Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 - 4) vs. (2 + 2) adducts.

The photochemical reactions of eleven synthetic DNA hairpins possessing a single TT step either in a base-paired stem or in a hexanucleotide linker have been investigated. The major reaction products have been identified as the cis-syn (2 + 2) adduct and the (6 - 4) adduct on the basis of their spectroscopic properties including 1D and 2D NMR spectra, UV spectra and stability or instability to photochemical cleavage. Product quantum yields and ratios determined by HPLC analysis allow the behaviour of the eleven hairpins to be placed into three groups: Group I in which the (2 + 2) adduct is the major product, as is usually the case for DNA, Group II in which comparable amounts of (2 + 2) and (6 - 4) adducts are formed, and Group III in which the major product is the (6 - 4) adduct.

Conformation of a dodecane DNA hairpin linker. Multiple gauche bonds cover the bases.

Alkane linkers derived from α,ω-alkane diols have been employed for the preparation of DNA mini-hairpins, which are suitable for studies of the spectroscopy and photochemistry of short base pair domains. The solution structure of a DNA hairpin having a n-dodecane linker and six AT base pairs has been determined using (1)H NMR data with restrained molecular dynamics. The chemical shifts of the 12 diastereotopic pairs of linker protons show a distribution of values depending on their locations within the shielding region of the ring-currents of the adjacent base pair.

Structure and stability of alkane-linked DNA hairpin conjugates.

The synthesis and properties of three related families of alkane-linked DNA hairpins are reported. The first possesses a dodecane linker (C12) and 2-8 AT base pairs. The second possesses six AT base pairs and straight chain alkane linkers having 8-16 methylenes.

DNA base-pair flipping with fluorescent perylenediimide pincers.

The synthesis, structure, and electronic spectra of a series of DNA hairpins possessing two perylenediimide (PDI) base pair surrogates are reported. The PDI chromophores are located in opposite strands of the hairpin base pair domain opposite abasic sites and are either adjacent to each other or separated by a variable number of AT or GC base pairs. Molecular modeling of the conjugate having adjacent PDI chromophores shows that they adopt a slipped, pi-stacked geometry with an angle of 40 degrees between the PDI long axes.

Structure and photoinduced electron transfer in DNA hairpin conjugates possessing a tethered 5'-pyrenecarboxamide.

The structure, spectroscopy, and photophysical behavior of a series of hairpin-forming conjugates possessing a 5'-tethered N-alkylpyrenecarboxamide chromophore have been investigated. Comparison of the NMR spectra of the conjugates and analogs lacking the tethered pyrene indicates that the pyrene does not behave as an end-capping group but rather is intercalated between the two terminal hairpin base pairs. An intercalated structure is also consistent with the thermodynamic parameters for hairpin formation and the steady state and transient spectral properties of the conjugates.

Photoinduced charge separation in pyrenedicarboxamide-linked DNA hairpins.

The synthesis and photophysical properties of the dihydroxypropylamide derivative of pyrene-1,6-dicaboxamide, its aniline dyad, and DNA conjugates are reported. The dicarboxamide serves as a hairpin linker for bis(oligonucleotide) conjugates having short base pair stems. The dihydroxypropyl derivative has a large fluorescence quantum yield and long singlet decay time, as determined by fluorescence and time-resolved broad band pump-probe spectroscopy.

ChipCheckII - predicting binding curves for multiple analyte strands on small DNA microarrays.

Incomplete binding, saturation, and cross-hybridization between partially complementary strands complicate the parallel detection of nucleic acids via DNA microarrays. Treating the competing equilibria governing binding to microarrays requires computational tools. We have developed the web-based program ChipCheckII that calculates total hybridization matrices for target strands interacting with probes on small DNA microarrays.

Isostable DNA.

The high fidelity detection of multiple DNA sequences in multiplex assays calls for duplexes whose stability is independent of sequence (isostable DNA), forming under universally stringent conditions. Nature did not evolve DNA to form isostable duplexes. Here we report how probe strands can be modified so that an all-A/T target strand is bound with the same or slightly higher affinity than the corresponding all-G/C strand with the same sequence of purines and pyrimidines.

Immunostimulatory CpG oligonucleotides form defined three-dimensional structures: results from an NMR study.

The DNA eicosamer 5'-TCCATGACGTTCCTGATGCT-3' is known to stimulate the innate immune system of vertebrae. The immunostimulatory activity is based on the activation of Toll-like receptor 9 (TLR9). While it is known that the CG dinucleotide of the eicosamer has to be unmethylated, the structural basis of the recognition of the DNA through the receptor remains unclear.

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).

ChipCheck--a program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays.

Presented here is the program ChipCheck that allows the computation of total hybridization equilibria for hybridization experiments involving small oligonucleotide arrays. The calculation requires the free energies of binding for all pairs of probes and targets as well as total strand concentrations and probe molecule numbers. ChipCheck has been tested computationally on microarrays with up to 100 spots and 42 target strands (4200 binding equilibria).

CpG oligonucleotides with modified termini and nicked dumbbell structure show enhanced immunostimulatory activity.

A series of 21 phosphodiester oligodeoxyribonucleotides containing the core sequence 5'-GACGTT-3' or related control sequences were prepared and tested for their immunostimulatory effect on murine macrophages. The range of structural modifications tested included substituents at 3'- or 5'-termini, N3-methylation of thymidine residues, and hexaethylene glycol linkers favoring nicked or cyclic dumbbell duplexes. Lipophilic and cationic substituents at the termini failed to increase the release of TNF-alpha and nitric oxide, but two new types of modification were found that enhance the stimulation of RAW264.