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

Genetic code symmetry and efficient design of GC-constrained coding sequences.

Matan Gavish1, Amnon Peled, Benny Chor

  • 1School of Physics, Tel Aviv University Ramat-Aviv, Tel-Aviv 69978, Israel.

Bioinformatics (Oxford, England)
|January 24, 2007
PubMed
Summary
This summary is machine-generated.

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

Irinotecan Modulates Immune Checkpoints in Neuroblastoma.

ImmunoTargets and therapy·2026
Same author

DSP502 combines dual inhibition of PD-L1 and PVR to trigger anti-cancer immune responses.

Molecular cancer therapeutics·2026
Same author

Harnessing smartphone RGB imagery and LiDAR point cloud for enhanced leaf nitrogen and shoot biomass assessment - Chinese spinach as a case study.

Frontiers in plant science·2025
Same author

Identification of Dinaciclib and Ganetespib as anti-inflammatory drugs using a novel HTP screening assay that targets IFNγ-dependent PD-L1.

Frontiers in immunology·2025
Same author

BKT300: A Novel Anti-Leukemic Small Molecule Targeting the Protein Regulator of Cytokinesis 1 (PRC1) Pathway.

Research square·2025
Same author

Targeting CCL24 in Inflammatory and Fibrotic Diseases: Rationale and Results from Three CM-101 Phase 1 Studies.

Drug safety·2024

We developed a fast algorithm to find optimal DNA sequences for cloning into phage display libraries. This method improves polymerase chain reaction (PCR) efficiency by considering guanine-cytosine (GC) base distribution.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Polymerase chain reaction (PCR) cloning of long DNA sequences (40-60 bases) into phage display libraries is inefficient.
  • PCR efficiency is significantly impacted by the guanine-cytosine (GC) base distribution within the amplified DNA sequence.
  • Finding optimal DNA inserts for PCR cloning presents a computational challenge due to the exponential increase in possible sequences with peptide length.

Purpose of the Study:

  • To develop an efficient computational method for identifying DNA sequences with optimal parameters for PCR cloning.
  • To address the challenge of low efficiency in cloning long DNA sequences into phage display libraries.
  • To optimize the selection of DNA inserts for improved PCR cloning success.

Main Methods:

Related Experiment Videos

  • Formulated the GC distribution requirements as a search problem.
  • Developed a linear time, 'one pass' algorithm for efficient identification of optimal DNA sequences.
  • Generalized the problem to accommodate non-standard genetic codes and solved it in polynomial time.

Main Results:

  • An efficient, linear time algorithm was developed to solve the PCR cloning optimization problem.
  • The algorithm leverages a newly observed symmetry in the standard genetic code.
  • The generalized problem for non-standard genetic codes was solved in polynomial time.

Conclusions:

  • The developed algorithm significantly improves the efficiency of identifying suitable DNA sequences for PCR cloning.
  • The findings offer a computational solution to a key bottleneck in phage display library construction.
  • The approach is adaptable to various genetic codes, enhancing its broader applicability.