Specificity of the ribosomal A site for aminoacyl-tRNAs (2009)
Dale, Taraka, Fahlman, Richard P., Olejniczak, Mikolaj, Uhlenbeck, Olke C.
Although some experiments suggest that the ribosome displays specificity for the identity of the esterified amino acid of its aminoacyl-tRNA substrate, a study measuring dissociation rates of several...
Elles, Lisa M. Sharpe, Uhlenbeck, Olke C.
Escherichia coli DEAD-box protein A (DbpA) is an ATP-dependent RNA helicase with specificity for 23S ribosomal RNA. Although DbpA has been extensively characterized biochemically, its biological...
Hammerhead redux: Does the new structure fit the old biochemical data? (2008)
Nelson, Jennifer A., Uhlenbeck, Olke C.
The cleavage rates of 78 hammerhead ribozymes containing structurally conservative chemical modifications were collected from the literature and compared to the recently determined crystal structure...
The 51-63 base pair of tRNA confers specificity for binding by EF-Tu (2007)
Sanderson, Lee E., Uhlenbeck, Olke C.
Elongation factor Tu (EF-Tu) exhibits significant specificity for the different elongator tRNA bodies in order to offset its variable affinity to the esterified amino acid. Three X-ray cocrystal...
Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis (2007)
Nelson, Jennifer A., Uhlenbeck, Olke C.
Analysis of the catalytic activity of identical mutations in the catalytic cores of nHH8, a very active “extended” hammerhead, and HH16, a less active “minimal” hammerhead, reveal that the...
Wang, Shuying, Hu, YaoXiong, Overgaard, Michael T., Karginov, Fedor V., Uhlenbeck, Olke C., McKay, David B.
The YxiN protein of Bacillus subtilis is a member of the DbpA subfamily of prokaryotic DEAD-box RNA helicases. Like DbpA, it binds with high affinity and specificity to segments of 23S ribosomal RNA...
Wang, Shuying, Hu, YaoXiong, Overgaard, Michael T., Karginov, Fedor V., Uhlenbeck, Olke C., McKay, David B.
The YxiN protein of Bacillus subtilis is a member of the DbpA subfamily of prokaryotic DEAD-box RNA helicases. Like DbpA, it binds with high affinity and specificity to segments of 23S ribosomal RNA...
Wang, Shuying, Hu, YaoXiong, Overgaard, Michael T., Karginov, Fedor V., Uhlenbeck, Olke C., McKay, David B.
The YxiN protein of Bacillus subtilis is a member of the DbpA subfamily of prokaryotic DEAD-box RNA helicases. Like DbpA, it binds with high affinity and specificity to segments of 23S ribosomal RNA...
Binding of misacylated tRNAs to the ribosomal A site (2005)
DALE, TARAKA, UHLENBECK, OLKE C.
To test whether the ribosome displays specificity for the esterified amino acid and the tRNA body of an aminoacyl-tRNA (aa-tRNA), the stabilities of 4 correctly acylated and 12 misacylated tRNAs in...
Karginov, Fedor V., Uhlenbeck, Olke C.
DExD/H proteins catalyze structural rearrangements in RNA by coupling ATP hydrolysis to the destabilization of RNA helices or RNP complexes. The Escherichia coli DExD/H protein DbpA specifically...
Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX (2000)
Shtatland, Timur, Gill, Stanley C., Javornik, Brenda E., Johansson, Hans E., Singer, Britta S., Uhlenbeck, Olke C., ...
Genomic SELEX is a method for studying the network of nucleic acid–protein interactions within any organism. Here we report the discovery of several interesting and potentially biologically...
Werner, Martina, Uhlenbeck, Olke C.
The ability of the hammerhead ribozyme to distinguish between matched and mismatched substrates was evaluated using two kinetically defined ribozymes that differed in the length and sequence of the...
Willis, Michael C., LeCuyer, Karen A., Meisenheimer, Kristen M., Uhlenbeck, Olke C., Koch, Tad H.
An analogue of the replicase translational operator of bacteriophage R17, that contains a 5-bromouridine at position –5 (RNA I), complexes with a dimer of the coat protein and photocrosslinks to...
