EM chromosome mapping using surface-spread polytene chromosomes

Electron micrographs as well as light micrographs of individual surface-spread polytene (SSP) chromosomes indicate more detailed banding patterns than standard squash preparations do. For EM preparations of SSP chromosomes a simple technique is described, avoiding thin-sectioning of chromosomes.     

Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies.

We have investigated loop-induced structural perturbation of the stem structure in hairpins d(GAATTCXnGAATTC) (X = A, T and n = 3, 4, 5 and 6) that contain an EcoRI restriction site in close proximity to the hairpin loop. Oligonucleotides containing either a T3 or a A3 loop were not hydrolyzed by the restriction enzyme and also showed only weak binding to EcoRI in the absence of the cofactor Mg2+. In contrast, hairpins with larger loops are hydrolyzed by the enzyme at the scission site next to the loop although the substrate with a A4 loop is significantly more resistant than the oligonucleotide containing a T4 loop. The hairpin structures with 3 loop residues were found to be thermally most stable while larger hairpin loops resulted in structures with lower melting temperatures. The T-loop hairpins are thermally more stable than the hairpins containing the same number of A residues in the loop. As judged from proton NMR spectroscopy and the thermodynamic data, the base pair closest to the hairpin loop did form in all cases studied. The hairpin loops did, however, affect the conformation of the stem structure of the hairpins. From 31P and 1H NMR spectroscopy we conclude that the perturbation of the stem structure is stronger for smaller hairpin loops and that the extent of the perturbation is limited to 2-3 base pairs for hairpins with T3 or A4 loops. Our results demonstrate that hairpin loops modulate the conformation of the stem residues close to the loop and that this in turn reduces the substrate activity for DNA sequence specific proteins.     

Electron microscopic band-interband pattern of polytene chromosomes in Drosophila nasuta albomicans. 2. Salivary gland chromosome 2L.

The band-interband pattern (division 28-52) of salivary gland chromosome 2L in Drosophila nasuta albomicans was studied by light (LM) and electron microscopy (EM) using squash preparations and surface-spread polytene (SSP) chromosome preparations, respectively. LM and EM maps were complied. Based on the digitized EM patterns of five homologous SSP chromosomes a computerized EM chromosome map was plotted. The EM pattern analysis showed a total number of 479 chromosome bands with an almost 83% increase compared with the LM analysis of squash preparations. By extrapolation of the data from 39% of the polytene genome analysed so far in D. n. albomicans, a total number of 2,926 chromosome bands was calculated. This is almost the same number of bands as was calculated earlier for Drosophila hydei using the same SSP chromosome preparation technique. The data in the literature concerning variations in the number of chromosome bands in different Drosophila species, the various chromosome preparation techniques adopted, and the different criteria used for the EM pattern analyses, are discussed.     

Length-dependent formation of parallel-stranded DNA in alternating AT segments

Parallel-stranded DNA can be formed from alternating AT segments and is not restricted exclusively to homooligomeric AT sequences. DNA oligonucleotides 3'-d(AT)nxC4(AT)n-3' (where x indicates the location of the 5'-5' phosphodiester linkage) form parallel-stranded hairpin structures at micromolar strand concentration for n = 4 or 5 but not for n = 6, 7. The spectral properties of the parallel-stranded structures are similar to those of the hairpin structures containing homooligomeric AT stems. However, parallel-stranded structures formed in alternating AT segments are significantly less stable than either their corresponding antiparallel control or the homooligomeric parallel AT hairpins as evidenced by their lower helix-coil transition enthalpy, melting temperature, and stability constant. This results in a remarkable polymorphism which is most pronounced for 3'-d(AT)5xC4(AT)5-3'. This oligonucleotide can exist as a parallel-stranded hairpin, coil, or concatameric antiparallel structure(s), depending on temperature and strand concentration. These results suggest simple guidelines for the design of parallel-stranded DNA. In addition, we present a model for the assessment of the stability of parallel-stranded duplex structures formed from AT base pairs based on their sequence.     

The use of surface spread polytene chromosomes for high resolution fluorescence microscopic analyses

The technique of surface spreading of polytene chromosomes is applied to fluorescence microscopy. With bisbenzimide Hoechst 33258 stained surface spread polytene chromosomes from the dipteran species Chironomus thummi piger, depiction of the band-interband structure is close to that of electron micrographs of the same enlargement.     

Tandem duplications in Drosophila melanogaster

In the tandem duplication Dp(1;1)Gr approximately one quarter of the euchromatic part of the X-chromosome is duplicated. Dp(1;1)Gr itself has no phenotypic effect, but it can be made visible by combining different alleles within the tandem duplication and the homologous X-chromosome. In heterozygous females crossing-over between the two X-chromosomes is strongly reduced while at the same time crossing-over in the distal regions of the autosomes is increased.     

DNA Duplexes Containing Alpha Anomeric Nucleotides and Polarity Reversals: Coexistence of Parallel and Antiparallel DNA

Abstract

Oligodeoxynucleotides that possess alpha anomeric nucleotides and polarity reversals show promise for application in the area of antisense therapy. Here we provide a survey of the spectroscopic, thermodynamic, and enzymatic techniques used in our laboratories to investigate model systems containing such unnatural features with the ultimate goal of designing a new class of more potent and effective antisense therapeutics.     

Multimodal Assessment of Long-Term Memory Recall and Reinstatement in a Combined Cue and Context Fear Conditioning and Extinction Paradigm in Humans

Learning to predict danger via associative learning processes is critical for adaptive behaviour. After successful extinction, persisting fear memories often emerge as returning fear. Investigation of return of fear phenomena, e.g. reinstatement, have only recently began and to date, many critical questions with respect to reinstatement in human populations remain unresolved. Few studies have separated experimental phases in time even though increasing evidence shows that allowing for passage of time (and consolidation) between experimental phases has a major impact on the results. In addition, studies have relied on a single psychophysiological dimension only (SCRs/SCL or FPS) which hampers comparability between different studies that showed both differential or generalized return of fear following a reinstatement manipulation. In 93 participants, we used a multimodal approach (fear-potentiated startle, skin conductance responses, fear ratings to asses fear conditioning (day 1), extinction (day 2) as well as delayed memory recall and reinstatement (day 8) in a paradigm that probed contextual and cued fear intra-individually. Our findings show persistence of conditioning and extinction memory over time and demonstrate that reinstated fear responses were qualitatively different between dependent variables (subjective fear ratings, FPS, SCRs) as well as between cued and contextual CSs. While only the arousal-related measurement (SCRs) showed increasing reactions following reinstatement to the cued CSs, no evidence of reinstatement was observed for the subjective ratings and fear-related measurement (FPS). In contrast, for contextual CSs, reinstatement was evident as differential and generalized reinstatement in fear ratings as well as generally elevated physiological fear (FPS) and arousal (SCRs) related measurements to all contextual CSs (generalized non-differential reinstatement). Returning fear after reinstatement likely depends on a variety of variables (experimental design, dependent measurements) and more systematic investigations with respect to critical determinants of reinstatement in humans are required.