title: Conformational and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments.
abstract: NMR studies were carried out on various equimolar mixtures consisting of a combination of oligomers: d(ACGGCT) (I). d(pACGGCT) (Ia), d(TGCAGT) (II), d(AGCCGTACTGCA) (III), d(TGCAGTACGGCT) (IV). It is shown that I + II + III (MI) and Ia + II + III (M2) form stable duplexes with nicks in the centre of the respective double helices. A close analysis of the NOESY experiments of M1 and M2 revealed that these fragments form B-DNA type duplex structures. A comparison of the chemical-shift data of the nicked duplexes with those of the intact duplex of III + IV (M3) demonstrated that only small local distortions occur when a nick is introduced. The chemical-shift profiles of M1 and M3 were used to obtain the thermodynamic data for the duplex/coil transitions. The profiles of M1 were analysed by means of a new thermodynamic model (TRIDUP). From the calculated thermodynamic data of M1 and M3 it is concluded that the melting behaviour of M1 occurs cooperatively. A ligation experiment demonstrated that the relatively small substrate (M2) was almost completely joined after an overnight incubation at 14 degrees C.
authors.affiliation: Gorlaeus Laboratories, University of Leiden, The Netherlands.
authors.forename: J M
authors.initials: JM
authors.lastname: Pieters
authors.forename: R M
authors.initials: RM
authors.lastname: Mans
authors.forename: H
authors.initials: H
authors.lastname: van den Elst
authors.forename: G A
authors.initials: GA
authors.lastname: van der Marel
authors.forename: J H
authors.initials: JH
authors.lastname: van Boom
authors.forename: C
authors.initials: C
authors.lastname: Altona
mesh_terms: D001483:Base Sequence; D004249:DNA Damage; D011088:DNA Ligases / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000302:isolation & purification; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000302:isolation & purification; D009841:Oligonucleotides; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D011088:DNA Ligases