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Updated: Jun 25, 2026

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA
10:15

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

Published on: July 6, 2012

Sequence-dependent pausing of single lambda exonuclease molecules.

Thomas T Perkins1, Ravindra V Dalal, Paul G Mitsis

  • 1Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA. tperkins@jila.colorado.edu

Science (New York, N.Y.)
|August 30, 2003
PubMed
Summary
This summary is machine-generated.

Lambda exonuclease digests DNA strands at a constant speed, but pauses at specific DNA sequences. These pauses, particularly at the GGCGA motif, may affect DNA recombination efficiency.

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Last Updated: Jun 25, 2026

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA
10:15

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Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
10:27

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Published on: July 8, 2019

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Lambda exonuclease is a key enzyme in DNA metabolism.
  • Understanding its enzymatic activity at a single-molecule level provides insights into DNA processing.
  • Previous studies have characterized its general processivity and directionality.

Purpose of the Study:

  • To investigate the single-molecule kinetics of lambda exonuclease digestion.
  • To identify sequence-specific pausing events during DNA degradation.
  • To correlate pausing with DNA sequence and potential biological implications.

Main Methods:

  • Single-molecule observation of lambda exonuclease activity.
  • Measurement of DNA digestion speed and pause durations.
  • Gel electrophoresis to identify strong pausing sequences.
  • Sequence analysis to correlate pauses with specific motifs.

Main Results:

  • Lambda exonuclease exhibits processive degradation at a near-constant speed (4 nm/s).
  • Digestion is punctuated by pauses of variable duration at specific locations.
  • Pauses are strand-specific and sequence-dependent, with a strong pause identified at the GGCGA motif.
  • The GGCGA motif is located in the left lambda cohesive end.

Conclusions:

  • Single-molecule analysis reveals nuanced kinetics of lambda exonuclease, including sequence-dependent pausing.
  • The identified GGCGA motif acts as a significant pause site.
  • Exonuclease inhibition at this motif may contribute to reduced recombination efficiency at the lambda cohesive end.