Replacement of RNA hairpins by in vitro selected tetranucleotides (1993)
Dichtl, Bernhard, Pan, Tao, DiRenzo, Anthony B., Uhlenbeck, Olke C.
An in vitro selection method based on the autolytic cleavage of yeast tRNAPhe by Pb2+ was applied to obtain tRNA derivatives with the anticodon hairpin replaced by four single-stranded nucleotides....
An ultraviolet light-induced crosslink in yeast tRNAphe (1992)
Behlen, Linda S., Sampson, Jeffrey R., Uhlenbeck, Olke C.
The irradiation of native or unmodified yeast tRNAphe by short wavelength UV light (260 nM) results In an Intramolecular crosslink that has been mapped to occur between C48 In the variable loop and...
Ruffner, Duane E., Uhlenbeck, Olke C.
A hammerhead domain of less than 50 nucleotides is responsible for a self-cleavage reaction in the replication of plant RNA pathogens. The hammerhead is composed of three helices joining at a central...
Sequence-dependent structural variations of hammerhead RNA enzymes (1990)
Heus, Hans A., Uhlenbeck, Olke C., Pardi, Arthur
The discovery of in vivo catalytic activity for the hammerhead RNA self-cleaving domain has led to the development of a new class of sequence-specific RNA endonucleases. Two such ribozymes have been...
Characterization of RNA hairpin loop stability (1988)
Groebe, Duncan R., Uhlenbeck, Olke C.
Fifteen RNA hairpins that share the same stem sequence and have homopolymer loops of A, C and U residues which vary in length from three to nine nucleotides were synthesized and their thermal...
A comparison of two phage coat protein-RNA interactions (1988)
Wu, Huey-Nan, Kastelic, Keith A., Uhlenbeck, Olke C.
The interaction between the coat protein of the group I bacteriophage fr with its translational operator site is compared with the previously studied R17 interaction. The sequence of the two RNA...
An RNA mutation that increases the affinity of an RNA-protein interaction (1987)
Lowary, Peggy T., Uhlenbeck, Olke C.
The introduction of a cytidine in place of one of the two single stranded uridines in the R17 replicase translational operator results in a much tighter binding to R17 coat protein. The complex...
Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates (1987)
Milligan, John F., Groebe, Duncan R., Witherell, Gary W., Uhlenbeck, Olke C.
A method is described to synthesize small RNAs of defined length and sequence using T7 RNA polymerase and templates of synthetic DNA which contain the T7 promoter. Partially single stranded templates...
Role of the constant uridine in binding of yeast tRNAPhe anticodon arm to 30S ribosomes (1982)
Uhlenbeck, Olke C., Lowary, Peggy T., Wittenberg, Wayne L.
Twenty-two anticodon arm analogues were prepared by joining different tetra penta and hexaribonucleotides to a nine nucleotide fragment of yeast tRNAPhe with T4 RNA ligase. The oligomer with the same...
Reactions at the termini of tRNA with T4 RNA ligase (1978)
Bruce, A.Gregory, Uhlenbeck, Olke C.
T4 RNA ligase will catalyze the addition of nucleoside 3′,5′-bisphos-phates Onto the 3′ terminus of tRNA resulting in a tRNA molecule one nucleotide longer with a 3′ terminal phosphate. Under...
Equimolar addition of oligoribonucleotides with T4 RNA ligase (1977)
Uhlenbeck, Olke C., Cameron, Vicki
T4 induced RNA ligase will join equimolar concentrations of two oligo-ribonucleotides, (Ap)3C and p(Up)5, to form a single product, (Ap)3Cp(Up) 5, in high yield. The presence of the 3′ phosphate on...
A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein
Johansson, Hans E., Dertinger, Dagmar, LeCuyer, Karen A., Behlen, Linda S., Greef, Charles H., Uhlenbeck, Olke C.
Most mutations in the sequence of the RNA hairpin that specifically binds MS2 coat protein either reduce the binding affinity or have no effect. However, one RNA mutation, a uracil to cytosine change...
