Publications
1996
Paillart J C, Marquet R, Skripkin E, Ehresmann C, Ehresmann B
Dimerization of retroviral genomic RNAs: structural and functional implications Journal Article
In: Biochimie, vol. 78, no. 7, pp. 639-653, 1996, ISBN: 8955907, (0300-9084 Journal Article Review Review, Academic).
Abstract | Links | BibTeX | Tags: Animals Base Sequence HIV-1/genetics Human Microscopy, DNA Support, Electron Molecular Sequence Data *Nucleic Acid Conformation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry/metabolism Rats Retroviridae/*genetics Sequence Analysis
@article{,
title = {Dimerization of retroviral genomic RNAs: structural and functional implications},
author = {J C Paillart and R Marquet 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=8955907},
isbn = {8955907},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {639-653},
abstract = {Retroviruses are a family of widespread small animal viruses at the origin of a diversity of diseases. They share common structural and functional properties such as reverse transcription of their RNA genome and integration of the proviral DNA into the host genome, and have the particularity of packaging a diploid genome. The genome of all retroviruses is composed of two homologous RNA molecules that are non-covalently linked near their 5' end in a region called the dimer linkage structure (DLS). There is now considerable evidence that a specific site (or sites) in the 5' leader region of all retroviruses, located either upstream or/and downstream of the major splice donor site, is involved in the dimer linkage. For MoMuLV and especially HIV-1, it was shown that dimerization is initiated at a stem-loop structure named the dimerization initiation site (DIS). The DIS of HIV-1 and related regions in other retroviruses corresponds to a highly conserved structure with a self-complementary loop sequence, that is involved in a typical loop-loop 'kissing' complex which can be further stabilized by long distance interactions or by conformational rearrangements. RNA interactions involved in the viral RNA dimer were postulated to regulate several key steps in retroviral cycle, such as: i) translation and encapsidation: the arrest of gag translation imposed by the highly structured DLS-encapsidation signal would leave the RNA genome available for the encapsidation machinery; and ii) recombination during reverse transcription: the presence of two RNA molecules in particles would be necessary for variability and viability of virus progeny and the ordered structure imposed by the DLS would be required for efficient reverse transcription.},
note = {0300-9084
Journal Article
Review
Review, Academic},
keywords = {Animals Base Sequence HIV-1/genetics Human Microscopy, DNA Support, Electron Molecular Sequence Data *Nucleic Acid Conformation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry/metabolism Rats Retroviridae/*genetics Sequence Analysis},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Berthoux L, Ottmann M, Darlix J L, Marquet R, Ehresmann B, Ehresmann C
In: J Virol, vol. 70, no. 12, pp. 8348-8354, 1996, ISBN: 8970954, (0022-538x Journal Article).
Abstract | Links | BibTeX | Tags: Animals COS Cells DNA, Genetic Virion *Virus Assembly, MARQUET, Non-U.S. Gov't Transcription, Nucleic Acid Support, PAILLART, Post-Translational Proviruses/genetics *RNA, Unité ARN, Viral *Regulatory Sequences, Viral HIV-1/*genetics/physiology Human Mutagenesis Protein Processing, Viral/*biosynthesis Gene Expression Genome
@article{,
title = {A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis},
author = {J C Paillart and L Berthoux and M Ottmann and J L Darlix and R Marquet and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8970954},
isbn = {8970954},
year = {1996},
date = {1996-01-01},
journal = {J Virol},
volume = {70},
number = {12},
pages = {8348-8354},
abstract = {In retroviruses, the genomic RNA is in the form of a 60S-70S complex composed of two identical genome-length RNA molecules tightly associated through numerous interactions. A major interaction, called the dimer linkage structure, has been found near the RNA 5' end and is probably involved in the control of translation, packaging, and recombination during proviral DNA synthesis. Recently, a small sequence corresponding to a stem-loop structure located in the 5' leader of human immunodeficiency virus type 1 (HIV-1) RNA was found to be required for the initiation of HIV-1 RNA dimerization in vitro and named the dimerization initiation site (E. Skripkin, J.-C. Paillart, R. Marquet, B. Ehresmann, and C. Ehresmann, Proc. Natl. Acad. Sci. USA 91: 4945-4949, 1994). To investigate the possible role of this 5' stem-loop in HIV-1 virion formation and infectivity, four mutant viruses were generated and analyzed in vivo. Results show that deletion of the stem-loop structure reduces infectivity by a factor of 10(3) whereas loop substitutions cause a decrease of 10- to 100-fold. The level of genomic RNA packaging was found to be decreased fivefold in mutants virions containing the stem-loop deletion and only twofold in the loop-substituted virions. Surprisingly, the second DNA strand transfer during reverse transcription was found to be severely impaired upon stem-loop deletion. Taken together, these results indicate that the stem-loop structure called the dimerization initiation site is a cis element acting on both genomic RNA packaging and synthesis of proviral DNA.},
note = {0022-538x
Journal Article},
keywords = {Animals COS Cells DNA, Genetic Virion *Virus Assembly, MARQUET, Non-U.S. Gov't Transcription, Nucleic Acid Support, PAILLART, Post-Translational Proviruses/genetics *RNA, Unité ARN, Viral *Regulatory Sequences, Viral HIV-1/*genetics/physiology Human Mutagenesis Protein Processing, Viral/*biosynthesis Gene Expression Genome},
pubstate = {published},
tppubtype = {article}
}
Marquet R, Paillart J C, Skripkin E, Ehresmann C, Ehresmann B
Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization. Book Chapter
In: Sarma, R H; Sarma, M H (Ed.): Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 20-24, 1995, vol. 2, pp. 61-72, Adenine Press, 1996.
