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.
Mondragon-Sanchez
J A
JA
Equipe de Spectroscopie Biomoleculaire, UMR CNRS 7033, UFR de Medicine, Universite Paris 13, 74, rue Marcel Cachin, F93017 Bobigny Cedex, France.
Liquier
J
J
Shafer
R H
RH
Taillandier
E
E
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