Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A·T base pairs of oligonucleotides immobilized on a 27 MHz quartz crystal microbalance

Hisao Matsuno, K. Niikura, Y. Okahata

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Abstract

We have systematically designed and synthesized six kinds of 16-17 mer alanine-based peptides containing four to six lysine (K) and one to four asparagine (N) residues to achieve the selective binding to A·T base pairs of DNA duplexes. The position and number of K and N residues were changed in the helical structure according to common features of the DNA-binding proteins, in which K and N residues are expected to interact electrostatically with phosphate groups and to interact with A·T base pairs by hydrogen bonding, respectively. The time courses of binding of these peptides to dA30·dT30 and dG30·dC30 duplexes immobilized on a 27 MHz quartz crystal microbalance (QCM) were studied in 10 mM phosphate buffer (pH 7.5) and 40 mM NaCl at 10 °C. The maximum binding amounts (Δmmax) on a nanogram scale and binding constants (Ka) could be obtained from the frequency decrease (mass increase) of the oligonucleotide-immobilized QCM. The conformation changes of the peptides upon binding to DNAs were monitored by circular dichroism (CD) spectroscopy. The four properly arranged N residues in the six-cationic K peptide, K6N4(d), resulted in a 5-fold higher affinity for A·T base pairs (Ka = 5.9 × 105 M-1) than for G·C base pairs (Ka = 1.2 × 105 M-1), and α-helices were clearly promoted by the binding to A·T base pairs from CD spectral changes.

Original languageEnglish
Pages (from-to)3615-3622
Number of pages8
JournalBiochemistry
Volume40
Issue number12
DOIs
Publication statusPublished - Mar 27 2001
Externally publishedYes

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Immobilized Nucleic Acids
Quartz Crystal Microbalance Techniques
Quartz crystal microbalances
Asparagine
Base Pairing
Alanine
Lysine
Peptides
Circular Dichroism
Phosphates
Circular dichroism spectroscopy
DNA
DNA-Binding Proteins
Dichroism
Conformations
Hydrogen Bonding
Hydrogen bonds
Buffers
Spectrum Analysis

All Science Journal Classification (ASJC) codes

  • Biochemistry

Cite this

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title = "Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A·T base pairs of oligonucleotides immobilized on a 27 MHz quartz crystal microbalance",
abstract = "We have systematically designed and synthesized six kinds of 16-17 mer alanine-based peptides containing four to six lysine (K) and one to four asparagine (N) residues to achieve the selective binding to A·T base pairs of DNA duplexes. The position and number of K and N residues were changed in the helical structure according to common features of the DNA-binding proteins, in which K and N residues are expected to interact electrostatically with phosphate groups and to interact with A·T base pairs by hydrogen bonding, respectively. The time courses of binding of these peptides to dA30·dT30 and dG30·dC30 duplexes immobilized on a 27 MHz quartz crystal microbalance (QCM) were studied in 10 mM phosphate buffer (pH 7.5) and 40 mM NaCl at 10 °C. The maximum binding amounts (Δmmax) on a nanogram scale and binding constants (Ka) could be obtained from the frequency decrease (mass increase) of the oligonucleotide-immobilized QCM. The conformation changes of the peptides upon binding to DNAs were monitored by circular dichroism (CD) spectroscopy. The four properly arranged N residues in the six-cationic K peptide, K6N4(d), resulted in a 5-fold higher affinity for A·T base pairs (Ka = 5.9 × 105 M-1) than for G·C base pairs (Ka = 1.2 × 105 M-1), and α-helices were clearly promoted by the binding to A·T base pairs from CD spectral changes.",
author = "Hisao Matsuno and K. Niikura and Y. Okahata",
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T1 - Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A·T base pairs of oligonucleotides immobilized on a 27 MHz quartz crystal microbalance

AU - Matsuno, Hisao

AU - Niikura, K.

AU - Okahata, Y.

PY - 2001/3/27

Y1 - 2001/3/27

N2 - We have systematically designed and synthesized six kinds of 16-17 mer alanine-based peptides containing four to six lysine (K) and one to four asparagine (N) residues to achieve the selective binding to A·T base pairs of DNA duplexes. The position and number of K and N residues were changed in the helical structure according to common features of the DNA-binding proteins, in which K and N residues are expected to interact electrostatically with phosphate groups and to interact with A·T base pairs by hydrogen bonding, respectively. The time courses of binding of these peptides to dA30·dT30 and dG30·dC30 duplexes immobilized on a 27 MHz quartz crystal microbalance (QCM) were studied in 10 mM phosphate buffer (pH 7.5) and 40 mM NaCl at 10 °C. The maximum binding amounts (Δmmax) on a nanogram scale and binding constants (Ka) could be obtained from the frequency decrease (mass increase) of the oligonucleotide-immobilized QCM. The conformation changes of the peptides upon binding to DNAs were monitored by circular dichroism (CD) spectroscopy. The four properly arranged N residues in the six-cationic K peptide, K6N4(d), resulted in a 5-fold higher affinity for A·T base pairs (Ka = 5.9 × 105 M-1) than for G·C base pairs (Ka = 1.2 × 105 M-1), and α-helices were clearly promoted by the binding to A·T base pairs from CD spectral changes.

AB - We have systematically designed and synthesized six kinds of 16-17 mer alanine-based peptides containing four to six lysine (K) and one to four asparagine (N) residues to achieve the selective binding to A·T base pairs of DNA duplexes. The position and number of K and N residues were changed in the helical structure according to common features of the DNA-binding proteins, in which K and N residues are expected to interact electrostatically with phosphate groups and to interact with A·T base pairs by hydrogen bonding, respectively. The time courses of binding of these peptides to dA30·dT30 and dG30·dC30 duplexes immobilized on a 27 MHz quartz crystal microbalance (QCM) were studied in 10 mM phosphate buffer (pH 7.5) and 40 mM NaCl at 10 °C. The maximum binding amounts (Δmmax) on a nanogram scale and binding constants (Ka) could be obtained from the frequency decrease (mass increase) of the oligonucleotide-immobilized QCM. The conformation changes of the peptides upon binding to DNAs were monitored by circular dichroism (CD) spectroscopy. The four properly arranged N residues in the six-cationic K peptide, K6N4(d), resulted in a 5-fold higher affinity for A·T base pairs (Ka = 5.9 × 105 M-1) than for G·C base pairs (Ka = 1.2 × 105 M-1), and α-helices were clearly promoted by the binding to A·T base pairs from CD spectral changes.

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