Abstract: A tip coating system for use with scanning tunneling microscope (STM) tips. The tip coating system includes a tip holder, a plate having a slot for receiving the tip and for holding a coating material, a heater for heating the coating material into a molten blob, a micropositioner for displacing the plate to and from the tip and for moving the tip within the slot so that selected portions of the tip contact the molten blob of coating material. The tip coating system is preferably controlled by electronic controllers, including a temperature controller for the heater. The tip coating system is used to insulate the tips with soft polymer coating material to ensure very low tip leakage current (on the order of about 1 pA typical).

Abstract: A method for introducing a site-specific mutation into a target polynucleotide sequence is presented. The method involves the use of an oligonucleotide capable of binding to the target sequence, either by triplex formation (mediated by Hoogsteen, reverse Hoogsteen or equivalent base pairing) or by Watson/Crick base pairing (in the presence of a recombinase enzyme). The oligonucleotide of the invention is modified by the covalent attachment of one or more electrophilic groups. When a modified oligonucleotide is bound to its target sequence, the electrophilic group is able to interact with a nearby nucleotide in the target sequence, causing a modification to the nucleotide that results in a change in nucleotide sequence. Compositions used in the practice of the method are also disclosed.

Abstract: Oligonucleotides (ODNs) include a sequence that is complementary to a target sequence in single stranded RNA, or single or double stranded DNA, and an alkylating function which after hybridization alkylates the target sequence. ODNs adapted for alkylating single stranded RNA, such as messenger RNA, are complementary to the target sequence in the Watson Crick sense. ODNs adapted for alkylating double stranded DNA have at least two alkylating functions and are complementary to the target sequence in the Hoogsteen or reverse Hoogsteen sense. With these ODNs both strands of the target sequence are alkylated. A third class of ODNs have at least approximately 26 nucleotide units in a continous sequence which are complementary to the target sequence of double stranded DNA, and the alkylating function is covalently attached to a nucleotide unit in the continuous sequence. Alkylation or cross-linking with this class of ODNs occurs in the presence of a recombinase enzyme.

Abstract: Covalently linked conjugates of oligonucleotides (ODNs) with a cyclopropapyrroloindole moiety or an analog thereof, selectively and efficiently alkylate and crosslink with nucleic acid sequences that are complementary to the base sequence of the ODN.

Abstract: Oligonucleotides containing 1-N-alkyl-6-thiopurine, 3-N-alkyl-4-thiopyrimidine and 5-N-alkyl-4-thiopyrazolopyrimidine bases and the corresponding 2'-O-alkylated or allylated nucleotides demonstrate potent antiviral activity in several assays, including the human immunodeficiency virus reverse transcriptase enzyme assay. The oligonucleotides of the invention contain approximately 5 to 99 nucleotide units, and may include, in addition to the above-noted N-alkylated and thiolated heterocyclic bases, the naturally occurring pyrimidine and purine bases.

Abstract: A tip and substrate preparation system for use with scanning probe microscopes (SPMs) includes a scanning tunneling microscope (STM) tip maker, STM tip coater, a substrate treatment method for producing clean, flat gold substrates for STM use and methods for preparing chemically activated substrates for use with an atomic force microscope (AFM). The tip maker includes a coater and an etcher which are preferably controlled by electronic controllers. The etcher provides fully automatic tip etching in a two-stage process in sodium hydroxide (NaOH) solution, permitting platinum alloys to be etched without the use of cyanide-containing chemicals. The coater is used to insulate the tips with soft polymer coatings so as to ensure very low tip leakage current (on the order of about 1 pA typical). The substrate treatment device comprises a quartz plate and a quartz torch for annealing substrates in a hydrogen flame.

Abstract: A covalently linked conjugate of an oligonucleotide (ODN) with a peptide and a carrier or targeting ligand (ODN-peptide-carrier) includes a therapeutic oligonucleotide which is capable of selectively binding to a target sequence of DNA, RNA or protein inside a target cell. The ODN is covalently linked to a peptide which is capable of being cleaved by proteolytic enzymes inside the target cell. The peptide, in turn is covalently linked to a carrier or targeting ligand moiety which facilitates delivery of the entire ODN-peptide-carrier conjugate into the cell, and preferably into a specific target tissue type. Inside the cell, the peptide is cleaved, releasing the ODN which, by binding to the target DNA, RNA or protein sequence, brings about a beneficial result.