Ditzler, Mark A., Sponer, Jirí, Walter, Nils G.
Despite numerous structural and biochemical investigations, the catalytic mechanism of hairpin ribozyme self-cleavage remains elusive. To gain insight into the coupling of active site dynamics with...
Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum (2007)
Hoerter, John A.H., Walter, Nils G.
Small interfering (si)RNAs have recently been used to therapeutically silence genes in vivo after intravenous systemic delivery. Further progress in the development of siRNA therapeutics will in part...
Trans-acting glmS catalytic riboswitch: Locked and loaded (2007)
Tinsley, Rebecca A., Furchak, Jennifer R.W., Walter, Nils G.
A recently discovered class of gene regulatory RNAs, coined riboswitches, are commonly found in noncoding segments of bacterial and some eukaryotic mRNAs. Gene up- or down-regulation is triggered by...
Sefcikova, Jana, Krasovska, Maryna V., Sponer, Jirí, Walter, Nils G.
The genome of the human hepatitis delta virus (HDV) harbors a self-cleaving catalytic RNA motif, the genomic HDV ribozyme, whose crystal structure shows the dangling nucleotides 5′ of the cleavage...
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation (2006)
TINSLEY, REBECCA A., WALTER, NILS G.
Pyrrolo-C (PC), or 3-[β-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G....
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation (2006)
TINSLEY, REBECCA A., WALTER, NILS G.
Pyrrolo-C (PC), or 3-[β-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G....
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation (2006)
TINSLEY, REBECCA A., WALTER, NILS G.
Pyrrolo-C (PC), or 3-[β-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G....
Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA (2005)
LAMBERT, MEREDITH NEWBY, HOERTER, JOHN A.H., PEREIRA, MIGUEL J.B., WALTER, NILS G.
Helix (H)27 from Escherichia coli 16S ribosomal (r)RNA is centrally located within the small (30S) ribosomal subunit, immediately adjacent to the decoding center. Bacterial 30S subunit crystal...
In the fluorescent spotlight: Global and local conformational changes of small catalytic RNAs (2002)
Walter, Nils G., Harris, Dinari A., Pereira, Miguel J. B., Rueda, David
RNA is a ubiquitous biopolymer that performs a multitude of essential cellular functions involving the maintenance, transfer, and processing of genetic information. RNA is unique in that it can carry...
Structural basis for heterogeneous kinetics: Reengineering the hairpin ribozyme
Esteban, José A., Walter, Nils G., Kotzorek, Gerd, Heckman, Joyce E., Burke, John M.
The RNA cleavage reaction catalyzed by the hairpin ribozyme shows biphasic kinetics, and chase experiments show that the slow phase of the reaction results from reversible substrate binding to an...
Single-molecule transition-state analysis of RNA folding
Bokinsky, Gregory, Rueda, David, Misra, Vinod K., Rhodes, Maria M., Gordus, Andrew, Babcock, Hazen P., ...
How RNA molecules fold into functional structures is a problem of great significance given the expanding list of essential cellular RNA enzymes and the increasing number of applications of RNA in...
Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance
Rueda, David, Bokinsky, Gregory, Rhodes, Maria M., Rust, Michael J., Zhuang, Xiaowei, Walter, Nils G.
The hairpin ribozyme is a minimalist paradigm for studying RNA folding and function. In this enzyme, two domains dock by induced fit to form a catalytic core that mediates a specific backbone...
Sekella, Phillip T, Rueda, David, Walter, Nils G
Recently, Breaker and coworkers engineered hammerhead ribozymes that rearrange from a catalytically inactive to an active conformation upon allosteric binding of a specific ligand. To monitor...
Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA
LAMBERT, MEREDITH NEWBY, HOERTER, JOHN A.H., PEREIRA, MIGUEL J.B., WALTER, NILS G.
Helix (H)27 from Escherichia coli 16S ribosomal (r)RNA is centrally located within the small (30S) ribosomal subunit, immediately adjacent to the decoding center. Bacterial 30S subunit crystal...
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation
TINSLEY, REBECCA A., WALTER, NILS G.
Pyrrolo-C (PC), or 3-[β-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G....
Structural basis for heterogeneous kinetics: Reengineering the hairpin ribozyme
Esteban, José A., Walter, Nils G., Kotzorek, Gerd, Heckman, Joyce E., Burke, John M.
The RNA cleavage reaction catalyzed by the hairpin ribozyme shows biphasic kinetics, and chase experiments show that the slow phase of the reaction results from reversible substrate binding to an...
Single-molecule transition-state analysis of RNA folding
Bokinsky, Gregory, Rueda, David, Misra, Vinod K., Rhodes, Maria M., Gordus, Andrew, Babcock, Hazen P., ...
