Manganese water-soluble porphyrin senses DNA conformation.
We have determined the sites that are preferentially cleaved by Mn(T4MPyP) (where T4MPyP is the dianion of 5, 10, 15, 20, tetrakis (4-N-methylpyridine)porphyrin) on synthetic DNAs and on both intrinsically curved and average-shaped natural DNA sequences. On the basis of cleavage selectivity and of DNase I footprinting we show that the recognition specificity by this compound is based on steric properties: the preferred conformation is a DNA minor groove narrower than average and dimensionally defined. This conclusion is reached on the basis of: (i) the localization of the preferential cleavage sites at the 3' extremity of short A-tracts, known to undergo minor groove directional narrowing; (ii) the effects of temperature on cleavage specificity on curved sequences; (iii) the localization of cleavage sites in synthetic constructs whose crystal and solution structure was previously defined, and in programmed sequence variants thereoff; (iv) the effects of base substitutions on cleavage efficiency; (v) DNase I footprinting analysis. Several of these evidences argue against the possibility that Mn(T4MPyP)/DNA site selection occurs on the basis of electrostatic potential effects.Mn(T4MPyP) provides a tool for the analysis of DNA conformation whose selectivity is complementary to that of DNase I and hydroxyl radicals.
Di Mauro
E
E
Fondazione "Istituto Pasteur Fondazione Cenci Bolognetti" c/o Dipartimento di Genetica e Biologia Molecolare, Università di Roma-La Sapienza, Italy. dimauro@axrma.uniroma1.it
Saladino
R
R
Tagliatesta
P
P
De Sanctis
V
V
Negri
R
R
D000818:Animals; D015374:Biosensing Techniques; D016831:Crithidia fasciculata; D004247:DNA / Q000737:chemistry*; D018983:DNA Footprinting; D018105:DNA, Kinetoplast / Q000737:chemistry; D003850:Deoxyribonuclease I / Q000378:metabolism; D008345:Manganese / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009942:Organometallic Compounds / Q000737:chemistry*; D011166:Porphyrins / Q000737:chemistry*
D018105:DNA, Kinetoplast; D009838:Oligodeoxyribonucleotides; D009942:Organometallic Compounds; D011166:Porphyrins; C114728:manganese(II) 5,10,15,20-tetrakis(4-N-methylpyridine)porphyrin; D008345:Manganese; D004247:DNA; D003850:Deoxyribonuclease I