A Synthetic DNA with Unusual Base‐Pairing

Abstract

The alternating polydeoxynucleotide poly[d(A-s4T) -d(A-s4T)] with 4-thiothymidine substituting for thymidine shows anomalous spectral and hydrodynamic properties which are inconsistent with a Watson-Crick structure but agree with a model of a left-handed double helix built up from Haschemeyer-Sobell (reversed Hoogsteen) base-pairs instead.Optical-rotatory-dispersion and circular-dichroism spectra exhibit a strong negative Cotton effect centered near 400 nm that is assigned to a n + n* transition of the thioamide chromophor and that is a t least unexpected if the sulfur atom participates in the hydrogen bridge. From the inversion of the Cotton effects between 370 and 400 nm with respect to the monomer or randomcoil state it is inferred that 4-thiothymidine attains the unusual syn conformation in the ordered polymer. At pH below 4.5 the polymer is protonated at N-1 of the deoxyadenosine residues and changes into a different helical conformation. As the inflection point of the proton-induced transition falls close to the basic p K of deoxyadenosine monophosphate, also N-1 (A) is probably not involved in hydrogen bonding. Therefore, only N-7 (A) and 0 -2 (s4T) remain as proton acceptors for base-pairing. The polymer undergoes cooperative temperature-dependent transitions in concentrated solutions of 1 : 1 electrolytes. Two more helical conformations are characterized by ultraviolet, optical-rotatory dispersion, and circular dichroism. I n addition, changes in hydrodynamic parameters, e.g. sedimentation coefficient, buoyant density and partial specific-volume are reported. A structural hysteresis is observed in a helix-helix transition and is discussed in terms of metastable states indicated from a phase diagram. Definition. A,, unit, the quantity of material contained in 1 ml of a solution which has an absorbance of 1 a t 345 nm, when measured in a 1-cm pathlength cell.can become less important relative to other factors under conditions of reduced solvent-solvent interactions which are met in solutions deviating from neutrality, in mixtures of water and organic solvents, and in concentrated salt solutions. These as well as chemical modification of the nucleosides may lead to some interference with the Watson-Crick structure and eventually favor even an alternative basepairing.I n this study the anomalous behaviour of a synthetic DNA is described which is distinctly different in structure from the usual Watson-Crick structure. The alternating polydeoxynucleotide poly[d(A-s*T) d(As4T)], prepared first enzymatically in this laboratory [7, 81, contains the analog nucleoside 4-thiothymidine instead of thymidine. Since in the Watson-Crick structure the 4-0x0 group of thymidine is involved in basepairing, substitution of this oxygen by sulfur should cause a t least some perturbation of the hydrogen bond. Therefore, the question of structure and stability of this biopolymer has intrigued us from the very beginning. As reported briefly [9], two interconvertible conformations differing in buoyant density were detected during...

Structure and Stability of Chemically Modified DNA Bases: Quantum Chemical Calculations on 16 Isomers of Diphosphocytosine

“…Modification of cytosine base to phosphorus-containing cytosine analogues, diphosphocytosine, is a good start point in this topic. Also, their existence in many tautomeric forms, like other nucleoside bases, seems to be crucial in order to explain the mutation occurring during DNA duplication [63][64][65][66]. Searching the literatures confirms that no previous studies include all numbers of cytosine tautomers.…”

Association of Cu2+with Uracil and Its Thio Derivatives: A Theoretical Study

“…[14] Moreover, their existence in many tautomeric forms seems to be crucial for explaining mutation occurring during DNA duplication. [15][16][17] Recently, we have studied [18] the stability of all tautomers of these compounds in the gas phase and the activation barriers that interconnect them, in order to identify the most stable tautomer and the most basic center for protonation. [18] More recently, to investigate whether the basicity of these compounds depends on binding type, we studied the association of thiouracil derivatives with Cu + .…”

Equilibrium geometry and gas‐phase proton affinity of 2‐thiouracil derivatives

“…Thiouracils are currently the subject of extensive theoretical and experimental investigations due to the wide variety of their biological activities 1–19. Thus, 2‐thiouracil constitutes an important derivative of the thiated pyrimidines.…”