The manipulation of genes at the molecular level presents a serious challenge, often requiring strategies that may not, at first, seem obvious. The basic problems are that genes are minute and that every cell contains thousands of them. Individual nucleotides cannot be seen, and no physical features mark the beginning or the end of a gene.

Let’s consider a typical situation faced by a molecular geneticist. Suppose we want to use bacteria to produce large quantities of a human protein. The first and most formidable problem is to find the gene that encodes the desired protein. A haploid human genome consists of 3.2 billion base pairs of DNA. Let’s assume that the gene that we want to isolate is 3000 bp long; our target gene occupies only one-millionth of the genome, so searching for our gene in the huge expanse of genomic DNA is more difficult than looking for the proverbial needle in a haystack. But, even if we are able to locate the gene, how do we separate it from the rest of the DNA?

If we succeed in locating and isolating the desired gene, we next need to insert it into a bacterial cell. Linear fragments of DNA are quickly degraded by bacteria, so the gene must be inserted in a stable form. It must also be able to successfully replicate or it will not be passed on when the cell divides. If we succeed in transferring our gene to bacteria in a stable form, we must still ensure that the gene is properly transcribed and translated.

Finally, the methods used to isolate and transfer genes are inefficient: of a million cells that are subjected to these procedures, only one cell might successfully take up and express the human gene. So we must search through many bacterial cells to find the one containing the recombinant DNA. We are back to the problem of the needle in a haystack.

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Although these problems might seem insurmountable, molecular techniques have been developed to overcome them, and human genes are now routinely transferred to bacterial cells in which the genes are expressed.