Tetraplex structure formation in the thrombin-binding DNA aptamer by metal cations measured by vibrational spectroscopy.
Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K(+), Pb(2+), Ba(2+), Sr(2+) and Mn(2+) has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2'endo/anti and C2'endo/syn deoxyguanosine glycosidic conformations and local B like form DNA phosphate geometries. Addition of Pb(2+) ions modifies the structure by interacting at the level of the guanine carbonyl groups. The very important downshift of the guanine C6=O6 carbonyl vibration mode in the TBA spectrum induced by the addition of one Pb(2+) ion per TBA molecule is in agreement with a localization of the metal ion between both guanine quartets. FTIR melting experiments show an important stabilization of the tetraplex structure upon addition of Pb(2+) ions (DeltaT = 15 degrees C). This strong interaction of lead cations may be correlated with a change in the geometry of the cage formed by the two guanine quartets. A similar but weaker effect is observed for barium and strontium cations.
Equipe de Spectroscopie Biomoleculaire, UMR CNRS 7033, UFR de Medicine, Universite Paris 13, 74, rue Marcel Cachin, F93017 Bobigny Cedex, France.
J A
JA
Mondragon-Sanchez
J
J
Liquier
R H
RH
Shafer
E
E
Taillandier
D052157:Aptamers, Nucleotide; D002412:Cations; D004247:DNA / Q000737:chemistry*; D017666:Deuterium Oxide; D006147:Guanine / Q000737:chemistry; D006358:Hot Temperature; D007477:Ions; D007854:Lead / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry* / Q000378:metabolism; D011188:Potassium / Q000737:chemistry; D013053:Spectrophotometry; D017550:Spectroscopy, Fourier Transform Infrared; D013696:Temperature; D013816:Thermodynamics; D013917:Thrombin / Q000737:chemistry*
D052157:Aptamers, Nucleotide; D002412:Cations; D007477:Ions; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; C081676:thrombin aptamer; D007854:Lead; D006147:Guanine; D004247:DNA; D013917:Thrombin; D017666:Deuterium Oxide; D011188:Potassium