How RNA molecules fold into functional structures is a problem of great significance given the expanding list of essential cellular RNA enzymes and the increasing number of applications of RNA in...
Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance
Rueda, David, Bokinsky, Gregory, Rhodes, Maria M., Rust, Michael J., Zhuang, Xiaowei, Walter, Nils G.
The hairpin ribozyme is a minimalist paradigm for studying RNA folding and function. In this enzyme, two domains dock by induced fit to form a catalytic core that mediates a specific backbone...
Sekella, Phillip T, Rueda, David, Walter, Nils G
Recently, Breaker and coworkers engineered hammerhead ribozymes that rearrange from a catalytically inactive to an active conformation upon allosteric binding of a specific ligand. To monitor...
Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA
LAMBERT, MEREDITH NEWBY, HOERTER, JOHN A.H., PEREIRA, MIGUEL J.B., WALTER, NILS G.
Helix (H)27 from Escherichia coli 16S ribosomal (r)RNA is centrally located within the small (30S) ribosomal subunit, immediately adjacent to the decoding center. Bacterial 30S subunit crystal...
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation
TINSLEY, REBECCA A., WALTER, NILS G.
Pyrrolo-C (PC), or 3-[β-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G....
Trapped water molecules are essential to structural dynamics and function of a ribozyme
Rhodes, Maria M., Réblová, Kamila, Šponer, Jiří, Walter, Nils G.
Ribozymes are catalytically competent examples of highly structured noncoding RNAs, which are ubiquitous in the processing and regulation of genetic information. Combining explicit-solvent molecular...
Sefcikova, Jana, Krasovska, Maryna V., Šponer, Jiří, Walter, Nils G.
The genome of the human hepatitis delta virus (HDV) harbors a self-cleaving catalytic RNA motif, the genomic HDV ribozyme, whose crystal structure shows the dangling nucleotides 5′ of the cleavage...
Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
Krasovska, Maryna V., Sefcikova, Jana, Réblová, Kamila, Schneider, Bohdan, Walter, Nils G., Šponer, Jiří
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry....
Molecular dynamics simulations of RNA: An in silico single molecule approach
McDowell, S. Elizabeth, ŠpačkovÁ, Nad'a, Šponer, Ji[rcaron]Í, Walter, Nils G.
RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out...
Under the microscope: Single molecule symposium at the University of Michigan, 2006
Walter, Nils G., Meiners, Jens-Christian, Meyhofer, Edgar, Neubig, Richard R., Sunahara, Roger K., Perkins, Noel C., ...
In recent years, a revolution has occurred in the basic sciences, which exploits novel single molecule detection and manipulation tools to track and analyze biopolymers in unprecedented detail. A...
Future of biomedical sciences: Single molecule microscopy
The behavior of single molecule defines whether a cell lives, dies, or responds to a specific drug treatment. Single molecule microscopies have begun to reveal the number, location, and...
Sefcikova, Jana, Krasovska, Maryna V., ŠpačkovÁ, Nad'a, Šponer, Ji[rcaron]Í, Walter, Nils G.
The self-cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme...
Trans-acting glmS catalytic riboswitch: Locked and loaded
Tinsley, Rebecca A., Furchak, Jennifer R.W., Walter, Nils G.
A recently discovered class of gene regulatory RNAs, coined riboswitches, are commonly found in noncoding segments of bacterial and some eukaryotic mRNAs. Gene up- or down-regulation is triggered by...
Focus on function: Single molecule RNA enzymology
Ditzler, Mark A., AlemÁn, Elvin A., Rueda, David, Walter, Nils G.
The ability of RNA to catalyze chemical reactions was first demonstrated 25 years ago with the discovery that group I introns and RNase P function as RNA enzymes (ribozymes). Several additional...
Liu, Shixin, Bokinsky, Gregory, Walter, Nils G., Zhuang, Xiaowei
Single-molecule FRET is a powerful tool for probing the kinetic mechanism of a complex enzymatic reaction. However, not every reaction intermediate can be identified via a distinct FRET value, making...
Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum
Hoerter, John A.H., Walter, Nils G.
Small interfering (si)RNAs have recently been used to therapeutically silence genes in vivo after intravenous systemic delivery. Further progress in the development of siRNA therapeutics will in part...
De Silva, Chamaree, Walter, Nils G.
Engineered “aptazymes” fuse in vitro selected aptamers with ribozymes to create allosteric enzymes as biosensing components and artificial gene regulatory switches through ligand-induced...
Ditzler, Mark A., Šponer, Jiří, Walter, Nils G.
Despite numerous structural and biochemical investigations, the catalytic mechanism of hairpin ribozyme self-cleavage remains elusive. To gain insight into the coupling of active site dynamics with...