Rodney E. Harrington

Atomic Force Microscopy Imaging of Double Stranded DNA and RNA

A procedure for imaging long DNA and double stranded RNA (dsRNA) molecules using Atomic Force Microscopy (AFM) is described. Stable binding of double stranded DNA molecules to the flat mica surface is achieved by chemical modification of freshly cleaved mica under mild conditions with 3-aminopropyltriethoxy silane. We have obtained striking images of intact lambda DNA, Hind III restriction fragments of lambda DNA and dsRNA from reovirus. These images are stable under repeated scanning and measured contour lengths are accurate to within a few percent. This procedure leads to strong DNA attachment, allowing imaging under water. The widths of the DNA images lie in the range of 20 to 80nm for data obtained in air with commercially available probes. The work demonstrates that AFM is now a routine tool for simple measurements such as a length distribution. Improvement of substrate and sample preparation methods are needed to achieve yet higher resolution.

Sequence-Dependent Kinks Induced in Curved DNA

In certain curved DNA fragments without AA dinucleotides, the gel retardation anomaly associated with curvature passes through a maximum with fragment length, indicating length (and electric field) dependent structural transitions in the DNA. We suggest that thermally induced stereochemical kinks in DNA are stabilized in the gel, thus relieving the effects of curvature. These kinks are shown to occur specifically at CA/TG and TA/TA stacks. Other physical and biological evidence points to frequent structural dislocations at CA and TA steps. These reversible sequence dependent kinks may therefore represent a novel class of structural protein-DNA recognition elements.

DNA curving and bending in protein–DNA recognition

Most biological events are regulated at the molecular level by site‐specific associations between specialized proteins and DNA. These associations may bring distal regions of the genome into functional contact or may lead to the formation of large multisubunit complexes capable of regulating highly site‐specific transactional events. It is now believed that sequence‐specific protein–DNA recognition and the ability of certain proteins to compete for multiple binding sites is regulated at several levels by the local structure and conformation of the binding partners. These encompass the micro structure of DNA, including its curvature, bending and flexing as well as conformational lability in the DNA‐binding domains of the proteins. Possible mechanisms for binding specificity are discussed in the context of specific nucleoprotein systems with particular emphasis given to the roles of DNA conformations in these interactions.

Potentiostatic deposition of DNA for scanning probe microscopy.

We describe a procedure for reversible adsorption of DNA onto a gold electrode maintained under potential control. The adsorbate can be imaged by scanning probe microscopy in situ. Quantitative control of a molecular adsorbate for microscopy is now possible. We found a potential window (between 0 and 180 mV versus a silver wire quasi reference) over which a gold (111) surface under phosphate buffer is positively charged, but is not covered with a dense adsorbate. When DNA is present in these conditions, molecules adsorb onto the electrode and remain stable under repeated scanning with a scanning tunneling microscope (STM). They become removed when the surface is brought to a negative charge. When operated at tunnel currents below approximately 0.4 nA, the STM yields a resolution of approximately 1 nm, which is better than can be obtained with atomic force microscopy (AFM) at present. We illustrate this procedure by imaging a series of DNA molecules made by ligating a 21 base-pair oligonucleotide. We observed the expected series of fragment lengths but small fragments are adsorbed preferentially.

New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility.

Publisher Summary This chapter discusses the unusual DNA structures with known sequence dependencies such as bends, and the relatively new concept of sequence-directed structural softness or flexibility, and correlates these with protein structural motifs wherever possible. It shows that analyses of consensus binding sequences in DNA can provide important clues both for identifying possible roles of localized DNA structures (or microstructures) in protein-DNA interactions and for interpreting these roles in structure-function terms. An important consequence is that most biological processes are modulated at the molecular level by the interactions of regulatory proteins with themselves or other proteins, and with their characteristic operator DNA. A corollary is that the trajectory of the DNA is precisely defined, particularly in large, multi-subunit nucleoprotein complexes. Because both of these factors are highly site specific, they can confer a corresponding level of site specificity to the processes they control, which include transcriptional regulation, the action of hormone receptors, and certain types of site-specific recombination, including the precise insertion of viral DNA into host genomes.

The organic crystallizing agent 2-methyl-2,4-pentanediol reduces DNA curvature by means of structural changes in A-tracts.

