Mismatching base-pair dependence of the kinetics of DNA-DNA hybridization studied by surface plasmon fluorescence spectroscopy.

Two single-stranded DNAs consisting of complementary base pairs except for one mismatching base pair (MM1) can form double-stranded DNA by molecular recognition. This type of duplex is not as stable as that formed by MM0. In order to add to a better understanding of the physical mechanism of the hybridization and dissociation processes at sensor (chip) surfaces, we studied the kinetics of the MM1 hybridization by surface plasmon fluorescence spectroscopy. Target DNA strands labelled with a fluorescent molecule Cy5 at the 5' end and hybridizing with the surface-attached probe DNA can be excited by the strong optical field of a surface plasmon resonance mode. The emitted fluorescence can be detected with high sensitivity. The affinity of a duplex was found to depend on the chemical nature, i.e. G-G, G-T etc., and on the position of the mismatching base pair along the 15mer duplex.

[1]  Anthony G. Frutos,et al.  Surface plasmon resonance imaging measurements of DNA hybridization adsorption and streptavidin/DNA multilayer formation at chemically modified gold surfaces , 1997 .

[2]  B. Nordén,et al.  Kinetics for hybridization of peptide nucleic acids (PNA) with DNA and RNA studied with the BIAcore technique. , 1997, Biochemistry.

[3]  J P Jost,et al.  Study of protein-DNA interactions by surface plasmon resonance (real time kinetics). , 1991, Nucleic acids research.

[4]  J. SantaLucia,et al.  Thermodynamics of internal C.T mismatches in DNA. , 1998, Nucleic acids research.

[5]  W. Knoll,et al.  Investigating the kinetics of DNA-DNA and PNA-DNA interactions using surface plasmon resonance-enhanced fluorescence spectroscopy. , 2001, Biosensors & bioelectronics.

[6]  Y. Okahata,et al.  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. , 2001, Biochemistry.

[7]  P. Nilsson,et al.  Analysis of oligonucleotide probe affinities using surface plasmon resonance: a means for mutational scanning. , 1997, Analytical biochemistry.

[8]  W. Knoll,et al.  Interfaces and thin films as seen by bound electromagnetic waves. , 1998, Annual review of physical chemistry.

[9]  J. Knight Geneticists' work in disarray as DNA-chip producer pulls the plug , 2001, Nature.

[10]  C. Halliwell,et al.  A factorial analysis of silanization conditions for the immobilization of oligonucleotides on glass surfaces. , 2001, Analytical chemistry.

[11]  F. Kirpekar,et al.  Detection of double-stranded DNA by IR- and UV-MALDI mass spectrometry. , 1999, Analytical chemistry.

[12]  How to Make a DNA Chip , 2002 .

[13]  W. Knoll,et al.  Complement hybridization from solution to surface-attached probe-oligonucleotides observed by surface-plasmon-field-enhanced fluorescence spectroscopy , 2000 .

[14]  Y. Okahata,et al.  Kinetic measurements of DNA hybridization on an oligonucleotide-immobilized 27-MHz quartz crystal microbalance. , 1998, Analytical chemistry.

[15]  J. SantaLucia,et al.  Thermodynamics and NMR of internal G.T mismatches in DNA. , 1997, Biochemistry.

[16]  Wolfgang Knoll,et al.  Surface-Plasmon Field-Enhanced Fluorescence Spectroscopy , 2000 .

[17]  B. Nordén,et al.  Thermodynamics of sequence-specific binding of PNA to DNA. , 2000, Biochemistry.

[18]  N. Sugimoto,et al.  Stabilization factors affecting duplex formation of peptide nucleic acid with DNA. , 2001, Biochemistry.

[19]  J. SantaLucia,et al.  Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. , 1999, Biochemistry.

[20]  J Wang,et al.  Mismatch-sensitive hybridization detection by peptide nucleic acids immobilized on a quartz crystal microbalance. , 1997, Analytical chemistry.

[21]  R. Service,et al.  Microchip Arrays Put DNA on the Spot , 1998, Science.

[22]  J. SantaLucia,et al.  Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. , 1998, Biochemistry.

[23]  S. Yamaguchi,et al.  Adsorption, immobilization, and hybridization of DNA studied by the use of quartz crystal oscillators , 1993 .

[24]  D. Yeung,et al.  Real-time detection and quantification of DNA hybridization by an optical biosensor. , 1995, Analytical chemistry.

[25]  P. Christen,et al.  Sequence-specific rates of interaction of target peptides with the molecular chaperones DnaK and DnaJ. , 1998, Biochemistry.