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The interaction of the antimicrobial peptide dicynthaurin with 1,2-dipalmitoyl-glycerophosphatidyl-glycerol is investigated in monolayers at the air-liquid interface. The adsorption of the peptide to the negatively charged lipid monolayer and the fluidization of the condensed chain lattice have indicated a direct link to the peptides' ability to expand the bacterial membrane.

Solid-state NMR spectroscopy was used to determine the conformation and membrane topology of the disulfide-stabilized antimicrobial peptide tachyplesin I (TP) in lipid layers. Results reveal that TP is immersed in the glycerol backbone region of the membrane and is oriented roughly parallel to the plane of the membrane.

The experiments that probe the sequence-selective binding of SJG-136 to both naked and cellular DNA are described using footprinting and enzyme inhibition techniques. A single-strand ligation PCR studies indicate that SJG-136 can reach the nucleus of cells and interact with genomic DNA with a similar sequence-selectivity to that occurring with naked DNA in vitro.

Research has been conducted on the cyclic allylic alcohols and amides. The oxidation of these compounds with OsO (sub)4/TMEDA has been carried out and and the study of the hydrogen bonding control which leads to syn isomer formation is presented.

The antimicrobial cyclic peptide, RTD-1, exhibits two physically distinct states of binding to lipid bilayers as shown by circular dichroism and X-ray lamellar diffraction techniques. However, RTD-1 shows differences in the nature of transition between the two states in contrast with other antimicrobial peptides. RTD-1 induced membrane thinning depends on the peptide-to-lipid-ratio.

The major DNA groove binding ditercalinium exhibits a GC-selective drug-DNA association in that it binds to the N(sup)7 of guanine to form complexes with GC base pairs. Data indicate that the major groove-oriented N(sup)7 of guanine is a key element of the molecular recognition process.

Quinoxaline antibiotics promote the binding of peptide nucleic acid to DNA, probably by opening the double helix. Peptide nucleic acids mimic DNA and are being developed as potential diagnostic and therapeutic agents.

A study of lipid bilayers that contain antimicrobial peptide protegrin-1 is presented. The usage of lamellar X-ray diffraction is discussed.

The properties of the beta-type antimicrobial peptide protegrin-1 were investigated. Protegrin-1 was analyzed in aligned lipid bilayers using oriented circular dichroism (OCD) and shown to exhibit two significantly distinct OCD spectra as a function of lipid composition, hydration condition and peptide concentration. These two distinct spectra allow the easy determination of the state of the peptide in aligned multilayers. However, the structural basis of the spectra cannot be determined due to lack of a theoretical approach.

The optimization of switch triple helix formation at the 5'CpG3' and 5'GpC3' junctions steps by combination of base triplets in Hoogsteen and in reverse Hoogsteen configurations was investigated. It was observed that the selection of the proper linker nucleotide in the switching third strand has an essential function in the interaction between oligonucleotides and alternating oligopurine/oligopyrimidine target sequences at various junctions.

A series of polymerase chain reaction synthesized DNA fragments was used to examine the binding of anticancer drug daunomycin to double-helical DNA by fluorescence titration and DNase I footprinting. The fragments allowed easier examination of the role of the 2-amino group in the minor groove. Results revealed that daunomycin binded preferentially to 5'(A/T)GC and 5'(A/T)CG triplets in the normal fragment. The fragments in which inosine was substituted for guanosine, diaminopurine was substituted for adenine and vice versa were used in the study.

Oligonucleotides forming triple helices can be synthesized by targeting a double-helical strand with a longer strand possessing the complementary base-pairing motif as the targeted strand. The compound benzopyridoquinoxaline (BPQ) has been found to remove the bulge formed by strands so that they become smooothly parallel triple helix structures. In addition, BPQ seems to facilitate triplet base pairing even in vivo, allowing the foromation of stable triple helices in the natural state.

Studies on the complex formed by the reaction of the hybrid ligand amsacrine-4-carboxamide-netropsin combilexin (NetAmsa) with DNA or chromatin were conducted using spectroscopy and biochemistry techniques. NetAmsa interacts with DNA by sequence-specific binding of the netropsin-like moiety of the ligand to the minor groove of DNA, by insertion of the acridine chromophore, or by threading of the methanesulfonanilino group into the major groove of DNA double helix.

A novel aproach to the efficient synthesis of a functionalized salen-copper complex has been developed. The salen-copper complex induces DNA cleavage through an interaction within a groove of the double helix. An unusual mode of binding to DNA and the DNA-cleaving properties is observed. The new butylamino side chain could lead to the modification of the chelate to support cellular transport and DNA recognition.

