a specific process, not resulting from simple annealing of denatured molecules. Next we used mutants of the DIS to test the formation of the extended duplex. Four pairs of transcomplementary mutants were designed in such a way that all pairs can form the loop-loop "kissing" complex, but only two of them can potentially form the extended duplex. All pairs of mutants form heterodimers whose thermal stability, dissociation constant, and dynamics were analyzed. Taken together, our results indicate that, in contrast with the interactions between natural sense and antisense RNAs, no extended duplex is formed during dimerization of HIV-1 RNA. We also showed that 55-mer sense RNAs containing the DIS are able to interfere with the preformed HIV-1 RNA dimer.},
note = {0027-8424
Journal Article},
keywords = {Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}