Direct observation of cotranscriptional folding in an adenine riboswitch.

PubWeight™: 1.13‹?› | Rank: Top 10%

🔗 View Article (PMC 3496414)

Published in Science on October 19, 2012

Authors

Kirsten L Frieda1, Steven M Block

Author Affiliations

1: Biophysics Program, Stanford University, Stanford, CA 94305, USA.

Articles citing this

Riboswitches in eubacteria sense the second messenger c-di-AMP. Nat Chem Biol (2013) 1.47

Toward giga-pixel nanoscopy on a chip: a computational wide-field look at the nano-scale without the use of lenses. Lab Chip (2013) 1.13

Hierarchy of RNA functional dynamics. Annu Rev Biochem (2014) 1.04

Decoding mechanisms by which silent codon changes influence protein biogenesis and function. Int J Biochem Cell Biol (2015) 1.04

On the importance of cotranscriptional RNA structure formation. RNA (2013) 1.01

Molecular mechanisms of transcription through single-molecule experiments. Chem Rev (2014) 0.98

Rigid DNA beams for high-resolution single-molecule mechanics. Angew Chem Int Ed Engl (2013) 0.94

Engineering modular 'ON' RNA switches using biological components. Nucleic Acids Res (2013) 0.89

The genetic code as expressed through relationships between mRNA structure and protein function. FEBS Lett (2013) 0.89

A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends Biochem Sci (2016) 0.86

Progress and challenges for chemical probing of RNA structure inside living cells. Nat Chem Biol (2015) 0.85

Single-molecule studies of riboswitch folding. Biochim Biophys Acta (2014) 0.85

Differences between cotranscriptional and free riboswitch folding. Nucleic Acids Res (2013) 0.82

Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element. Nucleic Acids Res (2013) 0.81

High-resolution optical tweezers for single-molecule manipulation. Yale J Biol Med (2013) 0.80

Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately predicted from the folding landscape. J Am Chem Soc (2013) 0.80

Cotranscriptional folding of a riboswitch at nucleotide resolution. Nat Struct Mol Biol (2016) 0.79

Riboswitch structure and dynamics by smFRET microscopy. Methods Enzymol (2014) 0.78

Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation. Nat Commun (2017) 0.78

Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization. Elife (2016) 0.77

A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning. J Mol Biol (2015) 0.77

Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context. J Biol Chem (2014) 0.77

Native Purification and Analysis of Long RNAs. Methods Enzymol (2015) 0.77

Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design. Wiley Interdiscip Rev RNA (2015) 0.76

Axial Optical Traps: A New Direction for Optical Tweezers. Biophys J (2015) 0.75

Effects of cooperation between translating ribosome and RNA polymerase on termination efficiency of the Rho-independent terminator. Nucleic Acids Res (2015) 0.75

Nanomanipulation of single RNA molecules by optical tweezers. J Vis Exp (2014) 0.75

Studies of RNA Sequence and Structure Using Nanopores. Prog Mol Biol Transl Sci (2016) 0.75

Single molecule recordings of lysozyme activity. Phys Chem Chem Phys (2013) 0.75

Conformational dynamics of the frameshift stimulatory structure in HIV-1. RNA (2017) 0.75

An excited state underlies gene regulation of a transcriptional riboswitch. Nat Chem Biol (2017) 0.75

Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding. Nucleic Acids Res (2017) 0.75

Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat Chem Biol (2017) 0.75

Articles cited by this

Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J Mol Biol (1990) 4.78

The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem (2009) 4.20

Folding of the adenine riboswitch. Chem Biol (2006) 3.95

Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol (2003) 3.84

The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell (2005) 3.62

Direct observation of hierarchical folding in single riboswitch aptamers. Science (2008) 3.22

The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry (2005) 2.98

Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev (2008) 2.47

Applied force reveals mechanistic and energetic details of transcription termination. Cell (2008) 2.45

Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control. Chembiochem (2007) 2.12

RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro. J Bacteriol (2000) 1.98

RNA folding during transcription. Annu Rev Biophys Biomol Struct (2006) 1.81

Bacterial RNA polymerase. Curr Opin Struct Biol (2001) 1.72

Thinking quantitatively about transcriptional regulation. Nat Rev Mol Cell Biol (2005) 1.66

Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc Natl Acad Sci U S A (1999) 1.58

Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet (2011) 1.46

Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J Mol Biol (1999) 1.43

Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A (2007) 1.36

A pH-responsive riboregulator. Genes Dev (2009) 1.33

mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol (2010) 1.28

Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing. Mol Cell (2006) 1.26

Functional topography of nascent RNA in elongation intermediates of RNA polymerase. Proc Natl Acad Sci U S A (1998) 1.23

Effect of transcription on folding of the Tetrahymena ribozyme. RNA (2003) 1.12

RNA folding during transcription by Escherichia coli RNA polymerase analyzed by RNA self-cleavage. Biochemistry (1990) 1.08

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci U S A (2012) 1.07

Encoding folding paths of RNA switches. Nucleic Acids Res (2006) 1.03

Articles by these authors

Optical trapping. Rev Sci Instrum (2004) 7.15

Direct observation of base-pair stepping by RNA polymerase. Nature (2005) 6.29

Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell (2003) 3.92

Kinesin moves by an asymmetric hand-over-hand mechanism. Science (2003) 3.83

An automated two-dimensional optical force clamp for single molecule studies. Biophys J (2002) 3.57

Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc Natl Acad Sci U S A (2006) 3.56

Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell (2006) 3.50

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature (2003) 3.50

Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science (2006) 3.49

Direct observation of hierarchical folding in single riboswitch aptamers. Science (2008) 3.22

Passive all-optical force clamp for high-resolution laser trapping. Phys Rev Lett (2005) 3.13

Coordination of opposite-polarity microtubule motors. J Cell Biol (2002) 3.04

Individual dimers of the mitotic kinesin motor Eg5 step processively and support substantial loads in vitro. Nat Cell Biol (2006) 2.73

Stepping and stretching. How kinesin uses internal strain to walk processively. J Biol Chem (2003) 2.60

High-resolution, single-molecule measurements of biomolecular motion. Annu Rev Biophys Biomol Struct (2007) 2.58

Applied force reveals mechanistic and energetic details of transcription termination. Cell (2008) 2.45

Simultaneous, coincident optical trapping and single-molecule fluorescence. Nat Methods (2004) 2.20

Sequence-dependent pausing of single lambda exonuclease molecules. Science (2003) 1.88

Backsteps induced by nucleotide analogs suggest the front head of kinesin is gated by strain. Proc Natl Acad Sci U S A (2006) 1.85

Forward and reverse motion of single RecBCD molecules on DNA. Biophys J (2004) 1.82

Single-molecule studies of RNA polymerase: motoring along. Annu Rev Biochem (2008) 1.80

Single-molecule, motion-based DNA sequencing using RNA polymerase. Science (2006) 1.69

Binding and translocation of termination factor rho studied at the single-molecule level. J Mol Biol (2012) 1.58

Combined optical trapping and single-molecule fluorescence. J Biol (2003) 1.52

Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proc Natl Acad Sci U S A (2012) 1.51

A universal pathway for kinesin stepping. Nat Struct Mol Biol (2011) 1.43

E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase. J Mol Biol (2010) 1.36

Picocalorimetry of transcription by RNA polymerase. Biophys J (2005) 1.33

Direct observation of the binding state of the kinesin head to the microtubule. Nature (2009) 1.32

Folding and unfolding single RNA molecules under tension. Curr Opin Chem Biol (2008) 1.26

Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing. Mol Cell (2006) 1.26

Statistical kinetics of macromolecular dynamics. Biophys J (2005) 1.24

Optical tweezers study life under tension. Nat Photonics (2011) 1.22

Single-molecule studies of RNA polymerase: one singular sensation, every little step it takes. Mol Cell (2011) 1.21

Measurement of the effective focal shift in an optical trap. Opt Lett (2005) 1.19

Eg5 steps it up! Cell Div (2006) 1.18

Resource Letter: LBOT-1: Laser-based optical tweezers. Am J Phys (2003) 1.17

Reconstructing folding energy landscapes by single-molecule force spectroscopy. Annu Rev Biophys (2014) 1.12

The importance of lattice defects in katanin-mediated microtubule severing in vitro. Biophys J (2002) 1.07

Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer. Proc Natl Acad Sci U S A (2012) 1.07

Precision steering of an optical trap by electro-optic deflection. Opt Lett (2008) 1.00

Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA. Mol Cell (2011) 0.97

RNA BIOCHEMISTRY. Factor-dependent processivity in human eIF4A DEAD-box helicase. Science (2015) 0.95

Force and premature binding of ADP can regulate the processivity of individual Eg5 dimers. Biophys J (2009) 0.92

Direct measurements of kinesin torsional properties reveal flexible domains and occasional stalk reversals during stepping. Proc Natl Acad Sci U S A (2009) 0.91

Kinesin steps do not alternate in size. Biophys J (2007) 0.90

Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proc Natl Acad Sci U S A (2014) 0.88

On the origin of kinesin limping. Biophys J (2009) 0.88

A not-so-cheap stunt. Science (2002) 0.88

Morphometric assessment of collagen accumulation in germinal matrix vessels of premature human neonates. Neuropathol Appl Neurobiol (2005) 0.87

Electrostatics of nucleic acid folding under conformational constraint. J Am Chem Soc (2012) 0.85

Efficient reconstitution of transcription elongation complexes for single-molecule studies of eukaryotic RNA polymerase II. Transcription (2012) 0.85

Anatomical analysis of the developing cerebral vasculature in premature neonates: absence of precapillary arteriole-to-venous shunts. Pediatr Res (2002) 0.82

Subependymal veins in premature neonates: implications for hemorrhage. Pediatr Neurol (2004) 0.81

Single-molecule studies of RNAPII elongation. Biochim Biophys Acta (2012) 0.80

An optical apparatus for rotation and trapping. Methods Enzymol (2010) 0.79

Temporal expression pattern of cerebrovascular endothelial cell alkaline phosphatase during human gestation. J Neuropathol Exp Neurol (2002) 0.78

Attitudes and expectations about music therapy for premature infants among staff in a neonatal intensive care unit. Altern Ther Health Med (2004) 0.78

Not so lame after all: kinesin still walks with a hobbled head. J Gen Physiol (2007) 0.78

Germinal matrix cells associate with veins and a glial scaffold in the human fetal brain. Brain Res Dev Brain Res (2005) 0.75

UK defence group's structure could limit its usefulness. Nature (2009) 0.75