The cooperative binding of the antitumor antibiotic echinomycin to DNA fragments with closely spaced CpG steps was studied by quantitative footprinting. The DNA fragments used were composed of a pair of ACGT sites together with an ACGT site and a TCGA site, which are either close to each other or are separated by two or four AT base pairs. Findings indicated that echinomycin cooperatively binds with the sequences ACGTACGT and TCGAACGT.

The two amino group of guanine highly influence the sequence specific cleavage of DNA by both bleomycin and calicheamicin. Addition of the 2-amino group into the adenine residues creates new cleavage sites and removal of 2-amino groups from guanine residues reduces the DNA cleavage. A total redistribution of the drug mediated cleavage sites occurs by the shifting of 2-amino groups from guanine to adenine residues. The results show close agrement with the NMR studies of bleomycin interaction.

Optical and gas electrophoretic techniques confirm the tight fitting of the distamycin moiety into the minor groove of DNA during binding reactions of DNA, as predicted by molecular modeling. The bending of the duplex toward the minor groove causes DNA helical distortion. The intercalation of the ellipticine chromophore remains unaffected during this binding process. Experiments employing the biscationic compound Distel (2+) prove these observations.

Electric linear dichroism spectroscopic studies of N-methylpyrrolecarboxamide-glycylanilinoacridine (MePyGA) reveal its preferential intercalation with GC-rich sequences. MePyGA stabilizes topoisomerase II-DNA cleavable complex and stimulates site-specific DNA cleavage. Removal of N-methylpyrrole unit cancels the preferential binding and site-specific-cleavage, suggesting the influence of 1 position substituent on the catalytic activities of topoisomerase II. Spectral and biochemical studies show that anilo group in MePyGA binds the tricyclic acridine moiety, the DNA binding domain and N-methylpyrrole moiety with the topoisomerase II-targeted chain.

The location of actinomycin molecules on a DNA lattice changes rapidly with time. Significant changes include increased antibiotic binding at the canonical preferred (GPC) sites along with reducing antibiotic presence at flanking sequences indicating lateral dislocation of the antibiotic molecules toward the best binding sites. The shuffling mechanism enables the appropriate selection of particular structural elements in the minor groove of the DNA helix by the antibiotic.

The DNA-binding capacity of echinomycin requires the presence of Hoogsteen A-T base pairs, which are determined by using 7-deazapurines. The tyrT fragment displays two strands which accept C7A and C7G through PCR. Hoogsteen pairs require a syn conformation of purine nucleotides next to the binding site. The possibility of this being caused by echinomycin is discussed. The influence of the Hoogsteen pairs on the total constancy of the complex is examined. Quantitative DNase I footprinting is employed to study compounds of echinomycin with ordinary and altered DNA. Echinomycin is also examined by being changed with DEPC and OsO4.

Analysis of seven antitumor intercalating agents show that the presence of a hydhoxyl substituent on the methyl group of position 4 does not influence the DNA sequence selectivity binding, and the presence of a chlorine atom at position 6 does not influence the ability of the drug to identify AT sequences selectively in DNA.

The interaction between amiloride and three defined-sequence DNA fragments was examined using nuclease footprinting methods. Results revealed that the diuretic follows a unique pattern of sequence-selective DNA recognition and that it binds to adenine and thymine residue-rich sites, often preferring those with 5'-TpX-3' steps. It was suggested that amiloride uses a pH-dependent tricyclic hydrogen bonded conformation to intercalate into DNA in solution. This theory was supported by findings showing the dissappearance of the footprinting pattern when the pH value exceeds the pKa.

Research was conducted on the binding of a distamycin-ellipticine hybrid molecule to DNA and chromatin. Results showed that the ellipticine moiety of the hybrid molecule dominates the binding reaction wth DNA. The hybrid was also observed to bind preferentially to the internucleosomal DNA upon introduction of chromatin. Researchers proposed a new hybrid ligand design having an additional positively-charged amidine side chain to affect higher DNA-binding affinity.

The DNA-binding properties of two netropsin-bithiazole hybrid molecules (compound 1 and compound 2) were investigated using electric linear dichroism and DNase I footprinting. Compound 1 associates with DNA via a minor goove-insertion of the netropsin group with the bithiazole group projecting away from the helix. The binding orientation of compound 2 typifies that of groups that specifically binds that minor groove. The two hybrid molecules preferentially bind specific nucleotide sequences.

