Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases.
Peracchi, A, Beigelman, L, Usman, N, Herschlag, D
We have synthesized 13 hammerhead ribozyme variants, each containing an abasic residue at a specific position of the catalytic core. The activity of each of the variants is significantly reduced. In...
Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization.
Narlikar, G J, Gopalakrishnan, V, McConnell, T S, Usman, N, Herschlag, D
A fundamental catalytic principle for protein enzymes in the use of binding interactions away from the site of chemical transformation for catalysis. We have compared the binding and reactivity of a...
Total chemical synthesis of a ribozyme derived from a group I intron.
Whoriskey, S K, Usman, N, Szostak, J W
We describe the complete chemical synthesis of a ribozyme that catalyzes template-directed oligonucleotide ligation. The specific activity of the synthetic ribozyme is nearly identical to that of the...
Crystal structure of an Okazaki fragment at 2-A resolution.
Egli, M, Usman, N, Zhang, S G, Rich, A
In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template...
Enzymatic aminoacylation of single-stranded RNA with an RNA cofactor.
Musier-Forsyth, K, Scaringe, S, Usman, N, Schimmel, P
A chemically synthesized single-stranded ribonucleotide tridecamer derived from the 3' end of Escherichia coli alanine tRNA can be charged with alanine in the presence of short complementary RNA...
Schmidt, S, Beigelman, L, Karpeisky, A, Usman, N, Sorensen, U S, Gait, M J
The hairpin ribozyme is a small self-cleaving RNA that can be engineered for RNA cleavage in trans and has potential as a therapeutic agent. We have used a chemical synthesis approach to study the...
Ordered differential display: a simple method for systematic comparison of gene expression profiles.
Matz, M, Usman, N, Shagin, D, Bogdanova, E, Lukyanov, S
A method for display of 3'-end restriction fragments of cDNAs is proposed, extending the idea reported recently. First, representative pools of such fragments are selectively amplified using PCR...
1-Deazaadenosine: synthesis and activity of base-modified hammerhead ribozymes.
Seela, F, Debelak, H, Usman, N, Burgin, A, Beigelman, L
The incorporation of 1-deazaadenosine (c1A, 1b) into a hammerhead ribozyme and the resulting catalytic activity is described. For this purpose the phosphoramidite 2a and the 3'-phosphonate 2b as well...
Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity.
Ogilvie, K K, Usman, N, Nicoghosian, K, Cedergren, R J
Chemical synthesis is described of a 77-nucleotide-long RNA molecule that has the sequence of an Escherichia coli Ado-47-containing tRNA(fMet) species in which the modified nucleosides have been...
Synthesis, deprotection, analysis and purification of RNA and ribozymes.
Wincott, F, DiRenzo, A, Shaffer, C, Grimm, S, Tracz, D, Workman, C, ...
Improvements in the synthesis, deprotection and purification of oligoribonucleotides are described. These advances allow for reduced synthesis and deprotection times, while improving product yield....
Synthesis and biological activities of a phosphorodithioate analog of 2',5'-oligoadenylate.
Beigelman, L, Matulic-Adamic, J, Haeberli, P, Usman, N, Dong, B, Silverman, R H, ...
To enhance the resistance of 2-5A (pppA2'p5'A2'p5'A) to degradation by exo- and endonucleases, a phosphorodithioate analog was synthesized using a solid-phase phosphite triester approach with...
An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain.
Chartrand, P, Harvey, S C, Ferbeyre, G, Usman, N, Cedergren, R
A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that...
Synthesis of 2'-modified nucleotides and their incorporation into hammerhead ribozymes.
Beigelman, L, Karpeisky, A, Matulic-Adamic, J, Haeberli, P, Sweedler, D, Usman, N
Several 2'-modified ribonucleoside phosphoramidites have been prepared for structure-activity studies of the hammerhead ribozyme. The aim of these studies was to design and synthesize catalytically...
Pon, R T, Usman, N, Damha, M J, Ogilvie, K K
Phosphoramidite reagents can phosphitylate guanine bases at the O6-position during solid phase synthesis and serious chain cleavage occurs if the base phosphitylation is not eliminated before the...
Green, R, Szostak, J W, Benner, S A, Rich, A, Usman, N
Two protected derivatives of the ribonucleoside inosine have been prepared to serve as building blocks for phosphoramidite-based synthesis of RNA. Two different synthetic routes address the unusual...
