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Structural imprints in vivo decode RNA regulatory mechanisms
TLDR
A novel biochemical approach, in vivo click selective 2′-hydroxyl acylation and profiling experiment (icSHAPE), is presented, which enables the first global view, to the authors' knowledge, of RNA secondary structures in living cells for all four bases.
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RNA SHAPE analysis in living cells.
TLDR
Two new chemical probes are designed, synthesized and demonstrated that enable selective 2'-hydroxyl acylation analyzed by primer extension in living cells to be analyzed bySHAPE.
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Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification.
N(6)-Methyladenosine (m(6)A) modification is hypothesized to control processes such as RNA degradation, localization, and splicing. However, the molecular mechanisms by which this occurs are unclear.…
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Active site tightness and substrate fit in DNA replication.
  • E. Kool
  • Biology
    Annual review of biochemistry
  • 2002
TLDR
The concept of active site tightness in DNA polymerases is discussed, and how it might influence steric (size and shape) effects of nucleotide selection in synthesis of a base pair is considered.
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Rolling Circle DNA Synthesis: Small Circular Oligonucleotides as Efficient Templates for DNA Polymerases.
TLDR
It is reported that small, single-stranded circular DNA oligonucleotides 26 to 74 nucleotides in size can behave as catalytic templates for DNA synthesis by several DNA polymerase enzymes, and it is demonstrated that the multimeric products can be cleaved enzymatically to short, sequence-defined oligodeoxynucleotide.
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Escherichia coli RNA polymerase activity observed using atomic force microscopy.
TLDR
The development of tapping-mode in fluid has made it possible to use AFM to follow biological processes at the molecular level and get new insights about the variability of activity of individual molecules bound to a surface, as well as confirming observations of the transcriptional activity of RNAP adsorbed onto mica.
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7SK-BAF axis controls pervasive transcription at enhancers
TLDR
It is shown that the 7SK small nuclear RNA (snRNA) inhibits enhancer transcription by modulating nucleosome position and uses distinct mechanisms to counteract the diverse consequences of pervasive transcription that distinguish super enhancers, enhancers and promoters.
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Hydrogen bonding, base stacking, and steric effects in dna replication.
  • E. Kool
  • Biology
    Annual review of biophysics and biomolecular…
  • 2001
TLDR
Recent studies have shed new light on the question of what physical forces cause a polymerase enzyme to insert a nucleotide into a strand of DNA and to choose the correct nucleotide over the incorrect ones.
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A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity.
  • S. Moran, R. Ren, E. Kool
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences…
  • 30 September 1997
TLDR
The synthesis of the 5'-triphosphate derivative of 1 and the study of its ability to be inserted into replicating DNA strands by the Klenow fragment of Escherichia coli DNA polymerase I find that this nucleotide derivative is a surprisingly good substrate for KF.
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A specific partner for abasic damage in DNA
TLDR
The results show that neither hydrogen bonds nor purine and pyrimidine structures are required to form a base pair with high efficiency and selectivity, and confirm that steric complementarity is an important factor in the fidelity of DNA synthesis.
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