Buoyant densities of natural and synthetic DNA's in CsCl and Cs₂SO₄ considered as sequence‐dependent properties

Abstract

SynopsisThe buoyant densities of natural and synthetic DNA's can be accurately interrelated if second-neighbor influences are taken into account. We derive the following expressions, based partly on the buoyant densities of six synthetic DNA's, for the buoyant densities p (g/cma) of DNA's having random sequences. In CsCI, In these equations, HG is the mole fraction of G : C base pairs in the DNA and the buoyant densities are calculated relative to densities for E. cola DNA of 1.703 and 1.426 (g/cm3) in CsCl and Cs~SOd, respectively.

Preparation and properties of the repeating sequence polymers d(A-I-C)n.d(I-C-T) n and d(A-G-C)n.d(G-C-T)n

“…The buoyant densities of d(A-G-C)"-d(G-C-T)" and d(A-I-C)"-d(I-C-T)" are 1.436 and 1.444 g/ml, respectively, in cesium sulfate and 1.718 and 1.716 g/ml, respectively, in cesium chloride. A buoyant density of 1.718 g/ml for d(A-G-C)"-d(G-C-T)" in cesium chloride is what one would expect on the basis of 67% G + C content (Schildkraut et al, 1962;Gray et al, 1974).…”

“…All of these measurements support the sequences we have assigned to these polymers. The synthesis of d(A-G-C)"-d(G-C-T)" and the determination of its buoyant density in cesium chloride and cesium sulfate have allowed us to derive general equations that express the buoyant density of a polymer in terms of its first-neighbor base frequencies (Gray et al, 1974). It is interesting to compare the nine have lower buoyant densities in cesium sulfate but higher buoyant densities in cesium chloride than their analogues containing hypoxanthine.…”

“…Snythetic DNAs with repeating nucleotide sequences have been instrumental in elucidation of the genetic code (Khorana et al, 1966) and in determination of repressor binding properties (Riggs et al, 1972). Synthetic DNA properties, such as buoyant density, have been used to derive relationships that describe the corresponding properties of natural DNA (Gray et al, 1974). Another type of model DNA has been used to study the influence of nucleotide composition in one region of a duplex DNA on the properties of a remote but contiguous region (Burd et al, 1975).…”

Recognition Mechanisms of DNA-Specific Enzymes

“…Detailed comparisons of a large number of synthetic polynucleotides and natural DNA's with respect to thermal transitions (57)(58)(59), buoyant density in CsCI and CS 2 -S04 (57,58,60), circular dichroic spectra (57)(58)(59), and wide-angle X-ray diffrac tion parameters (61,62) indicate that the physicial properties and, by inference, the structure of a DNA are dictated by its primary nucleotide sequence. 3 For example, infrared linear-dichroism measurements of oriented films (64) and in dependent X-ray diffraction data (55,65) demonstrate that the high-humidity form of poly(dA).poly(dT) differs from the standard B conformation and does not un dergo the transition to the A fo rm.…”