Related Experiment Video
Updated: May 22, 2026
06:18
Frequency and Distribution of Crossovers in Caenorhabditis elegans Meiosis by SNP Genotyping using Real-time PCR
Published on: July 11, 2025
Algorithms for optimizing cross-overs in DNA shuffling
Lu He1, Alan M Friedman, Chris Bailey-Kellogg
1Dept of Computer Science, Dartmouth College, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA.
BMC Bioinformatics
|April 28, 2012
Summary
This study introduces CODNS, a novel DNA shuffling method that enables recombination of more diverse gene parents. This approach generates predictable and optimized chimeric libraries for protein engineering.
Area of Science:
- Protein Engineering
- Molecular Biology
- Bioinformatics
Background:
- DNA shuffling creates gene libraries by recombining parent genes for selection.
- Current DNA shuffling is limited to homologous sequences and lacks control over recombination.
- This limits its application to closely related gene families.
Purpose of the Study:
- To develop efficient methods for DNA shuffling with diverse parents.
- To generate more predictable and optimized chimeric gene libraries.
- To extend the scope and control of DNA shuffling.
Main Methods:
- Developed CODNS (cross-over optimization for DNA shuffling) using dynamic programming algorithms.
- Optimized local sequence identity and free energy approximation for annealing.
- Implemented algorithms to control recombination frequency and localization by creating nucleotide runs.
Main Results:
- CODNS efficiently selects codons and allocates substitutions for targeted recombination.
- Demonstrated effectiveness with diverse parents including GAR transformylases, DNA polymerases (Pol X and β), and beta-lactamases.
- Successfully promoted recombination between distantly related genes (down to 15% sequence identity).
Conclusions:
- The new DNA shuffling approach supports significantly more diverse parents.
- The method is more deterministic, leading to predictable chimeric library generation.
- Protein engineers gain enhanced control for creating diverse and optimized gene libraries.
Related Concept Videos
02:08Gene Conversion
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
01:30Crossing Over
Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I, duplicated...
01:34Crossing Over
Unlike mitosis, meiosis aims for genetic diversity in its creation of haploid gametes. Dividing germ cells first begin this process in prophase I, where each chromosome—replicated in S phase—is now composed of two sister chromatids (identical copies) joined centrally.
The homologous pairs of sister chromosomes—one from the maternal and one from the paternal genome—then begin to align alongside each other lengthwise, matching corresponding DNA positions in a process called synapsis.
In order to...
The homologous pairs of sister chromosomes—one from the maternal and one from the paternal genome—then begin to align alongside each other lengthwise, matching corresponding DNA positions in a process called synapsis.
In order to...
02:32Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
02:13Overview of Transposition and Recombination
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
02:53Conservative Site-specific Recombination and Phase Variation
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...