Molecular Dynamics Study for the Base Sequence Recognition Probe of Nucleic Acids Modified with the Pyrenyl Group

Kazuhiro SASAa*, Takeshi UNOb, Haruhisa HAYASHIc and Hidehiko NAKANOa

aDepartment of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo
2167 Shosha, Himeji, Hyogo, 671-2201, JAPAN
bDepartment of Management and Information Sciences, Hiroshima Prefectural University
562 Nanatuka, Shobara, Hiroshima, 727-0023, JAPAN
cLibrary and Academic Information Center, University of Hyogo
2167 Shosha, Himeji, Hyogo, 671-2201, JAPAN

(Received: March 8, 2007; Accepted for publication: May 7, 2007; Published on Web: July 20, 2007)

It is known that RNA modified with the pyrenyl group (pyren-RNA) which uses the pyrene moiety as a fluorescent chromophore shows a remarkable increase in fluorescence when the double helix is formed with the complementary strand RNA, compared to the single strand pyrene-RNA, and that this phenomenon is not seen with DNA. For the purpose of designing a sequence recognition probe based on these phenomena, detailed data of the pyrenyl moiety in the pyrene-RNA and pyrene-DNA of double stranded structures are observed with MD simulation. In addition, the influence of mismatched combination of base in the complementary strand was examined. As a result, it was revealed that in the full-match double stranded pyrene-DNA the pyrene moiety stays inside the helix but in the full-match double stranded pyrene-RNA pyrene was thrusted out of the helix. Mismatch sequence in the pyrene-RNAdouble strand influenced the behavior of the pyrenyl moiety when the mismatch position was located close to the pyrene modified position.

Keywords: Base sequence recognition probe, Pyrene, DNA, RNA, Molecular dynamics

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