Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

An interactive dot matrix system for locating potentially significant features in nucleic acid molecules.

B A Shapiro1, R Nussinov, L E Lipkin

  • 1Laboratory of Mathematical Biology, National Cancer Institute, Frederick Cancer Research Facility, Maryland 21701.

Journal of Biomolecular Structure & Dynamics
|April 1, 1987
PubMed
Summary

A new computer system reveals non-random DNA sequence patterns. Alternating purine-pyrimidine doublets were found in regulatory regions, suggesting a biological significance beyond chance.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Mutations in LZTR1 drive human disease by dysregulating RAS ubiquitination.

Science (New York, N.Y.)·2018
Same author

Modeling of RNA nanotubes using molecular dynamics simulation.

European biophysics journal : EBJ·2014
Same author

Contribution of salt bridges toward protein thermostability.

Journal of biomolecular structure & dynamics·2012
Same author

GOSSIP: a method for fast and accurate global alignment of protein structures.

Bioinformatics (Oxford, England)·2011
Same author

Ultraviolet B irradiation and activation of protein kinase D in primary mouse epidermal keratinocytes.

Oncogene·2010
Same author

Towards drugs targeting multiple proteins in a systems biology approach.

Current topics in medicinal chemistry·2007

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • DNA structure is influenced by purine and pyrimidine sequences.
  • Understanding sequence variations is key to identifying regulatory elements.
  • Previous methods lacked interactive visualization for pattern discovery.

Purpose of the Study:

  • To develop an interactive system for analyzing DNA sequence patterns.
  • To identify significant features related to DNA helix distortions.
  • To investigate variations in purine and pyrimidine patterns within DNA.

Main Methods:

  • Developed an interactive computer system utilizing a dot matrix approach.
  • Generated comparison matrices based on Calladine-Dickerson rules.
  • Utilized adjustable parameters for visual enhancement and pattern identification.

Related Experiment Videos

Main Results:

  • Identified potentially significant features linked to DNA helix distortions.
  • Discovered a non-random pattern of alternating purine-pyrimidine doublets.
  • Observed this pattern predominantly in DNA regulatory regions.

Conclusions:

  • The discovered purine-pyrimidine pattern in regulatory regions exceeds probabilistic expectations.
  • The interactive system facilitates the discovery of previously unknown DNA sequence patterns.
  • This finding may have implications for understanding gene regulation.