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Artificial DNA, PNA & XNA (1)
Journal of Nucleic Acids (1)
Kawakami, Junji (2)
Yamaguchi, Yoshie (2)
Ananthanawat, Cheeraporn (1)
Srisuwannaket, Choladda (1)
Sugimoto, Naoki (1)
Suparpprom, Chaturong (1)
Tanaka, Yuko (1)
Vilaivan, Chotima (1)
Vilaivan, Tirayut (1)
Year of Publication
Triplet Analysis That Identifies Unpaired Regions of Functional RNAs
Journal of Nucleic Acids
We developed a novel method for analyzing RNA sequences, deemed triplet analysis, and applied the method in an in vitro RNA selection experiment in which HIV-1 Tat was the target. Aptamers are nucleic acids that bind a desired target (bait), and to date, many aptamers have been identified by in vitro selection from enough concentrated libraries in which many RNAs had an obvious consensus primary sequence after sufficient cycles of the selection. Therefore, the higher-order structural features of the aptamers that are indispensable for interaction with the bait must be determined by additional investigation of the aptamers. In contrast, our triplet analysis enabled us to extract important information on functional primary and secondary structure from minimally concentrated RNA libraries. As a result, by using our method, an important unpaired region that is similar to the bulge of TAR was readily predicted from a partially concentrated library in which no consensus sequence was revealed by a conventional sequence analysis. Moreover, our analysis method may be used to assess a variety of structural motifs with desired function.
Pyrrolidinyl peptide nucleic acid with α/β-peptide backbone
Artificial DNA, PNA & XNA
We describe herein a new conformationally constrained analog of PNA carrying an alternating α/β amino acid backbone consisting of (2′R,4′R)-nucleobase-subtituted proline and (1S,2S)-2-aminocyclopentanecarboxylic acid (acpcPNA). The acpcPNA has been synthesized and evaluated for DNA, RNA and self-pairing properties by thermal denaturation experiments. It can form antiparallel hybrids with complementary DNA with high affinity and sequence specificity. Unlike other PNA systems, the thermal stability of acpcPNA·DNA hybrid is largely independent of G+C contents, and is generally higher than that of acpcPNA·RNA hybrid with the same sequence. Thermodynamic parameters analysis suggest that the A·T base pairs in the acpcPNA·DNA hybrids are enthalpically stabilized over G·C pairs. The acpcPNA also shows a hitherto unreported behavior, namely the inability to form self-pairing hybrids. These unusual properties should make the new acpcPNA a potentially useful candidate for various applications including microarray probes and antigene agents.
peptide nucleic acid; nucleic acid; DNA recognition; RNA recognition; pre-organization; foldamer; α/β-peptide
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