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A recoding method to improve the humoral immune response to an HIV DNA vaccine.

Huang Y, Krasnitz M, Rabadan R, Witten DM, Song Y, Levine AJ, Ho DD, Robins H - PLoS ONE (2008)

Bottom Line: Transfecting the recoded DNA sequence into a human kidney cell line results in doubling the gag protein expression level compared to the codon optimized version.We then turn both sequences into DNA vaccines and compare induced antibody response in a murine model.Our sequence, which has the motifs removed, induces a five-fold increase in gag antibody response compared to the codon optimized vaccine.

View Article: PubMed Central - PubMed

Affiliation: Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America.

ABSTRACT
This manuscript describes a novel strategy to improve HIV DNA vaccine design. Employing a new information theory based bioinformatic algorithm, we identify a set of nucleotide motifs which are common in the coding region of HIV, but are under-represented in genes that are highly expressed in the human genome. We hypothesize that these motifs contribute to the poor protein expression of gag, pol, and env genes from the c-DNAs of HIV clinical isolates. Using this approach and beginning with a codon optimized consensus gag gene, we recode the nucleotide sequence so as to remove these motifs without modifying the amino acid sequence. Transfecting the recoded DNA sequence into a human kidney cell line results in doubling the gag protein expression level compared to the codon optimized version. We then turn both sequences into DNA vaccines and compare induced antibody response in a murine model. Our sequence, which has the motifs removed, induces a five-fold increase in gag antibody response compared to the codon optimized vaccine.

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Example of shuffling procedure.The procedure to get the maximal entropy distribution (MED) involves a set of randomized iterations. The triplets of nucleotides coding for each amino acid are permuted randomly among themselves. This is an illustrative example of a mock short protein with eight amino acids. The shuffling procedure randomly permutes L1, L2, L3, and L4 and separately permutes H1, H2, and H3. Each iteration produces a new sequence. For this example, there are 12 different combinations for the leucines and three combinations for the histidines resulting in 36 unique sequences. They are weighted in the shuffling procedure so that the MED is attained in the limit of a large number of iterations.
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pone-0003214-g003: Example of shuffling procedure.The procedure to get the maximal entropy distribution (MED) involves a set of randomized iterations. The triplets of nucleotides coding for each amino acid are permuted randomly among themselves. This is an illustrative example of a mock short protein with eight amino acids. The shuffling procedure randomly permutes L1, L2, L3, and L4 and separately permutes H1, H2, and H3. Each iteration produces a new sequence. For this example, there are 12 different combinations for the leucines and three combinations for the histidines resulting in 36 unique sequences. They are weighted in the shuffling procedure so that the MED is attained in the limit of a large number of iterations.

Mentions: The first step in the algorithm is the creation of a background sequence to compare with the human genome. This background is a completely randomized version of the coding sequences from the human genome subject to the constraints of amino acid order and codon usage in each gene. We design a Monte Carlo program that randomly permutes the codons for each amino acid within each gene. Figure 3 is an illustrative example.


A recoding method to improve the humoral immune response to an HIV DNA vaccine.

Huang Y, Krasnitz M, Rabadan R, Witten DM, Song Y, Levine AJ, Ho DD, Robins H - PLoS ONE (2008)

Example of shuffling procedure.The procedure to get the maximal entropy distribution (MED) involves a set of randomized iterations. The triplets of nucleotides coding for each amino acid are permuted randomly among themselves. This is an illustrative example of a mock short protein with eight amino acids. The shuffling procedure randomly permutes L1, L2, L3, and L4 and separately permutes H1, H2, and H3. Each iteration produces a new sequence. For this example, there are 12 different combinations for the leucines and three combinations for the histidines resulting in 36 unique sequences. They are weighted in the shuffling procedure so that the MED is attained in the limit of a large number of iterations.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2529374&req=5

pone-0003214-g003: Example of shuffling procedure.The procedure to get the maximal entropy distribution (MED) involves a set of randomized iterations. The triplets of nucleotides coding for each amino acid are permuted randomly among themselves. This is an illustrative example of a mock short protein with eight amino acids. The shuffling procedure randomly permutes L1, L2, L3, and L4 and separately permutes H1, H2, and H3. Each iteration produces a new sequence. For this example, there are 12 different combinations for the leucines and three combinations for the histidines resulting in 36 unique sequences. They are weighted in the shuffling procedure so that the MED is attained in the limit of a large number of iterations.
Mentions: The first step in the algorithm is the creation of a background sequence to compare with the human genome. This background is a completely randomized version of the coding sequences from the human genome subject to the constraints of amino acid order and codon usage in each gene. We design a Monte Carlo program that randomly permutes the codons for each amino acid within each gene. Figure 3 is an illustrative example.

Bottom Line: Transfecting the recoded DNA sequence into a human kidney cell line results in doubling the gag protein expression level compared to the codon optimized version.We then turn both sequences into DNA vaccines and compare induced antibody response in a murine model.Our sequence, which has the motifs removed, induces a five-fold increase in gag antibody response compared to the codon optimized vaccine.

View Article: PubMed Central - PubMed

Affiliation: Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America.

ABSTRACT
This manuscript describes a novel strategy to improve HIV DNA vaccine design. Employing a new information theory based bioinformatic algorithm, we identify a set of nucleotide motifs which are common in the coding region of HIV, but are under-represented in genes that are highly expressed in the human genome. We hypothesize that these motifs contribute to the poor protein expression of gag, pol, and env genes from the c-DNAs of HIV clinical isolates. Using this approach and beginning with a codon optimized consensus gag gene, we recode the nucleotide sequence so as to remove these motifs without modifying the amino acid sequence. Transfecting the recoded DNA sequence into a human kidney cell line results in doubling the gag protein expression level compared to the codon optimized version. We then turn both sequences into DNA vaccines and compare induced antibody response in a murine model. Our sequence, which has the motifs removed, induces a five-fold increase in gag antibody response compared to the codon optimized vaccine.

Show MeSH