Solvent-accessible surfaces of nucleic acids

Alden, Charles J.; Kim, Sung‐Hou

doi:10.1016/0022-2836(79)90268-7

Cited by 168 publications

(96 citation statements)

References 32 publications

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“…2, e and f). From (19,28) we obtain a long-range effect of netropsin affecting 20 base pairs on each side of the bound drug. This extremely large effect is paralleled by findings in a solution study of the DNA interaction with distamycin A (32), which structure is similar to netropsin, where one drug mole- Hydration of DNA in the saturated netropsin complex is increased The hydration of DNA films can be easily monitored by the intensity of the water stretching vibration band at 3400 cm 1 (10).…”

Section: Resultsmentioning

confidence: 99%

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Infrared linear dichroism of oriented DNA-ligand complexes prepared with the wet-spinning method

Fritzsche¹,

Rupprecht

Richter³

1984

Nucl Acids Res

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Oriented DNA films prepared by the wet-spinning technique have been complexed with several ligands: the anthracycline antibiotic violamycin BI, the dipeptide L-carnosine, and the oligopeptide antibiotic netropsin. The formation of the DNA-ligand complexes is accompanied by dramatic changes of the conformational flexibility of DNA. The B-A transition which occurs usually between 80% and 70% relative humidity (RH) is more or less suppressed by the ligands. Violamycin BI at a total ligand per DNA base pair ratio, r , of '0.03 and L-carnosine at rt X' 1.5 inhibit the B-A transition of "'18 and "'0.25 base pairs per ligand molecule, respectively. Netropsin at rt = 0.2 induces a very stable B-DNA even at rather low RH (23 %). The total hydration of this complex is significantly higher than for a drug-free DNA film. Netropsin-DNA complexes at r of 0.02 and 0.01 result in an inhibition of "45 base pairs pe4 drug molecule with respect to the B-A transition.

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Section: Resultsmentioning

confidence: 99%

“…The (19). Finally, rt of the L-carnosine -DNA complex was determined colorimetrically to be 1.5 (+ 0.2) taking into account the hydration of DNA at ambient RH (20).…”

Section: Corp (Usa)mentioning

confidence: 99%

Infrared linear dichroism of oriented DNA-ligand complexes prepared with the wet-spinning method

Fritzsche¹,

Rupprecht

Richter³

1984

Nucl Acids Res

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“…Therefore, the modified bases at the recognition sequences of these unusual phage DNAs might simply not make proper contact with the enzymes' binding or catalysis sites. This is especially likely to be the case for at least some of these enzymes because, in the B conformation, the 5-position of C and T residues is prominently exposed (43,44).…”

Section: Discussionmentioning

confidence: 99%

Digestion of highly modified bacteriophage DNA by restriction endonucleases

et al. 1982

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The ability of thirty Type II restriction endonucleases to cleave five different types of highly modified DNA has been examined. The DNA substrates were derived from relatively large bacteriophage genomes which contain all or most of the cytosine or thymine residues substituted at the 5-position.These substituents were a proton (PBS1 DNA), a hydroxymethyl group (SPO1 DNA), a methyl group (XP12 DNA), a glucosylated hydroxymethyl group (T4 DNA), or a phosphoglucuronated, glucosylated 4,5-dihydroxypentyl group (SP15 DNA). Although PBS1 DNA and SPO1 DNA were digested by most of the enzymes, they were cleaved much more slowly than was normal DNA by many of them. 5-Methylcytosine-rich XP12 DNA and the multiply modified T4 and SP15 DNAs were resistant to most of these endonucleases. The only enzyme that cleaved all five of these DNAs was TaqI, which fragmented them extensively.

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“…The result is a concomitant decrease in solvent-accessible surface area, a loss of bound water, and an increase in the entropy of the solution, which accompanies the release of water from the DNA surface. 9 In addition, the loss of water at high-ionic-strength conditions greatly reduces the electrostatic penalty for placing the negatively charged DNA adjacent to the negatively charged silica surface. Finally, when the pH of the solution is lowered from 8 to 5, an increase in surface hydroxyl groups on the silica phase occurs, thereby increasing the ability of the silica to form hydrogen bonds with the DNA in solution and decreasing the free hydroxyls that compete with DNA for hydrogen bonding sites on the silica surface.…”

Section: Silica-based Purification Of Nasmentioning

confidence: 99%