Molecular details of quinolone–DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it

Quinolones are antibacterial drugs that are thought to bind preferentially to disturbed regions of DNA. They do not fall into the classical categories of intercalators, groove binders or electrostatic binders to the backbone. We solved the 3D structure of the DNA duplex (ACGCGU-NA)(2), where NA denotes a nalidixic acid residue covalently linked to the 2′-position of 2′-amino-2′-deoxyuridine, by NMR and restrained torsion angle molecular dynamics (MD). In the complex, the quinolones stack on G:C base pairs of the core tetramer and disrupt the terminal A:U base pair. The displaced dA residues can stack on the quinolones, while the uracil rings bind in the minor groove. The duplex-bridging interactions of the drugs and the contacts of the displaced nucleotides explain the high UV-melting temperature for d(ACGCGU-NA)(2) of up to 53°C. Further, non-covalently linked complexes between quinolones and DNA of the sequence ACGCGT can be generated via MD using constraints obtained for d(ACGCGU-NA)(2). This is demonstrated for unconjugated nalidixic acid and its 6-fluoro derivative. The well-ordered and tightly packed structures thus obtained are compatible with a published model for the quinolone–DNA complex in the active site of gyrases

An experimental and theoretical investigation of the photophysics of 1-hydroxy-2-naphthoic acid

Photophysical and photochemical properties of 1-hydroxy-2-naphthoic acid (1,2-HNA) have been investigated experimentally by steady state and time domain fluorescence measurements and theoretically by Hartree-Fock (HF), configuration interaction at the single excitation (CIS) level, density functional theoretic (DFT), and semiempirical (AM1) methods. 1,2-HNA exhibits normal fluorescence that depends on its concentration, nature of the solvent, pH, temperature, and wavelength of excitation. It seems to form different emitting species in different media, akin to 3-hydroxy-2-naphthoic acid (3,2-HNA). The large Stokes shifted emission observed at pH 13 is attributed to species undergoing excited-state intramolecular proton transfer. Nonradiative transition seems to increase on protonation and decrease on deprotonation. AM1(PECI=8) calculations predict the absorption maximum (λ<SUB>max</SUB>=335.9 nm) in reasonable agreement with experiment (λ<SUB>max</SUB>=352 nm) for the neutral 1,2-HNA. They also predict a red shift in absorption on protonation and a blue shift on deprotonation as observed experimentally. CIS calculations tend to overestimate the energy gap and hence underestimate the absorption maxima between the ground and the excited electronic states of 1,2-HNA and its protonated and deprotonated forms. However, they do predict correctly that the excited state intramolecular proton transfer is likely to occur in the deprotonated form of 1,2-HNA and not in the neutral and the protonated forms. A single minimum is found in the potential energy profile for the ground state as well as the first excited state of 1,2-HNA and its protonated species. In contrast, a double minimum with a nominal barrier in between is predicted for the ground state and also the first three excited states of the deprotonated species. The keto form of the deprotonated species is found to be slightly less stable than the enol form in all the states investigated

Mutation Screening Of Patients With Leber Congenital Amaurosis Or The Enhanced S-Cone Syndrome Reveals A Lack Of Sequence Variations In The Nrl Gene

Purpose: To determine if mutations in the retinal transcription factor gene NRL are associated with retinopathies other than autosomal dominant retinitis pigmentosa (adRP). Methods: Genomic DNA was isolated from blood samples obtained from 50 patients with Leber Congenital Amaurosis (LCA), 17 patients with the Enhanced S-Cone Syndrome (ESCS), and a patient with an atypical retinal degeneration that causes photoreceptor rosettes with blue cone opsin. The 5' upstream region (putative promoter), untranslated exon 1, coding exons 2 and 3, and exon-intron boundaries of the NRL gene were analyzed by direct sequencing of the PCR-amplified products. Results: Complete sequencing of the NRL gene in DNA samples from this cohort of patients revealed only one nucleotide change. The C->G transversion at nucleotide 711 of NRL exon 3 was detected in one LCA patient; however, this change did not alter the amino acid (L237L). Conclusions: No potential disease causing mutation was identified in the NRL gene in patients with LCA, ESCS, or the atypical retinal degeneration. Together with previous studies, our results demonstrate that mutations in the NRL gene are not a major cause of retinopathy. To date, only missense changes have been reported in adRP patients, and sequence variations are rare. It is possible that the loss of NRL function in humans is associated with a more complex clinical phenotype due to its expression in pineal gland in addition to rod photoreceptors.Wo

Mutation screening of patients with Leber congenital amaurosis or the enhanced S-cone syndrome reveals a lack of sequence variations in the NRL gene

Purpose: To determine if mutations in the retinal transcription factor gene NRL are associated with retinopathies other than autosomal dominant retinitis pigmentosa (adRP). Methods: Genomic DNA was isolated from blood samples obtained from 50 patients with Leber Congenital Amaurosis (LCA), 17 patients with the Enhanced S-Cone Syndrome (ESCS), and a patient with an atypical retinal degeneration that causes photoreceptor rosettes with blue cone opsin. The 5' upstream region (putative promoter), untranslated exon 1, coding exons 2 and 3, and exon-intron boundaries of the NRL gene were analyzed by direct sequencing of the PCR-amplified products. Results: Complete sequencing of the NRL gene in DNA samples from this cohort of patients revealed only one nucleotide change. The C->G transversion at nucleotide 711 of NRL exon 3 was detected in one LCA patient; however, this change did not alter the amino acid (L237L). Conclusions: No potential disease causing mutation was identified in the NRL gene in patients with LCA, ESCS, or the atypical retinal degeneration. Together with previous studies, our results demonstrate that mutations in the NRL gene are not a major cause of retinopathy. To date, only missense changes have been reported in adRP patients, and sequence variations are rare. It is possible that the loss of NRL function in humans is associated with a more complex clinical phenotype due to its expression in pineal gland in addition to rod photoreceptors