Unique base-pair breathing dynamics in PNA-DNA hybrids 1 1Edited by I. Tinoco

Leijon, Mikael; Sehlstedt, Ulrica; Nielsen, Peter E.; Gräslund, Astrid

doi:10.1006/jmbi.1997.1153

Cited by 20 publications

(20 citation statements)

References 49 publications

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“…Imino Proton Exchange-The exchange times of the imino protons were obtained from inversion recovery times of the NMR resonances as described previously (9). Addition of an exchange catalyst yields in the limit of infinite catalyst concentration the kinetic parameters for the base pair opening (Equation 1).…”

Section: Resultsmentioning

confidence: 99%

“…The carrier frequency was centered in the imino proton region. The exchange time at a particular base concentration [B], ex [B] , was obtained from the recovery time T rec [B] as described (9,13).…”

Section: Methodsmentioning

confidence: 99%

“…the opening is asymmetric, no information is provided on the fluctuations of the cytosine base. However, no evidence exists that base pair opening is asymmetric in the DNA double helix, although this appears to be the case in PNA-DNA hybrid (9). Furthermore, the cytosine base is not recognized itself by the methyltransferases.…”

Section: ј-C-c-t-t-t-c-g-a-a-a-g-g-3јmentioning

confidence: 99%

“…For GC base pairs, lifetimes about 10 times longer than for AT base pairs usually have been observed (12), as one might expect from the presence of an additional hydrogen bond in the GC base pair. However, most studies have concerned isolated GC base pairs (9,11,(13)(14)(15)(16). Representative values for isolated GC base pair lifetimes are compiled in Table I.…”

mentioning

confidence: 99%

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High Base Pair Opening Rates in Tracts of GC Base Pairs

Dornberger

Leijon

Fritzsche

1999

Journal of Biological Chemistry

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148

157

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Sequence-dependent structural features of the DNA double helix have a strong influence on the base pair opening dynamics. Here we report a detailed study of the kinetics of base pair breathing in tracts of GC base pairs in DNA duplexes derived from 1 H NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of infinite exchange catalyst concentration, the exchange times of the guanine imino protons of the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The implication of these findings for the structural principles governing spontaneous helix opening as well as the DNA-binding specificity of the cytosine-5-methyltransferases, where flipping of the cytosine base has been observed, are discussed.Many DNA-binding proteins are highly selective in their recognition of particular DNA sequences. Besides sequencespecific hydrogen bonding and van der Waals interactions, sequence-dependent structure and dynamics of DNA are likely to play an important role in DNA-protein interaction. In addition, the adaptability of a DNA sequence element to structural changes necessary for sequence-specific interaction is important in recognition (1).Base pair opening is required in many fundamental processes in the cell, for example, transcription and recombination. Recently, base pair opening was found to participate in a novel mode of protein-DNA interaction. The crystal structures of the M.HhaI 1 and M.HaeIII cytosine-5-methyltransferases in complex with their DNA recognition sequences showed the target base completely flipped out from the helix (2, 3). Cytosine-5-methyltransferases usually recognize a sequence of four GC base pairs (4). M.HhaI and M.HaeIII recognize 5Ј-GCGC-3Ј and 5Ј-GGCC-3Ј, respectively. A pertinent question is whether these enzymes actively expel the target base from the helix stack or capture a transient spontaneous opening. It has been shown that M.HhaI binds more tightly when a mismatch is created in the recognition sequence by replacing the target cytosine by any other base or an abasic site but not 5mC (5, 6). The enhanced binding was attributed to the lower energy required for opening a mismatched base pair upon formation of the binary complex. Hence, the base pair dynamics at the cytosine target site seems to contribute to the specificity of the cytosine-5-methyltransferases. These findings prompted us to investigate the base pair dynamics of tracts of GC base pairs.Measurements of base pair dynamics yield information about stability and structure of the double helix. Furthermore, studies of base pair opening in DNA interacting with drugs (7, 8) and hybridized with uncharged PNA (peptide nucleic acids) (9) have provided new clues to the m...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: ј-C-c-t-t-t-c-g-a-a-a-g-g-3јmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

High Base Pair Opening Rates in Tracts of GC Base Pairs

Dornberger

Leijon

Fritzsche

1999

Journal of Biological Chemistry

Self Cite

148

157

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“…PNA probes serving as shielding layer dilutes effective surface charge density and considerable depression of transmembrane ionic current was observed consequently. PNA probes act as binding sites for negatively charged single-stranded DNA [45][46][47]. PNA/DNA hybridization was confirmed by increased ionic current and current rectifications.…”

Section: Dna Sensorsmentioning

confidence: 94%

Applications of polymer single nanochannels in biosensors

et al. 2013

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There are many elaborate masterpieces exist in natural world. Learning from nature, people developed serial intelligent biomimetic devices. Biomimetic smart nanochannels received widespread attention for mimicking biological processes in bodies. Excellent stability, tailorable surface characteristics and nano-size effects rend polymer single nanochannel an ideal candidate for constructing sensitive and reproducible biosensors. Nanochannels are responsive for special analytes while appropriate recognition elements are modified in channels wall. In this review, we summarized recent works in contructing biosensors that are using polymer single nanochannels for detecting various analytes. polymer, single, nanochannels, biosensors, ion track-etchingCitation:

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Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application

Bian,

Pei,

Gao

et al. 2024

Adv Healthcare Materials

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Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.

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Unique base-pair breathing dynamics in PNA-DNA hybrids 1 1Edited by I. Tinoco

Cited by 20 publications

References 49 publications

High Base Pair Opening Rates in Tracts of GC Base Pairs

High Base Pair Opening Rates in Tracts of GC Base Pairs

Applications of polymer single nanochannels in biosensors

Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application

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