In vitro selection of RNAs that bind to the human immunodeficiency virus type-1 gag polyprotein

Lochrie, Michael A.; Waugh, Sheela; Pratt, Dickson G.; Clever, Jared L.; Parslow, Tristram G.; Polisky, Barry

doi:10.1093/nar/25.14.2902

Cited by 97 publications

(92 citation statements)

References 50 publications

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“…The consensus sequence for the high affinity RNA ligand to HIV-1 MA derived from screening of random 76-mer and 31-mer libraries as described previously (30,31), yielding a consensus, 5Ј-GGAAU UAAUA GUAGC-3Ј (Sel15). We also prepared a 25-mer stem-loop (Sel25) version of Sel15 that retained its high MA binding affinity; its sequence is 5Ј-GGACA GGAAU UAAUA GUAGC UGUCC-3Ј.…”

Section: Methodsmentioning

confidence: 99%

Analysis of Small Molecule Ligands Targeting the HIV-1 Matrix Protein-RNA Binding Site

Alfadhli

McNett

Eccles

et al. 2013

Journal of Biological Chemistry

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Section: Methodsmentioning

confidence: 99%

Analysis of Small Molecule Ligands Targeting the HIV-1 Matrix Protein-RNA Binding Site

Alfadhli

McNett

Eccles

et al. 2013

Journal of Biological Chemistry

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“…SL1 also participates in the initiation of RNA dimerization [66,77]. SL3 contains a specific binding site for HIV-1 NC [81][82][83], although cooperative binding to multiple loops has also been suggested [84]. However, an important distinction is that a continuous, discrete, transferable element analogous to that of MLV [71,72] has not been defined for any lentivirus.…”

Section: Encapsidation Determinantsmentioning

confidence: 99%

FIV: from lentivirus to lentivector

Saenz

Poeschla

2004

J. Gene Med.

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SummaryMolecular virological understanding of the feline immunodeficiency virus (FIV) life cycle is increasing, facilitating rational derivation of improved vectors from this non-primate lentivirus. The packaging signal has been mapped, a central DNA flap has been identified, and class I integrase mutants have been validated. Vector systems with improved effectiveness and safety profiles are being applied by a number of laboratories in several pre-clinical models, with demonstrated efficacy in human tissues. The comparative lentivirological research that facilitates FIV vector development may also yield insights into the still enigmatic molecular basis for a signature lentiviral property with pathogenetic and therapeutic importance: permanent transgene integration in non-dividing cells. This review discusses virological aspects of lentiviral vector development, as well as some recent controversies and applications.

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“…Nucleocapsid protein is known to have a preference for G/U-containing sequences (Berglund et al 1997;Fisher et al 1998;Kim et al 2002). In addition, in vitro selection studies have shown that RNA ligands selected for nucleocapsid binding end with a self-complementary sequence located in a stem-loop structure (Lochrie et al 1997). These features are similar to presumed features of the -SL1 region.…”

Section: Regulation Of Hiv-2 Rna Dimerizationmentioning

confidence: 99%

A structural linkage between the dimerization and encapsidation signals in HIV-2 leader RNA

Lanchy

Ivanovitch

Lodmell

2003

RNA

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The 5 untranslated leader region of retroviral RNAs contains noncoding information that is essential for viral replication, including signals for transcriptional transactivation, splicing, primer binding for reverse transcription, dimerization of the genomic RNA, and encapsidation of the viral RNA into virions. These RNA motifs have considerable structural and functional overlap. In this study, we investigate the conformational dynamics associated with the use and silencing of a sequence in HIV-2 RNA that is involved in genomic RNA dimerization called stem-loop 1 (SL1) and its relationship with a flanking sequence that is known to be important for encapsidation of viral RNAs. We demonstrate that a long-distance intramolecular interaction between nucleotides located upstream of the primer-binding site domain and nucleotides encompassing the Gag translation start codon functionally silences SL1 as a dimerization element. This silencing can be relieved by mutation or by hybridization of an oligonucleotide that disrupts the long-distance interaction. Furthermore, we identify a palindrome within the packaging/ encapsidation signal (just 5 of SL1) that can either serve as an efficient dimerization signal itself, or can mediate SL1 silencing through base pairing with SL1. These results provide a tangible link between the functions of genomic RNA dimerization and encapsidation, which are known to be related, but whose physical relationship has been unclear. A model is proposed that accounts for observations of dimerization, packaging, and translation of viral RNAs during different phases of the viral replication cycle.

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In vitro selection of RNAs that bind to the human immunodeficiency virus type-1 gag polyprotein

Cited by 97 publications

References 50 publications

Analysis of Small Molecule Ligands Targeting the HIV-1 Matrix Protein-RNA Binding Site

Analysis of Small Molecule Ligands Targeting the HIV-1 Matrix Protein-RNA Binding Site

FIV: from lentivirus to lentivector

A structural linkage between the dimerization and encapsidation signals in HIV-2 leader RNA

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