Use of intrinsic binding energy for catalysis by an RNA enzyme
Hertel, Klemens J., Peracchi, Alessio, Uhlenbeck, Olke C., Herschlag, Daniel
The contribution of several individual ribozyme⋅substrate base pairs to binding and catalysis has been investigated using hammerhead ribozyme substrates that were truncated at their 3′ or 5′...
Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX
Shtatland, Timur, Gill, Stanley C., Javornik, Brenda E., Johansson, Hans E., Singer, Britta S., Uhlenbeck, Olke C., ...
Genomic SELEX is a method for studying the network of nucleic acid–protein interactions within any organism. Here we report the discovery of several interesting and potentially biologically...
The tRNA Specificity of Thermus thermophilus EF-Tu
Asahara, Haruichi, Uhlenbeck, Olke C.
By introducing a GAC anticodon, 21 different Escherichia coli tRNAs were misacylated with either phenylalanine or valine and assayed for their affinity to Thermus thermophilus elongation factor Tu...
Modulation of tRNAAla identity by inorganic pyrophosphatase
Wolfson, Alexey D., Uhlenbeck, Olke C.
A highly sensitive assay of tRNA aminoacylation was developed that directly measures the fraction of aminoacylated tRNA by following amino acid attachment to the 3′-32P-labeled tRNA. When applied...
Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA
Diges, Camille M., Uhlenbeck, Olke C.
Escherichia coli DbpA is a member of the DEAD/H family of proteins which has been shown to have robust ATPase activity only in the presence of a specific region of 23S rRNA. A series of bimolecular...
Use of T4 RNA ligase to construct model substrates for a ribosomal RNA maturation endonuclease
Meyhack, Bernd, Pace, Bernadette, Uhlenbeck, Olke C., Pace, Norman R.
RNase M5 of Bacillus subtilis specifically cleaves a 179-nucleotide precursor 5S rRNA to yield mature 5S rRNA (116 nucleotides) and two fragments derived from the termini. Possible recognition...
Interaction of Escherichia coli DbpA with 23S rRNA in different functional states of the enzyme
Karginov, Fedor V., Uhlenbeck, Olke C.
DExD/H proteins catalyze structural rearrangements in RNA by coupling ATP hydrolysis to the destabilization of RNA helices or RNP complexes. The Escherichia coli DExD/H protein DbpA specifically...
Binding of misacylated tRNAs to the ribosomal A site
DALE, TARAKA, UHLENBECK, OLKE C.
To test whether the ribosome displays specificity for the esterified amino acid and the tRNA body of an aminoacyl-tRNA (aa-tRNA), the stabilities of 4 correctly acylated and 12 misacylated tRNAs in...
Wang, Shuying, Hu, Yaoxiong, Overgaard, Michael T., Karginov, Fedor V., Uhlenbeck, Olke C., McKay, David B.
The YxiN protein of Bacillus subtilis is a member of the DbpA subfamily of prokaryotic DEAD-box RNA helicases. Like DbpA, it binds with high affinity and specificity to segments of 23S ribosomal RNA...
A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein
Johansson, Hans E., Dertinger, Dagmar, LeCuyer, Karen A., Behlen, Linda S., Greef, Charles H., Uhlenbeck, Olke C.
Most mutations in the sequence of the RNA hairpin that specifically binds MS2 coat protein either reduce the binding affinity or have no effect. However, one RNA mutation, a uracil to cytosine change...
Use of intrinsic binding energy for catalysis by an RNA enzyme
Hertel, Klemens J., Peracchi, Alessio, Uhlenbeck, Olke C., Herschlag, Daniel
The contribution of several individual ribozyme⋅substrate base pairs to binding and catalysis has been investigated using hammerhead ribozyme substrates that were truncated at their 3′ or 5′...
Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX
Shtatland, Timur, Gill, Stanley C., Javornik, Brenda E., Johansson, Hans E., Singer, Britta S., Uhlenbeck, Olke C., ...
Genomic SELEX is a method for studying the network of nucleic acid–protein interactions within any organism. Here we report the discovery of several interesting and potentially biologically...
The tRNA Specificity of Thermus thermophilus EF-Tu
Asahara, Haruichi, Uhlenbeck, Olke C.
