A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation

Lustig, Brooke; Lin, Nina; Smith, Stephen M.; Jernigan, Robert L.; Jeang, Kuan‐Teh

doi:10.1093/nar/23.17.3531

Cited by 6 publications

(5 citation statements)

References 36 publications

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“…But X-ray crystallographic data indicated 3 additional stabilizing base pairs in the internal loop (see Fig. The calculations also identify stacking stabilized structures with these augmenting base pair constraints that are consistent with the overall threedimensional structure indicated for the various hammerhead ribozyme structures determined by X-ray and FRET methods [13]. Klug and coworkers describe these as helix stem II augmenting base pairs, referring to the whole structure as augmented stem II helix [25].…”

Section: The Physical Structure Of Ribozymessupporting

confidence: 63%

“…It turns out that catalysis can be preserved for even truncated hammerhead structures [13]. Jeang and coworkers utilized for such structures an iterative thermal cycling method [29] to detect reduced activities reliably.…”

Section: The Physical Structure Of Ribozymesmentioning

confidence: 99%

“…The lattice and molecular dynamics calculations indicate significant flexibility for the hammerhead, including near the cleavage site [13,32]. There are at least two features of protein enzyme-substrate interaction, the general importance of flexibility and specificity, which could be applied to hammerhead ribozymes.…”

Section: The Physical Structure Of Ribozymesmentioning

confidence: 99%

“…A minimal hammerhead ribozyme cleaves target RNA containing a GUX consensus (X can be C, U or A) generating 2',3' cyclic phosphate and 5' hydroxy termini. In these regards, we have previously analyzed the conformation of a small hammerhead ribozyme by lattice calculation [13], and we have reported on several vector systems for high-level intracellular expression of anti-HIV-1 hammerhead ribozymes [14][15][16]. Cleavage efficiency of hammerhead ribozymes can be modulated by RNA-binding proteins such as HIV-1 p7 nucleocapsid protein which affects annealing/melting of RNA helices.…”

Section: Introductionmentioning

confidence: 99%

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Chemistry and Biochemistry of 2, 5-Oligoadenylate-Based Antisense Strategy

Adah

Bayly

Cramer³

et al. 2001

CMC

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This review describes the application of a natural defense mechanism to develop effective agents for the post-transcriptional control of gene expression. 2-5A is a unique 2',5'-phosphodiester bond linked oligoadenylate, (pp)p5'A2'(p5'A)(n), that is elaborated in virus-infected interferon-treated cells. The 2-5A system is an RNA degradation pathway that is an important mechanistic component of interferon's action against certain viruses. It may also play a role in the anticellular effects of interferon and in general RNA decay. A major player in the 2-5A-system is the latent and constitutive 2-5A-dependent ribonuclease (RNase L) which upon activation by 2-5A, degrades RNA. This RNase L enzyme can be recruited for antisense therapeutics by linking it to an appropriate oligonucleotide targeted to a chosen RNA. Syntheses of 2-5A, its analogues, 2-5A-antisense, and its modifications are detailed herein. Applications of 2-5A-antisense to particular targets such as HIV, PKR, chronic myelogenous leukemia, telomerase, and respiratory syncytical virus are described.

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Section: The Physical Structure Of Ribozymessupporting

confidence: 63%

Section: The Physical Structure Of Ribozymesmentioning

confidence: 99%

Section: The Physical Structure Of Ribozymesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Chemistry and Biochemistry of 2, 5-Oligoadenylate-Based Antisense Strategy

Adah

Bayly

Cramer³

et al. 2001

CMC

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“…As alluded to above, viruses with RNA genomes represent perhaps the most suitable vehicles for overexpression of RNA effectors (e.g., ribozymes). We have previously characterized a small ribozyme that cleaves a highly conserved sequence in the U5 region of the HIV-1 LTR (6,16). Because we encountered limitations with other expression strategies, it was of interest for us to explore alphavirus to deliver ribozymes into cells.…”

Section: Construction Of An Alphavirus Ribozyme Vectormentioning

confidence: 99%

Efficient expression by an alphavirus replicon of a functional ribozyme targeted to human immunodeficiency virus type 1

Smith

Maldarelli

Jeang

1997

J Virol

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Intracellular applications of ribozymes have been limited partly by the availability of suitable high-expression systems. For RNA effectors, consideration of an RNA virus vector system for delivery and expression is reasonable. We show that alphavirus replicons can be highly efficient nonintegrating ribozyme-expressing vectors. Using a hammerhead ribozyme targeted to a highly conserved sequence in the U5 region of the human immunodeficiency virus type 1 (HIV-1) long terminal repeat, we demonstrate that a full-length 8.3-kb Semliki Forest virus ribozyme (SFVRz) chimeric RNA maintains catalytic activity. SFVRz is packaged into viral particles, and these particles transduce mammalian cells efficiently. SFVRz-transduced BHK cells were found to produce large amounts of genomic and subgenomic forms of ribozyme-containing RNAs that are functional in cleaving a U5-tagged mRNA. The RNase protection assay shows that HIV-1 U5-chloramphenicol acetyltransferase mRNA expressed intracellularly from an RNA polymerase II promoter is quantitatively eliminated in SFVRz-transduced BHK cells.

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Flexibility of BIV TAR-Tat: Models of Peptide Binding

Hsieh

Collins

Blomquist

et al. 2002

Journal of Biomolecular Structure and Dynamics

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A new approach in determining local residue flexibility from base-amino acid contact frequencies is applied to the twelve million lattice chains modeling BIV Tat peptide binding to TAR RNA fragment. Many of the resulting key features in flexibility correspond to RMSD calculations derived from a set of five NMR derived structures (X. Ye, R. A. Kumar, and D. J. Patel, Protein Data Bank: Database of three-dimensional structures determined from NMR (1996)) and binding studies of mutants (L. Chen and A. D. Frankel, Proc. Natl. Acad. Sci. USA 92, 5077-5081 (1995)). The lattice and RMSD calculations facilitate the identification of peptide hinge regions that can best utilize the introduction of Gly or other flexible residues. This approach for identifying potential sites amenable to substitution of more flexible residues to enhance peptide binding to RNA targets could be a useful design tool.

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A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation

Cited by 6 publications

References 36 publications

Chemistry and Biochemistry of 2, 5-Oligoadenylate-Based Antisense Strategy

Chemistry and Biochemistry of 2, 5-Oligoadenylate-Based Antisense Strategy

Efficient expression by an alphavirus replicon of a functional ribozyme targeted to human immunodeficiency virus type 1

Flexibility of BIV TAR-Tat: Models of Peptide Binding

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