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2 edition of Design of B-form specific DNA binding oligonucleotide analogues found in the catalog.

Design of B-form specific DNA binding oligonucleotide analogues

Jane S. Hogeland

Design of B-form specific DNA binding oligonucleotide analogues

investigations of novel recognition moieties for triple helix formation

by Jane S. Hogeland

  • 17 Want to read
  • 35 Currently reading

Published .
Written in English

    Subjects:
  • Oligonucleotides.,
  • DNA.

  • Edition Notes

    Statementby Jane S. Hogeland.
    The Physical Object
    Pagination103 leaves, bound. :
    Number of Pages103
    ID Numbers
    Open LibraryOL18009623M

    A Scatchard plot for binding to poly(dA-dT) determined by solvent partition and spectrophotometric methods shows marked evidence of cooperativity with an intrinsic association constant x 10(4. SELEX-derived oligonucleotides, possessing shapes that interact with target molecules, provide a great alternative to rational design of specific oligonucleotide-based ligands. A great advantage of this approach is that it allows fast and simple selection of the tight-binding molecules from an enormous number of variants.

    T m is defined as Temperature of melting or, more accurately, as temperature of midtransition. This term is often used for nucleic acids (DNA and RNA, oligonucleotides and polynucleotides). A thermal denaturation experiment determines the stability of the secondary structure of a DNA or RNA and aids in the choice of the sequences for antisense oligomers or PCR primers. The exact ratio of BNA to DNA monomers is dependent on the target Tm value, the length of the oligo, GC%, and target sequence. In general, more than 50% of amer DNA oligo should be modified by BNA-NC units and contain a phosphate group at the 3'-end. BNA oligos bind more effectively than LNA or PNA oligos. Probe Design Example for PCR Clamping.

    Synthetic oligonucleotides are used extensively in laboratories as primers for polymerase chain reactions (PCR) and DNA sequencing, probes to visualise a specific DNA or RNA, tools to study gene function, and biopharmaceutical drugs for treating various diseases [1,2]. A combination of the binding models for the simultaneous recognition of both grooves of DNA led to the design of a polyamide–oligonucleotide ligand that binds to a specific DNA sequence with an.


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Design of B-form specific DNA binding oligonucleotide analogues by Jane S. Hogeland Download PDF EPUB FB2

Design of B-form specific DNA binding oligonucleotide analogues: investigations of novel recognition moieties for triple helix formationAuthor: Jane S.

Hogeland. Design of B-form specific DNA binding oligonucleotide analogues: investigations of novel recognition moieties for triple helix formation By Download PDF (3 MB).

The CpG dyad, an important genomic feature in DNA methylation and transcriptional regulation, is an attractive target for small molecules. To assess the utility of minor groove binding oligomers for CpG recognition, we screened a small library of hairpin pyrrole-imidazole polyamides targeting the sequence 5′-CGCG-3′ and assessed their sequence specificity using an unbiased next Cited by: PNA oligonucleotides can also be used in PCR, enhancing the amplification of specific DNA products.

Locked nucleic acid (LNA) Locked nucleic acid (LNA) is an unnatural conformationally restricted oligonucleotide analogue bearing a close structural resemblance to DNA, but possessing monomer units with a 2′-O-4′-C-methylene bridge.

The integrity of the DNA double helix is largely determined by specific hydrogen bonding between bases of the component strands and by stacking of successive base-pairs. Base analogues that do not discriminate between A, G, C and T in the complementary strand of a duplex can be described as “universal” and are a means of overcoming sequence Cited by: Triplexes are formed when the oligonucleotide binds to homopurine:homopyrimidine sequences in duplex DNA in a sequence-specific manner whereby a few mismatches in the triplex binding code can.

Sequence-specific binding and cleavage of duplex DNA by a radioiodinated, intercalator-linked, triplex-forming oligonucleotide. Nuclear Medicine and Biology23 (4),   Oligonucleotide design for assembling long sequences. Several programmes have been developed to automatically design oligonucleotides for long sequence synthesis, based on specification of the oligonucleotide length and Tm threshold.

A N-methylated quinolinium probe NSQ functionalized with a groove binder analogue was designed and synthesized. NSQ has been developed as a duplex or G-Quadruplex light-up fluorescent probe.

