This is a cool question, but it seems awfully tricky. There ware ways to render sequences temporarily unreadable chemically (e.g. Intercalating agents), but these methods are generally incompatible with organism biology (e.g. They're toxic) and they can be reversed by careful DNA purification.
Sequences can be made difficult to sequence due to being highly repetitive or GC rich, but such sequences are often also unstable. Moreover, this obstacle can be overcome by brute force methods (e.g. high coverage sequencing)
There are ways of making uracil tolerant bacteria strains that incorporate uracil into genomic and plasmid DNA, and some sequencing polymerases may not be able to read it with high fidelity.
This is a cool question, but it seems awfully tricky. There ware ways to render sequences temporarily unreadable chemically (e.g. Intercalating agents), but these methods are generally incompatible with organism biology (e.g. They're toxic) and they can be reversed by careful DNA purification.
Sequences can be made difficult to sequence due to being highly repetitive or GC rich, but such sequences are often also unstable. Moreover, this obstacle can be overcome by brute force methods (e.g. high coverage sequencing)
There are ways of making uracil tolerant bacteria strains that incorporate uracil into genomic and plasmid DNA, and some sequencing polymerases may not be able to read it with high fidelity.
I largely agree with Peter. You'd really need to explain the problem you're trying to solve, otherwise it's really difficult to help. If I understand you correctly I think you're probably going about this the wrong way.
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