Direct evidence for the presence of left-handed conformation in a supramolecular assembly of polynucleotides

Abstract

Hexammine cobalt(lIl) chloride (Co(NH3)63+) provokes a B-DNA -4 Z-DNA -+ P-DNA conformational transition in poly(dG-dC).poly(dG-dC) and poly(dG-m5dC).poly(dG-m5dC). The circular dichroism spectrum of '-DNA is characterized by a manyfold increase of positive ellipticity in the range of 300-225 nm and the complete absence of a negative peak. In order to ascertain the helical handedness of '-DNA, we used a recently developed enzyme immunoassay technique. This method consisted of treating the polynucleotides with Co(NH3)63+ to convert them to the Z-or '-DNA forms and immobilizing these conformations on a microtiter plate.The plates were subsequently treated with a monoclonal anti-Z-DNA antibody Z22, alkaline phosphatase conjugated, affinity purified immunoglobulins, and the phosphatase substrate. The enzyme-substrate reaction was monitored by reading the absorbance at 405 nm with a microplate autoreader. The monoclonal anti-Z-DNA antibody had no reactivity to the B-DNA form, but bound strongly to both the Z-and '-DNA forms, showing that Co(NH3)63+-induced '-DNA form of the polynucleotides exists in the left-handed Z-DNA conformation. INTRODQUCTIONMultivalent ions like Co(NH3)63+ and Ru(NH3)63+ are excellent promoters of the transition of poly(dG-dC).poly(dG-dC) and poly(dG-m5dC).poly(dG-m5dC) from their usual right-handed B-DNA form to the left-handed Z-DNA conformation at micromolar concentrations of these counterions (1-4). Increasing concentrations of Co(NH3)63+ are also known to provoke a supramolecular organization of the polynucleotides from the Z-DNA form to a '-DNA form (5-6). The '-DNA form is a believed to be a twisted, tightly packaged assembly of DNA.Several agents, including polylysine, spermine, ethylene glycol, and salt are known to convert native DNAs to the '-DNA form (7-9). The formation of this structural form of DNA is characterized by a large (10-to 100-fold) increase in the intensity of the molar ellipticity of DNA in circular dichroism (CD) spectroscopic measurements. This property has presented a basic problem in interpreting the CD spectrum of '-DNA and assigning its helical handedness. This uncertainty has recently led to the conclusion that '-DNA is the end product in the

ACC/AHA/SCAI 2005 guideline update for percutaneous coronary intervention—summary article: A report of the American college of cardiology/American heart association task force on practice guidelines(ACC/AHA/SCAI writing committee to update the 2001 guidelines for percutaneous coronary intervention)

“…In contrast to the CD spectrum of the DNA in the buffer solution, in the RMs with w 0 = 10, 15, and 20, the spectra show (spectrum of the DNA in RM at w 0 = 20 is shown in Figure 4a) following common features: (i) an increase in both positive and negative molar ellipticities, (ii) a shift in crossover point, (iii) a negative absorption at around 260 nm, and (iv) an appreciable absorption at longer wavelengths. The spectral characteristics are consistent with the formation of aggregated form of the genomic DNA 18, 36…”

Ligand–DNA interaction in a nanocage of reverse micelle

“…The DNA structures in the RM up to 300 mM AOT are similar in nature, which is consistent with the aggregated form of the DNA in the nanospace. 18,36 In 400 mM AOT RM (Figure 10c), the DNA structure is somewhat different than those in 100-300 mM AOT RMs with w 0 ¼ 20, particularly increased absorption in the negative direction ($250 nm) relative to that in the positive direction ($300 nm). However, the overall feature of the CD spectrum (Figure 10c) is also consistent with the aggregated form of the DNA.…”

“…The spectral characteristics are consistent with the formation of aggregated form of the genomic DNA. 18,36 The intensity distribution of the scattered light from DLS measurement on the RM (w 0 ¼ 20, [AOT] ¼ 100 mM) in the presence and absence of the genomic DNA is shown in Figure 4b. The expected hydrodynamic diameter of the RMs at this hydration level is $9 nm.…”

The Effects of Cobalt-Hexammine and Cobalt-Pentammine Cations on the Solution Structure of Calf-Thymus DNA. DNA Condensation and Structural Features Studied by FTIR Difference Spectroscopy

“…The hexammine cobalt cation was also used to monitor the condensation of DNA in vitro (3). Similarly, it has been used as an excellent agent to induce B to Z to 'I'-DNA conformational changes (4)(5)(6). The crystal structures of several DNA and RNA complexes containing cobalt-hexammine cation were reported in the literature (6)(7).…”