The characteristics of NSQ toward DNA structures were investigated through both experimental and modeling studies. Live HeLa cell imaging studies of NSQ showed its nuclear specific localization. Benzopyridoindole and benzopyridoquinoxaline derivatives were conjugated to a mer oligonucleotide at either of two different positions: the 5‘ end or an internucleotide position in the center of the mer.

These oligonucleotide−intercalator conjugates were then tested for their ability to form stable DNA triple helices with a DNA target duplex under physiological conditions. All of the. Dervan PB. Design of sequence-specific DNA-binding molecules. Science.

Apr 25; ()– Gravatt GL, Baguley BC, Wilson WR, Denny WA. DNA-directed alkylating agents. Synthesis and antitumor activity of DNA minor groove-targeted aniline mustard analogues of pibenzimol (Hoechst ) J Med Chem. Dec 9; 37 (25)– Sapphyrin−Oligonucleotide Conjugates. Novel Sequence-Specific DNA Photomodifying Agents with Increased Binding Affinity.

Journal of the American Chemical Society(49), DOI: /jal. Triple Helix-Forming Oligonucleotides Conjugated to Indolocarbazole Poisons Direct Topoisomerase I-Mediated DNA Cleavage to a Specific Site. Bioconjugate Chemistry12 (4), DOI: /bck.

Paul A. Wender and, Raok Jeon. Triplex-forming oligonucleotides (TFOs) bind to specific sequences in the DNA double helix via hydrogen bonding interactions.

TFOs have been shown to down-regulate gene expression, to induce targeted genomic DNA modifications, to stimulate DNA recombination, and. The DNA maintains a B-form structure. Netropsin-diazene has fulfilled all of the design criteria, binding to the DNA duplex studied in the minor groove of the central AAAA tract in a mode, preventing diyl dimerization and other side reactions from occurring.

binding of a desmetallo-porphyrin conjugate of hoechst to dna. iii. strong binding to single-strand oligonucleotides. Nucleosides, Nucleotides and Nucleic Acids20 (),   INTRODUCTION. Specific targeting of transcription factors by small molecules is an attractive concept that has been difficult to realize.

Recently, mithramycin (MTM; Figure Figure1), 1), a DNA binding aureolic acid natural product, was identified in high-throughput screening of 50 small molecules as a highly potent (low-nanomolar) and modestly selective inhibitor of abnormal oncogenic. Bicyclic nucleoside analogues with a fixed N-type conformation, 2′-O,4′-C-methyleneuridine and -cytidine, were incorporated into oligonucleotides, and the binding efficiency of the modified.

A detailed understanding of the chemical principles for binding specific sites on double-helical DNA with oligodeoxynucleotides (or their analogues) by triple-strand formation would provide a pivotal first step in the development of a novel chemotherapeutic strategy of genetic targeting.

This could ultimately enable precise inactivation of. Title: Design of B-Form Specific DNA Binding Oligonucleotide Analogues. Investigations of Novel Recognition Moieties For Triple Helix Formation. Abstract approved: Dwight D. Weller Oligonucleotides are capable of forming triple helices by binding within the major groove of a DNA duplex target.

While DNA within the cell is believed to be in the. Introduction. Oligonucleotide-directed triple helix formation is a highly specific strategy for designing potential artificial gene repressors ().In vitro experiments provide evidence that triplexes can block DNA binding proteins and inhibit transcription initiation (2,9–13).Recognition of homopurine/homopyrimidine sequences involves hydrogen bonds between oligonucleotide bases and purine.It was reported by Paris et al () that specific DNA sequences can be detected by utilising oligonucleotides containing pyrene-modified C-nucleoside.

In addition, Lewis et al () have indicated that oligonucleotide probes labelled by a bis-pyrenyl group at the 5'-terminus can be used to observe hybridisation with a target DNA [ 34 ].A comprehensive review of contemporary antisense oligonucleotides drugs and therapeutic principles, methods, applications, and research Oligonucleotide-based drugs, in particular antisense oligonucleotides, are part of a growing number of pharmaceutical and biotech programs progressing to treat a wide range of indications including cancer, cardiovascular, neurodegenerative, neuromuscular.