Contemporary predictive models for sequence-dependent DNA structure provide a good estimation of overall DNA curvature in most cases. However, the two current models differ fundamentally in their view of the origin of DNA curvature. An earlier model that associates DNA bending primarily, although not exclusively, with stretches of adenines (A-tracts) is based on results of comparative gel retardation, cyclization kinetics, hydroxyl radical cutting, and other solution measurements. It represents an intersection of wedge and junction models. More recently, a non-A-tract bending model has been proposed, built on structural results from x-ray crystallography and molecular modeling. In this view, A-tracts are proposed to be straight and rigid, whereas mixed sequence DNA is bent. Because a key premise of the non-A-tract bending model is the crystallographic observation that A-tracts are straight, we have examined the effect in solution of 2-methyl-2,4-pentanediol (MPD), an organic solvent used in crystal preparation for crystallographic DNA structure determinations. Using cyclization analysis, DNase I cutting, chemical probing, and electron microscopy on DNA oligomers with and without A-tracts, we show that the presence of MPD in solution dramatically affects A-tracts and that the effect is specific to these sequence elements. Combined with the previous observation that MPD affects gel mobility of curved sequences with A-tracts, our findings support the bent A-tract model and call for caution in the interpretation of crystallographic results on DNA structure as these are presently obtained.

Messenger RNA induction in cellular salt tolerance of Alfalfa (Medicago sativa)

A salt tolerant alfalfaMedicago sativa L. cell line (HG2-N1) has been selected for growth in 171 mM NaCl. The salt tolerance characteristic is stable and is retained after growth in absence of salt selection for two months.In vitro translation was used to compare mRNA composition from the salt tolerant HG2-N1 and parent salt sensitive HG2 cell lines grown in the presence and absence of 171 mM NaCl. The results suggest that the mRNA composition differs between HG2-N1 and HG2 in a number of RNA species. The salt tolerant HG2-N1 shows both increases and decreases in specific polypeptides as compared to HG2. Many of the enhanced polypeptide bands from mRNA in the salt tolerant HG2-N1 variant appear to be constitutively expressed, since they can be detected from HG2-N1 cells grown in presence and absence of NaCl, but the expression of a few bands may depend on the presence of added NaCl. Most enhanced polypeptides, which are detected from mRNA in the salt tolerant variant HG2-N1 (grown on NaCl) are different from polypeptide bands enhanced in the salt sensitive HG2 line as a result of 24 hour salt stress. Similar results were obtained from two dimensional analysis ofin vivo labeled polypeptides. At least one isolated cDNA clone shows selective expression of mRNA in salt tolerant cells grown in NaCl. These results indicate that adaptive mechanisms for salt tolerance may differ in some aspects from acute stress mechanisms.

Histone variants and acetylated species from the alfalfa plant Medicago sativa

The histones from the alfalfa plant Medicago sativa have been characterized in terms of type variants and levels of acetylation. Histones were isolated directly from total plant tissue (callus), eliminating the need to develop methods for nuclear isolation. An acid-urea-polyacrylamide gel with a transverse Triton X-100 gradient resolved and identified in a single gel at least one type of histone H4, two variant forms of histone H2B, two variant forms of histone H3, and four variant forms of histone H2A from a crude histone preparation. Histone H4 was present 25% in an unmodified state and 75% as monomodified, presumably as monoacetylated histone. Both histone H3 variants displayed five bands, consistent with up to four internal sites of acetylation. The two H3 variants differed in their steady-state level of acetylation, suggesting that they may reside in different chromatin environments. Several histone H1 species were identified by solubility and cross-reactivity with antiserum raised against the globular part of bovine H1(0), indicating conservation of epitopes between histone H1 of mammals and higher plants.

p53 Binding to Nucleosomal DNA Depends on the Rotational Positioning of DNA Response Element

The sequence-specific binding to DNA is crucial for the p53 tumor suppressor function. To investigate the constraints imposed on p53-DNA recognition by nucleosomal organization, we studied binding of the p53 DNA binding domain (p53DBD) and full-length wild-type p53 protein to a single p53 response element (p53RE) placed near the nucleosomal dyad in six rotational settings. We demonstrate that the strongest p53 binding occurs when the p53RE in the nucleosome is bent in the same direction as observed for the p53-DNA complexes in solution and in co-crystals. The p53RE becomes inaccessible, however, if its orientation in the core particle is changed by ∼180°. Our observations indicate that the orientation of the binding sites on a nucleosome may play a significant role in the initial p53-DNA recognition and subsequent cofactor recruitment.

Western blotting of histones from acid-urea-Triton-and sodium dodecyl sulfate-polyacrylamide gels

We have developed a method for histone transfer from acid-urea-Triton (AUT)-polyacrylamide gels to nitrocellulose filters which prevents the interference of Triton X-100 with the binding of histones to nitrocellulose. Equilibration of AUT gels in 50 mM acetic acid and 0.5% sodium dodecyl sulfate (SDS) allowed displacement of Triton by SDS without loss of band resolution. Electrotransfer of all histone species from treated AUT gels or from equilibrated SDS gels was complete within 1 h in a transfer buffer of Tris-glycine with SDS for increased transfer efficiency and methanol for histone binding. Nitrocellulose with a pore size of 0.2 micron was optimal for histone detection.