Efficient modification of RNA by porphyrin cation photochemistry: monitoring the folding of coaxially stacked RNA helices in tRNA(Phe) and the human immunodeficiency virus type 1 rev response element RNA.
Coaxially stacked RNA helices are a determined of RNA tertiary structure, but their presence is rarely detected using conventional chemical modification methods. In this report we describe a porphyrin ion photoreaction that enables one to monitor RNA stacking interactions and the folding of coaxially stacked RNA helices. The porphyrin cations meso-tetrakis(4-N-methylpyridyl)porphine, meso-tetrakis-(para-N-trimethylanilinium)porphine, and meso-tetrakis(2-N-methylpyridyl)porphine were used to characterize tRNA(Phe) and the human immunodeficiency virus type-I Rev response element RNA. Nucleosides at the bases of contiguous RNA helices in each RNA are efficiently modified by the porphyrin cations following irradiation of porphyrin-RNA mixtures. These photomodifications are markedly reduced for RNA equilibrated in ionic buffers that lead to enhanced stabilization of coaxially stacked helices. The porphyrin cation photoreaction specifically modifies G18, G20, and G34 in the tRNA folding produced by Mg(II). These nucleobases are exposed to solvent in the native tRNA structure and thus available to stack with solvent-borne porphyrin molecules. The describe porphyrin cation photochemical method provides a novel approach to study the solvent accessibility of nucleobases in RNA structure and to monitor the folding of coaxially stacked helices in RNA.
Celander
D W
DW
Department of Microbiology, University of Illinois at Urbana-Champaign 61801, USA. dcelande@uiuc.edu
Nussbaum
J M
JM
D000814:Aniline Compounds / Q000494:pharmacology; D001483:Base Sequence; D017931:DNA Primers; D015694:Gene Products, rev / Q000378:metabolism*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008665:Metalloporphyrins / Q000494:pharmacology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects / Q000528:radiation effects; D010777:Photochemistry; D011166:Porphyrins / Q000494:pharmacology*; D012360:RNA, Transfer, Phe / Q000737:chemistry* / Q000187:drug effects / Q000528:radiation effects; D012367:RNA, Viral / Q000737:chemistry* / Q000187:drug effects / Q000528:radiation effects; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013329:Structure-Activity Relationship; D013698:Templates, Genetic; D014158:Transcription, Genetic; D054321:rev Gene Products, Human Immunodeficiency Virus
D000814:Aniline Compounds; D017931:DNA Primers; D015694:Gene Products, rev; D008665:Metalloporphyrins; D011166:Porphyrins; D012360:RNA, Transfer, Phe; D012367:RNA, Viral; D054321:rev Gene Products, Human Immunodeficiency Virus; C099421:tetra(4-N-trimethylanilinium)porphine; C021096:tetra(4-N-methylpyridyl)porphine; C050950:tetrakis(N-methyl-4-pyridiniumyl)porphine manganese(III) complex