title: Melting of model HIV-1 stem-loop 1 RNA dimers monitored by 2-aminopurine fluorescence.
abstract: Viral maturation of HIV-1 involves refolding of its genomic RNA, which is believed to include a rearrangement of the SL1 stem-loop from a metastable conformation called kissing loop dimer (KD) to a stable one termed extended dimer (ED). To investigate this rearrangement in vitro we have studied the thermal melting of the RNA dimers formed by slightly modified 23-nucleotide SL1 RNA of HIV-1 Mal. Local structural changes in the RNA dimers during the melting were monitored by changes in the fluorescence of 2-aminopurine (2AP) incorporated in predetermined positions of RNA. We have shown that the stem regions of both preformed KD and ED melt in the temperature interval from 75 ° C to 90 ° C. Kissing loop interface of the KD RNA is found to be disrupted at lower temperatures from 20 ° C to 55 ° C, at which the stem regions remain intact. Conversion of the preformed KD to ED overcoming the kinetic barrier occurs between 55 ° C and 65 ° C. The melting of "loop-loop" regions in both preformed and newly formed EDs takes place around 70 ° C. Our finding that thermoinduced KD-to-ED conversion is preceded by transient dissociation of loop-loop interface disagrees with a common idea of strand exchange without disruption of loop-loop-contact.
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia. livshits@eimb.ru
authors.forename: Mikhail A
authors.initials: MA
authors.lastname: Livshits
authors.forename: Dmitry N
authors.initials: DN
authors.lastname: Kaluzhny
authors.forename: Elvira E
authors.initials: EE
authors.lastname: Minyat
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry; D019281:Dimerization; D005453:Fluorescence; D015497:HIV-1 / Q000235:genetics* / Q000378:metabolism; D055029:Inverted Repeat Sequences / Q000235:genetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral; D015075:2-Aminopurine