Solid-state NMR experiments were conducted to determine the site-specific conformation, dynamic, and lipid interaction of the transduction domain of HIV-1 TAT peptide in anionic lipid bilayers. The random coil structure of TAT and another cell-penetrating peptide (CPP), penetratin, suggested that the lack of amphipathic structure is essential for rapid translocation of the Arg-rich CPPs across the lipid membrane without causing permanent damages to the membrane integrity.

Several NMR studies are conducted to explain the structure and properties of the chemokine-derived antimicrobial peptide interleukin-8[alpha] (IL-8[alpha]). The results of the interaction of the peptide with the detergent micelles and oriented lipid bilayers are also discussed.

Solid-state NMR was used to study the structure and lipid interaction of two cationic residues, [Arg.sub.10] and [Lys.sub.13], in the cell-penetrating peptide (CPP) penetratin. The data obtained from solid-state NMR confirmed the existance of guanidinium-phosphate interactions in penetratin and also confirmed stronger structural role of guanidinium groups than ammonium groups in the lipid-assisted translocation of CPPs across liquid-crystalline cell membranes.

Nuclear magnetic resonance (NMR) study was conducted to study and compare the dynamics and depth of insertion of two tachyplesin-I (TP-I) linear analogs, TPF4 and TPA4, in lipid bilayers. The active TP-I and TPF4 were found to exhibit large-amplitude motions on the NMR timescales, while the inactive TPA4 was immobilized.

The structure of Mini-B, a functional fragment of surfactant protein B, in the presence of micelles composed of the anionic detergent sodium dodecyl sulfate (SDS) was determined by employing solution NMR. Mini-B was found to consist of amphipathic surface with a large positively charged patch on one face of the peptide and a large hydrophobic patch on the opposite face.

Solid-state NMR method is used for measuring the [super 13]C-[super 31]P distances for an Arg-rich [beta]-hairpin antimicrobial peptide (PG-1) in the lipid membrane in order to understand the insertion of charged amino acid residues into the hydrophobic part of lipid layers. The results have suggested that the molecular mechanism for toroidal pore formation is guanidinium-phosphate complexation, which has neutralized the guanidinium ions before they are inserted into the membrane.

The tertiary structure of retrocyclin-2 is determined in a membrane-mimicking environment and a well-defined [beta]-hairpin structure is present in the presence of SDS micelles. The ability to self-associate has contributed to the high-affinity binding of retrocyclins for glycoproteins by increasing the valency and increasing the ability of retrocyclins to cross-link cell surface glycoproteins.

The dynamics of membrane disruption by antimicrobial peptide protegrin-1 (PG-1) on dimyristoyl-sn-glycero-phosphocholine-supported bilayer patches obtained through atomic force microscopy is reported. The action of PG-1 is found to be concentration-dependent.

The aggregation and packing of a membrane-disruptive beta-hairpin antimicrobial peptide, protegrin-1 (PG-1), in the solid state are investigated to understand its oligomerization and hydrogen-bonding propensity. The intermolecular packing of PG-1 found in the solid state is consistent with its oligomerization in lipid bilayers.

A (super 19)F spin diffusion magic-angle-spinning NMR technique is described to determine the oligomeric state of peptides bound to the lipid bilayer. Magnetization transfer between chemically equivalent but orientally different (super 19)F spins on different molecules reduces the (super 19)F magnetization in an exchange experiment.

NMR is used to determine the structure of a C-terminal fragment of human SP-B that includes residues 63-78. Structure determination was performed in the fluorinated alcohol hexafluoro-2-propanol (HFIP) and in sodium dodecyl sulfate (SDS) micelles.

The interaction of a beta-hairpin antimicrobial peptide, protegrin-1 is investigated by using solid state NMR. The protegrin-1 induces the formation of an isotropic phase in anionic bilayers containing phosphatidyglycerol.

Results demonstrate that the beta-sheet antimicrobial peptide, protegrin-1, aggregates establish contact with the surface and the hydrophobic center of 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidylcholine bilayers.

The interaction of antimicrobial peptides with lipopolysaccharide (LPS) bilayers is studied to understand how antimicrobial peptides interact with the LPS monolayer on the outer membrane of Gramnegative bacteria. The results imply that antimicrobial peptides readily penetrate the LPS monolayer of the outer membrane.

The application of a designed dipeptide conjugate as a convenient footprinting reagent capable of operating through a novel semiquinone mechanism is presented. The results indicate that the novel semiquinone footprinting approach as an attractive alternative to the popular DNase I footprinting method.