By introducing a GAC anticodon, 21 different Escherichia coli tRNAs were misacylated with either phenylalanine or valine and assayed for their affinity to Thermus thermophilus elongation factor Tu...
Modulation of tRNAAla identity by inorganic pyrophosphatase
Wolfson, Alexey D., Uhlenbeck, Olke C.
A highly sensitive assay of tRNA aminoacylation was developed that directly measures the fraction of aminoacylated tRNA by following amino acid attachment to the 3′-32P-labeled tRNA. When applied...
Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA
Diges, Camille M., Uhlenbeck, Olke C.
Escherichia coli DbpA is a member of the DEAD/H family of proteins which has been shown to have robust ATPase activity only in the presence of a specific region of 23S rRNA. A series of bimolecular...
Use of T4 RNA ligase to construct model substrates for a ribosomal RNA maturation endonuclease
Meyhack, Bernd, Pace, Bernadette, Uhlenbeck, Olke C., Pace, Norman R.
RNase M5 of Bacillus subtilis specifically cleaves a 179-nucleotide precursor 5S rRNA to yield mature 5S rRNA (116 nucleotides) and two fragments derived from the termini. Possible recognition...
Interaction of Escherichia coli DbpA with 23S rRNA in different functional states of the enzyme
Karginov, Fedor V., Uhlenbeck, Olke C.
DExD/H proteins catalyze structural rearrangements in RNA by coupling ATP hydrolysis to the destabilization of RNA helices or RNP complexes. The Escherichia coli DExD/H protein DbpA specifically...
Binding of misacylated tRNAs to the ribosomal A site
DALE, TARAKA, UHLENBECK, OLKE C.
To test whether the ribosome displays specificity for the esterified amino acid and the tRNA body of an aminoacyl-tRNA (aa-tRNA), the stabilities of 4 correctly acylated and 12 misacylated tRNAs in...
Wang, Shuying, Hu, Yaoxiong, Overgaard, Michael T., Karginov, Fedor V., Uhlenbeck, Olke C., McKay, David B.
The YxiN protein of Bacillus subtilis is a member of the DbpA subfamily of prokaryotic DEAD-box RNA helicases. Like DbpA, it binds with high affinity and specificity to segments of 23S ribosomal RNA...
The 51–63 base pair of tRNA confers specificity for binding by EF-Tu
Sanderson, Lee E., Uhlenbeck, Olke C.
Elongation factor Tu (EF-Tu) exhibits significant specificity for the different elongator tRNA bodies in order to offset its variable affinity to the esterified amino acid. Three X-ray cocrystal...
Elles, Lisa M. Sharpe, Uhlenbeck, Olke C.
Escherichia coli DEAD-box protein A (DbpA) is an ATP-dependent RNA helicase with specificity for 23S ribosomal RNA. Although DbpA has been extensively characterized biochemically, its biological...
Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis
Nelson, Jennifer A., Uhlenbeck, Olke C.
Analysis of the catalytic activity of identical mutations in the catalytic cores of nHH8, a very active “extended” hammerhead, and HH16, a less active “minimal” hammerhead, reveal that the...
Hammerhead redux: Does the new structure fit the old biochemical data?
Nelson, Jennifer A., Uhlenbeck, Olke C.
The cleavage rates of 78 hammerhead ribozymes containing structurally conservative chemical modifications were collected from the literature and compared to the recently determined crystal structure...
Specificity of the ribosomal A site for aminoacyl-tRNAs
Dale, Taraka, Fahlman, Richard P., Olejniczak, Mikołaj, Uhlenbeck, Olke C.
Although some experiments suggest that the ribosome displays specificity for the identity of the esterified amino acid of its aminoacyl-tRNA substrate, a study measuring dissociation rates of several...
Sharpe Elles, Lisa M., Sykes, Michael T., Williamson, James R., Uhlenbeck, Olke C.
Escherichia coli DbpA is an ATP-dependent RNA helicase with specificity for hairpin 92 of 23S ribosomal RNA, an important part of the peptidyl transferase center. The R331A active site mutant of DbpA...