Scaringe, S A, Francklyn, C, Usman, N
The preparation of fully protected diisopropylamino-beta-cyanoethyl ribonucleoside phosphoramidites with regioisomeric purity greater than 99.95% is described. It is demonstrated that the combination...
Characterization of HIV-1 REV protein: binding stoichiometry and minimal RNA substrate.
Cook, K S, Fisk, G J, Hauber, J, Usman, N, Daly, T J, Rusche, J R
The HIV-1 REV protein binds to the stem II region of the REV-responsive element (RNA). Studies to further define the RNA sequence and structure specifically bound by REV protein identify a minimal...
Large scale chemical synthesis, purification and crystallization of RNA-DNA chimeras.
RNA-DNA chimeras, in which both DNA and RNA monomers are site-specifically substituted in the same strand, may be prepared only by chemical synthesis. Biochemical studies have revealed a number of...
The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG).
Teng, M K, Usman, N, Frederick, C A, Wang, A H
The crystal structure of the complex between the dodecamer d(CGCGAATTCGCG) and a synthetic dye molecule Hoechst 33258 was solved by X-ray diffraction analysis and refined to an R-factor of 15.7% at...
Template-directed primer extension catalyzed by the Tetrahymena ribozyme.
Bartel, D P, Doudna, J A, Usman, N, Szostak, J W
The Tetrahymena ribozyme has been shown to catalyze an RNA polymerase-like reaction in which an RNA primer is extended by the sequential addition of pN nucleotides derived from GpN dinucleotides,...
Inhibition of vascular smooth muscle cell proliferation by ribozymes that cleave c-myb mRNA.
Jarvis, T C, Alby, L J, Beaudry, A A, Wincott, F E, Beigelman, L, McSwiggen, J A, ...
Proliferation of injured smooth muscle cells contributes to the reocclusion or restenosis of coronary arteries that often occurs following angioplasty procedures. We have identified and optimized...
Minasov, G, Matulic-Adamic, J, Wilds, C J, Haeberli, P, Usman, N, Beigelman, L, ...
Chemically modified nucleotide analogs have gained widespread popularity for probing structure-function relationships. Among the modifications that were incorporated into RNAs for assessing the role...
Tereshko, V, Wallace, S T, Usman, N, Wincott, F E, Egli, M
The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Hüsken et al., Biochemistry, 1996,...
Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases.
Peracchi, A, Beigelman, L, Usman, N, Herschlag, D
We have synthesized 13 hammerhead ribozyme variants, each containing an abasic residue at a specific position of the catalytic core. The activity of each of the variants is significantly reduced. In...
Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization.
Narlikar, G J, Gopalakrishnan, V, McConnell, T S, Usman, N, Herschlag, D
A fundamental catalytic principle for protein enzymes in the use of binding interactions away from the site of chemical transformation for catalysis. We have compared the binding and reactivity of a...
Total chemical synthesis of a ribozyme derived from a group I intron.
Whoriskey, S K, Usman, N, Szostak, J W
We describe the complete chemical synthesis of a ribozyme that catalyzes template-directed oligonucleotide ligation. The specific activity of the synthetic ribozyme is nearly identical to that of the...
Crystal structure of an Okazaki fragment at 2-A resolution.
Egli, M, Usman, N, Zhang, S G, Rich, A
In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template...
Enzymatic aminoacylation of single-stranded RNA with an RNA cofactor.
Musier-Forsyth, K, Scaringe, S, Usman, N, Schimmel, P
A chemically synthesized single-stranded ribonucleotide tridecamer derived from the 3' end of Escherichia coli alanine tRNA can be charged with alanine in the presence of short complementary RNA...
Schmidt, S, Beigelman, L, Karpeisky, A, Usman, N, Sorensen, U S, Gait, M J
The hairpin ribozyme is a small self-cleaving RNA that can be engineered for RNA cleavage in trans and has potential as a therapeutic agent. We have used a chemical synthesis approach to study the...
Ordered differential display: a simple method for systematic comparison of gene expression profiles.
Matz, M, Usman, N, Shagin, D, Bogdanova, E, Lukyanov, S
A method for display of 3'-end restriction fragments of cDNAs is proposed, extending the idea reported recently. First, representative pools of such fragments are selectively amplified using PCR...
1-Deazaadenosine: synthesis and activity of base-modified hammerhead ribozymes.
Seela, F, Debelak, H, Usman, N, Burgin, A, Beigelman, L
The incorporation of 1-deazaadenosine (c1A, 1b) into a hammerhead ribozyme and the resulting catalytic activity is described. For this purpose the phosphoramidite 2a and the 3'-phosphonate 2b as well...
Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity.
Ogilvie, K K, Usman, N, Nicoghosian, K, Cedergren, R J
Chemical synthesis is described of a 77-nucleotide-long RNA molecule that has the sequence of an Escherichia coli Ado-47-containing tRNA(fMet) species in which the modified nucleosides have been...
Synthesis, deprotection, analysis and purification of RNA and ribozymes.
Wincott, F, DiRenzo, A, Shaffer, C, Grimm, S, Tracz, D, Workman, C, ...
Improvements in the synthesis, deprotection and purification of oligoribonucleotides are described. These advances allow for reduced synthesis and deprotection times, while improving product yield....
Synthesis and biological activities of a phosphorodithioate analog of 2',5'-oligoadenylate.
Beigelman, L, Matulic-Adamic, J, Haeberli, P, Usman, N, Dong, B, Silverman, R H, ...
To enhance the resistance of 2-5A (pppA2'p5'A2'p5'A) to degradation by exo- and endonucleases, a phosphorodithioate analog was synthesized using a solid-phase phosphite triester approach with...
An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain.
Chartrand, P, Harvey, S C, Ferbeyre, G, Usman, N, Cedergren, R
A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that...
Synthesis of 2'-modified nucleotides and their incorporation into hammerhead ribozymes.
Beigelman, L, Karpeisky, A, Matulic-Adamic, J, Haeberli, P, Sweedler, D, Usman, N
Several 2'-modified ribonucleoside phosphoramidites have been prepared for structure-activity studies of the hammerhead ribozyme. The aim of these studies was to design and synthesize catalytically...
Pon, R T, Usman, N, Damha, M J, Ogilvie, K K
Phosphoramidite reagents can phosphitylate guanine bases at the O6-position during solid phase synthesis and serious chain cleavage occurs if the base phosphitylation is not eliminated before the...
Green, R, Szostak, J W, Benner, S A, Rich, A, Usman, N
Two protected derivatives of the ribonucleoside inosine have been prepared to serve as building blocks for phosphoramidite-based synthesis of RNA. Two different synthetic routes address the unusual...
Scaringe, S A, Francklyn, C, Usman, N
The preparation of fully protected diisopropylamino-beta-cyanoethyl ribonucleoside phosphoramidites with regioisomeric purity greater than 99.95% is described. It is demonstrated that the combination...
Characterization of HIV-1 REV protein: binding stoichiometry and minimal RNA substrate.
Cook, K S, Fisk, G J, Hauber, J, Usman, N, Daly, T J, Rusche, J R
The HIV-1 REV protein binds to the stem II region of the REV-responsive element (RNA). Studies to further define the RNA sequence and structure specifically bound by REV protein identify a minimal...
Large scale chemical synthesis, purification and crystallization of RNA-DNA chimeras.
RNA-DNA chimeras, in which both DNA and RNA monomers are site-specifically substituted in the same strand, may be prepared only by chemical synthesis. Biochemical studies have revealed a number of...
The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG).
Teng, M K, Usman, N, Frederick, C A, Wang, A H
The crystal structure of the complex between the dodecamer d(CGCGAATTCGCG) and a synthetic dye molecule Hoechst 33258 was solved by X-ray diffraction analysis and refined to an R-factor of 15.7% at...
Template-directed primer extension catalyzed by the Tetrahymena ribozyme.
Bartel, D P, Doudna, J A, Usman, N, Szostak, J W
The Tetrahymena ribozyme has been shown to catalyze an RNA polymerase-like reaction in which an RNA primer is extended by the sequential addition of pN nucleotides derived from GpN dinucleotides,...
Inhibition of vascular smooth muscle cell proliferation by ribozymes that cleave c-myb mRNA.
Jarvis, T C, Alby, L J, Beaudry, A A, Wincott, F E, Beigelman, L, McSwiggen, J A, ...
Proliferation of injured smooth muscle cells contributes to the reocclusion or restenosis of coronary arteries that often occurs following angioplasty procedures. We have identified and optimized...
Minasov, G, Matulic-Adamic, J, Wilds, C J, Haeberli, P, Usman, N, Beigelman, L, ...
Chemically modified nucleotide analogs have gained widespread popularity for probing structure-function relationships. Among the modifications that were incorporated into RNAs for assessing the role...
Tereshko, V, Wallace, S T, Usman, N, Wincott, F E, Egli, M
The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Hüsken et al., Biochemistry, 1996,...