Free bases spread out and absorb more source

FIGURE 21.18 Absorption of UV Radiation by Nucleic Acids

All nucleic acids absorb UV light by the aromatic rings of the bases. The phosphate backbone (pink line or black dots) is not involved in UV absorption. The structure of the nucleic acid dictates how much light the aromatic rings absorb. On the right side of the light bulb, free nucleotides are shown spread out such that each ring can absorb the UV light. Overall, the free nucleotides absorb more UV. In contrast, as shown on the left, the aromatic rings are stacked along the phosphate backbone in a nucleic acid polymer. In this configuration the rings shield each other and absorb less UV light.

The PNA backbone is very stable and is not degraded by any naturally occurring nucleases or proteases. PNA can be used to bind to and block target sequences of DNA in purine-rich regions and prevent transcription of DNA to give mRNA. It can also bind to RNA and prevent translation of mRNA into protein; i.e., it acts like antisense RNA. PNA is useful for laboratory applications and may also be used clinically in the near future. For example, antisense PNA that inhibits the translation of gag-pol mRNA of HIV-1 has been shown to reduce virus production by 99 percent in tissue culture. Similarly, antisense PNA can stop the in vitro translation of Ha-ras and bcl-2 mRNA (both from cancer cells). In the case of bcl-2, PNA was also shown to inhibit gene expression by binding to the DNA at a purine-rich tract.

The major problem with using PNA clinically is that it penetrates cells poorly— much worse than natural nucleic acids. Recent developments suggest that PNA can enter cells effectively if it is coupled to other molecules that are taken up readily or if it is carried by positively charged liposomes.


The concentration of DNA or RNA is usually measured by absorption of ultraviolet light.

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