Stabilization of Triple-Helical Nucleic Acids by Basic Oligopeptides

Potaman, Vladimir N.; Sinden, Richard R.

doi:10.1021/bi00045a033

Cited by 43 publications

(39 citation statements)

References 60 publications

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“…9). This contrasts with studies done with basic oligopeptides, which indicated that high positive charge densities were best for stabilizing intermolecular and intramolecular triplexes (57,58). However, without knowing the three-dimensional structure of Stm1p, it is difficult to predict the exact charge density on any part of its surface.…”

Section: Stm1 a Purine Motif Triplex Dna-binding Proteinmentioning

confidence: 81%

The Yeast STM1 Gene Encodes a Purine Motif Triple Helical DNA-binding Protein

Nelson

Musso

Dyke

2000

Journal of Biological Chemistry

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The formation of triple helical DNA has been evoked in several cellular processes including transcription, replication, and recombination. Using conventional and affinity chromatography, we purified from Saccharomyces cerevisiae whole-cell extract a 35-kDa protein that avidly and specifically bound a purine motif triplex (with a K d of 61 pM) but not a pyrimidine motif triplex or duplex DNA. Peptide microsequencing identified this protein as the product of the STM1 gene. Confirmation that Stm1p is a purine motif triplex-binding protein was obtained by electrophoretic mobility shift assays using either bacterially expressed, recombinant Stm1p or whole-cell extracts from stm1⌬ yeast. Stm1p has previously been identified as G4p2, a G-quartet nucleic acidbinding protein. This suggests that some proteins actually recognize features shared by G4 DNA and purine motif triplexes, e.g. Hoogsteen hydrogen-bonded guanines. Genetically, the STM1 gene has been identified as a multicopy suppressor of mutations in several genes involved in mitosis (e.g. TOM1, MPT5, and POP2). A possible role for multiplex DNA and its binding proteins in mitosis is discussed.It has long been recognized that, under the proper conditions, certain DNA sequences preferentially adopt a structure composed of three nucleic acid strands (1). Triple helical or triplex DNA is a thermodynamically favored structure characterized by a third pyrimidine-rich (Py triplex) 1 or purine-rich (Pu triplex) DNA strand located within the major groove of a homopurine/homopyrimidine stretch of duplex DNA (reviewed in Ref. 2). Both intermolecular triplexes, where the third stand originates from a separate DNA molecule, and intramolecular triplexes (H-DNA), where the third stand originates from a proximal site on the same DNA molecule as its duplex acceptor, have been described. In intermolecular and intramolecular triplexes, stable interaction of the third strand is achieved through either specific Hoogsteen (Py triplex) or reverse Hoogsteen (Pu triplex) hydrogen bonding to the homopurine strand of the duplex, with the third strand adopting either a parallel (Py triplex) or antiparallel (Pu triplex) orientation relative to the homopurine acceptor. Base triplets in the pyrimidine motif include T*AT and C ϩ

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Section: Stm1 a Purine Motif Triplex Dna-binding Proteinmentioning

confidence: 81%

The Yeast STM1 Gene Encodes a Purine Motif Triple Helical DNA-binding Protein

Nelson

Musso

Dyke

2000

Journal of Biological Chemistry

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“…Side-chain and main-chain atoms may interact with a particular DNA base-pair of another chain or with more than one base-pair supporting each other in interwoven hydrogen-bonding networks. These stabilize the contacts between the bases, forming a triple helix on the DNA adsorbed to the electrode surface (Shin and Koo, 1996;Potaman and Sinden, 1995;and Soyfer and Potaman, 1995). Hoogsteen (1959) explained the hydrogen bonds in the triple base pairing by considering the third strand positioned in the major groove of a WatsonCrick base pairing.…”

Section: Dna-biosensormentioning

confidence: 99%

Voltammetric behaviour of mitoxantrone at a DNA-biosensor

Oliveira-Brett

Macedo

Raimundo

et al. 1998

Biosensors and Bioelectronics

113

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The surface of an electrochemical glassy carbon electrode was modified with a layer of double-stranded DNA (dsDNA) or with double-stranded DNA conditioned in single-stranded DNA (ssDNA) and was used to investigate mitoxantrone-DNA interactions. Differential pulse and square wave voltammetry were applied to develop an electroanalytical procedure for the determination of mitoxantrone and evaluate its interaction with dsDNA or ssDNA immobilized on the electrode surface. The results demonstrate that MTX interaction with DNA is not specific to either guanine or adenine bases. The kinetics of the mitoxantrone-DNA interaction is slow and damage to DNA was followed with time.

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“…Triplex may either pre-form locally in an otherwise double-stranded DNA or form during polymerization between the nascent and folded template strands (7,9). DNA polymerization-based primer extension analysis at elevated temperatures worked well in our experiments with mirror-repeated sequences of moderate (G+C) content and relatively high (G+C) content but rather imperfect mirror symmetry (15)(16)(17). However, during structural studies of a largely Pu·Py sequence in intron 21 from the polycystic kidney disease-associated gene PKD1 (18) the primer extension approach proved difficult for a very (G+C)-rich mirror repeat (74% G+C; Fig.…”

Section: Introductionmentioning

confidence: 64%

Overcoming a barrier for DNA polymerization in triplex-forming sequences

Potaman¹

1999

Nucleic Acids Research

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Folded structures in the DNA template, such as hairpins and multi-stranded structures, often serve as pause and arrest sites for DNA polymerases. DNA polymerization is particularly difficult on mirrorrepeated homopurine·homopyrimidine templates where triple-stranded (triplex) structures may form between the nascent and folded template strands. In order to use a linear PCR amplification approach for the structural analysis of DNA in mirror-repeated sequences we modified a conventional protocol. The barrier for DNA synthesis can be eliminated using an oligonucleotide that hybridizes with the template to prevent its folding and is subsequently displaced by the progressing polymerase. The described approach is potentially useful for sequencing and analysis of chemical adducts and point mutations in a variety of sequences prone to the formation of folded structures, such as long hairpins and quadruplexes.

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Stabilization of Triple-Helical Nucleic Acids by Basic Oligopeptides

Cited by 43 publications

References 60 publications

The Yeast STM1 Gene Encodes a Purine Motif Triple Helical DNA-binding Protein

The Yeast STM1 Gene Encodes a Purine Motif Triple Helical DNA-binding Protein

Voltammetric behaviour of mitoxantrone at a DNA-biosensor

Overcoming a barrier for DNA polymerization in triplex-forming sequences

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