Final answer:
The efficiency of plasmid cloning declines with larger inserts because larger DNA molecules are more difficult to handle, more prone to errors, less likely to transform, and replicate less efficiently. Alternative vectors like bacteriophages or YACs can accommodate larger inserts, reducing the number of clones to screen in large genomes.
Step-by-step explanation:
Plasmid cloning efficiency decreases with an increased size of the insert due to several factors. Larger inserts can be more difficult to handle during the recombination process, and they are more prone to genetic rearrangements or losses during bacterial replication. Also, the efficiency of transformation, where bacterial cells take up the plasmid, decreases as plasmid size increases. This is because large DNA molecules are less efficiently packaged into competent cells and suffer greater possibilities of degradation or structural compromise. Moreover, larger plasmids amplify less well, as they are replicated and partitioned less efficiently during cell division.
Greater insert size necessitates the use of alternative cloning vectors like bacteriophage or Yeast Artificial Chromosomes (YACs), which are capable of accommodating larger fragments of DNA. This allows for the screening of fewer clones to identify the gene or sequence of interest within large genomes, such as mammalian genomes which have more than 2 billion base pairs. In contrast, a typical cDNA insert in a plasmid is rarely longer than 1000 base pairs, greatly increasing the number of clones that would need to be screened to find a specific sequence.
To summarize the considerations of cloning efficiency with respect to the vector and insert size, using plasmids for larger inserts is inefficient and thus necessitates more effective vectors like bacteriophages for larger genomic libraries. These considerations play a pivotal role in the strategy of molecular cloning and affect the outcome of the cloning experiments significantly.