Links | BibTeX | Tags: MARQUET, PAILLART, Unité ARN
@inbook{,
title = {Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization.},
author = {R Marquet and J C Paillart and E Skripkin and C Ehresmann and B Ehresmann},
editor = {R H Sarma and M H Sarma},
url = {http://books.google.fr/books?hl=fr&id=SOpqAAAAMAAJ&q=Marquet#search_anchor},
year = {1996},
date = {1996-01-01},
booktitle = {Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 20-24, 1995},
volume = {2},
pages = {61-72},
publisher = {Adenine Press},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
1994
Skripkin E, Paillart J C, Marquet R, Ehresmann B, Ehresmann C
Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro Journal Article
In: Proc Natl Acad Sci U S A, vol. 91, no. 11, pp. 4945-4949, 1994, ISBN: 8197162, (0027-8424 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Binding Sites Biopolymers HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation Nucleotides/chemistry RNA, MARQUET, Non-U.S. Gov't, Nucleic Acid Support, PAILLART, Unité ARN, Viral/*chemistry Repetitive Sequences
@article{,
title = {Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro},
author = {E Skripkin and J C Paillart and R Marquet and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8197162},
isbn = {8197162},
year = {1994},
date = {1994-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {91},
number = {11},
pages = {4945-4949},
abstract = {The diploid genome of all retroviruses is made of two homologous copies of RNA intimately associated near their 5' end, in a region called the dimer linkage structure. Dimerization of genomic RNA is thought to be important for crucial functions of the retroviral life cycle (reverse transcription, translation, encapsidation). Previous in vitro studies mapped the dimer linkage structure of human immunodeficiency virus type 1 (HIV-1) in a region downstream of the splice donor site, containing conserved purine tracts that were postulated to mediate dimerization, through purine quartets. However, we recently showed that dimerization of HIV-1 RNA also involves sequences upstream of the splice donor site. Here, we used chemical modification interference to identify nucleotides that are required in unmodified form for dimerization of a RNA fragment containing nucleotides 1-707 of HIV-1 RNA. These nucleotides map exclusively in a restricted area upstream of the splice donor site and downstream of the primer binding site. They are centered around a palindromic sequence (GUGCAC279) located in a hairpin loop. Our results support a model in which dimer formation is initiated by the annealing of the palindromic sequences, possibly by a loop-loop interaction between the two monomers. Further experiments show that the deletion of the stem-loop or base substitutions in the loop abolish dimerization, despite the presence of the previously postulated dimer linkage structure. On the other hand, deletions of the purine tracts downstream of the splice donor site do not prevent dimerization. Therefore, we conclude that the palindromic region represents the dimerization initiation site of genomic RNA.},
note = {0027-8424
Journal Article},
keywords = {Base Sequence Binding Sites Biopolymers HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation Nucleotides/chemistry RNA, MARQUET, Non-U.S. Gov't, Nucleic Acid Support, PAILLART, Unité ARN, Viral/*chemistry Repetitive Sequences},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Marquet R, Skripkin E, Ehresmann B, Ehresmann C
Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA Journal Article
In: J Biol Chem, vol. 269, no. 44, pp. 27486-27493, 1994, ISBN: 7961663, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence DNA Mutational Analysis HIV-1/*chemistry Heat Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry Structure-Activity Relationship Support
@article{,
title = {Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA},
author = {J C Paillart and R Marquet and E Skripkin and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7961663},
isbn = {7961663},
year = {1994},
date = {1994-01-01},
journal = {J Biol Chem},
volume = {269},
number = {44},
pages = {27486-27493},
abstract = {The genome of all retroviruses consists in two homologous RNA molecules associated near their 5' end in a region called the dimer linkage structure. Dimerization of genomic RNA is thought to be important for several functions of the retroviral cycle such as encapsidation, reverse transcription, and translation. In human immunodeficiency virus type 1 (HIV-1), a region downstream of the splice donor site was initially postulated to mediate dimerization. However, we recently showed that the dimerization initiation site is located upstream of the splice donor site and suggested that dimerization may initiate through a loop-loop interaction. Here, we show that single base mutations in the palindromic loop of the dimerization initiation site completely abolish dimerization, while introduction of compensatory mutations restores the process. Furthermore, two single nucleotide mutants that are unable to form homodimers efficiently codimerize, while the wild type RNA and the compensatory mutant, which both form homodimers, are unable to codimerize. These results unambiguously prove the interaction between the palindromic loops of each monomer. By contrast, none of the deletions that we introduced downstream of the splice donor site abolishes dimerization. However, deletions of two purine tracts located in the vicinity of the initiation codon of the gag gene significantly decrease the thermal stability of the HIV-1 RNA dimer.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA Mutational Analysis HIV-1/*chemistry Heat Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
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}
}
1992
Rippe K, Fritsch V, Westhof E, Jovin T M
Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex Journal Article
In: EMBO J, vol. 11, no. 10, pp. 3777-3786, 1992, ISBN: 1396571, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF
@article{,
title = {Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex},
author = {K Rippe and V Fritsch and E Westhof and T M Jovin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1396571},
isbn = {1396571},
year = {1992},
date = {1992-01-01},
journal = {EMBO J},
volume = {11},
number = {10},
pages = {3777-3786},
abstract = {The oligonucleotides d[(G-A)7G] and d[(G-A)12G] self-associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double-helical structure (psRR-DNA) in which the two polypurine strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B-DNA. We have characterized psRR-DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer-excimer fluorescence of oligonucleotides end-labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4-9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force-field analysis in which the parallel-stranded d(G-A)n helix is right-handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H.O6 and N6H.N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left-handed Z-DNA. The related sequence d[(GAAGGA)4G] also forms a parallel-stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR-DNA in recombination, gene expression and the stabilization of genomic structure.},
note = {0261-4189
Journal Article},
keywords = {Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}