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Death by DNA Shuffling

press-release

 

The Institute of Science in Society

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http://www.i-sis.org.uk

 

General Enquiries sam

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ISIS Director m.w.ho

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Death by DNA Shuffling

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Geneticists can now create millions of new viruses and bacteria in a matter of

minutes in the laboratory. And there is no regulation to stop them from being

effectively released. Dr. Mae-Wan Ho reports.

 

A complete version of this paper with diagram and references is posted on ISIS

Members’ website (http://www.i-sis.org.uk/full/deathByDNAShufflingFull.php).

Membership details here (http://www.i-sis.org.uk/membership.php).

 

Willem P.C. Stemmer of Affymax Research Institute in Palo Alto, California,

published a paper in the Proceedings of the National Academy Science in 1994,

describing a technique for rapidly shuffling and recombining DNA in the

laboratory that appears to generate recombinant proteins with greatly improved

performances.

 

According to Stemmer, computer simulation studies had demonstrated the

importance of recombining segments of genes in evolution, rather than single

base changes. To put this into practice, he devised a method for reassembling

genes from random gene fragments in the test tube.

 

The DNA of the gene is digested with the enzyme deoxyribonuclease 1 (DNAse 1)

into random 10 to 50 bp (base-pair) fragments. These fragments are heated up to

separate the two strands and made to re-anneal (pair up again) in the presence

of a DNA polymerase, an enzyme that synthesize DNA.

 

The separated strands of DNA pair up according to complementary base sequences

in homologous DNA (DNA with similar base sequences from the same species or

related species); and a shorter sequence paired to a longer one will ‘prime’ the

synthesis of DNA using the longer sequence as a template, until the complete

double stranded DNA is restored. With fragments re-annealing in a random way,

the DNA polymerase can switch templates many times in the course of reassembly,

and that is how different recombinants are generated. A simplified diagram of

what is achieved in a typical experiment is shown in Figure 1.

 

Figure 1 DNA shuffling. Different variants of a gene or a DNA sequence,

represented by the different colours are fragmented and reassembled to generate

millions of recombinants all at once. See complete version

 

The recombinants are cloned into a vector and introduced into bacteria for rapid

screening.

 

In this way, many variants of any gene can be rapidly recombined, even variants

from different species. Larger pieces of DNA such as entire plasmids, viral and

bacterial genomes can also be recombined. To increase the variety of

recombinants, short pieces of synthetic DNA can be added into the mixture. Even

non-homologous DNA, from totally unrelated species can be recombined.

 

In the very first experiment reported, Stemmer claimed to have produced a

recombinant of a beta-lactamase that increased resistance to a beta-lactam

antibiotic by 16 000 fold. When this recombinant is ‘backcrossed’ to the

parental gene using the same DNA shuffling technique, which he later calls,

‘molecular breeding’, an enzyme that was 32 000 times as effective as the wild

type enzyme was obtained.

 

Previously, researchers have used other methods to introduce random errors, such

as the polymerase chain reaction (PCR), but that gave only a 16 fold improvement

at best. And ‘rational design’ based on known structure of the enzyme did no

better. So the results obtained with DNA shuffling seem out of this world.

 

Stemmer has since set up a California-based company, Maxygen, Inc. to exploit

the technology. In a series of papers between 1998 and 2002, he and his

coworkers in Maxygen and other companies have used the technique to obtain

greatly improved proteins, such as green fluorescent protein, fucosidase,

subtilisin, thymidine kinase and interferon-alpha, as well as improved

retroviral vectors and bacterial strains of Streptomyces and Lactobacillus.

 

In the experiment on retroviral genomes, 6 mouse leukaemia viruses (MLV) were

recombined in a single round, giving a library of 5 million replicating

recombinant viruses. Among them were completely new viruses that infect Chinese

Hamster Ovary cells, which none of the original MLV was capable of infecting,

and recombinant viruses that were 30 to 100 times more stable than the parental

strains, and hence much better for gene therapy.

 

So far, such experiments appear to have been carried out exclusively by Maxygen

Inc. or by the company in collaboration with other companies, and therefore not

independently replicated as far as the remarkable successes are concerned.

 

There is no doubt, however, that the procedure itself is dangerous. As these

researchers have amply demonstrated, recombination is the major route to

generating new viruses and bacteria. Some of the recombinant viruses and

bacteria could well be lethal.

 

What precautions have they taken with regard to the recombinants and vectors

used, to prevent them from being released into the environment? Are the

recombinant viruses and bacteria, or their DNA, strictly contained within the

laboratory?

 

Current regulation on contained use of genetically engineered micro-organism is

highly inadequate, and we have repeatedly pointed this out to our regulators. In

Europe, ‘tolerated releases’ are allowed, and this include not only transgenic

wastes consisting of dead bacteria and cells (with plenty of transgenic DNA),

but also certain living bacteria deemed, by the companies concerned, not to pose

a threat to health or the environment.

 

With unregulated experiments like these, who need bio-terrorists?

 

A complete version of this paper with diagram and references is posted on ISIS

Members’ website (http://www.i-sis.org.uk/full/deathByDNAShufflingFull.php).

Membership details here (http://www.i-sis.org.uk/membership.php).

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This article can be found on the I-SIS website at

http://www.i-sis.org.uk/deathByDNAShuffling.php

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General Enquiries sam

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