Simple method of DNA stretching on glass substrate for fluorescence image and spectroscopy

Study of biological molecule DNA has contributed to developing many breaking thoughts and wide applications in multidisciplinary fields, such as genomic, medical, sensing and forensic fields. Stretching of DNA molecules is an important supportive tool for AFM or spectroscopic studies of DNA in a single molecular level. In this article, we established a simple method of DNA stretching (to its full length) that occurred on a rotating negatively-charged surface of glass substrate. The isolation of a single DNA molecule was attained by the two competitive forces on DNA molecules, that is, the electrostatic attraction developed between the positively charged YOYO-1 stained DNA and the negatively charged substrate, and the centrifugal force of the rotating substrate, which separates the DNA aggregates into the single molecule. Density of stretched DNA molecules was controlled by selecting the specific parameters such as spinning time and rates, loading volume of DNA-dye complex solution etc. The atomic force microscopy image exhibited a single DNA molecule on the negatively-charged substrate in an isolated state. Further, the photoluminescence spectra of a single DNA molecule stained with YOYO-1 were achieved using the method developed in the present study, which is strongly believed to effectively support the spectroscopic analysis of DNA in a single molecular level.

[1]  A. M. Brett,et al.  Atomic Force Microscopy of DNA Immobilized onto a Highly Oriented Pyrolytic Graphite Electrode Surface , 2003 .

[2]  A. Bensimon,et al.  Encephalitozoon cuniculi (Microspora) genome: physical map and evidence for telomere-associated rDNA units on all chromosomes. , 2000, Nucleic acids research.

[3]  K. Takata,et al.  DNA Staining for Fluorescence and Laser Confocal Microscopy , 1997, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[4]  Hyun Jun Kim,et al.  Confocal Raman spectroscopy of single poly(3-methylthiophene) nanotubes , 2007 .

[5]  Vlastimil Masek,et al.  Raman spectroscopy of DNA modified by intrastrand cross-links of antitumor cisplatin. , 2007, Journal of structural biology.

[6]  S Povey,et al.  Dynamic molecular combing: stretching the whole human genome for high-resolution studies. , 1997, Science.

[7]  B. Berge,et al.  Observation by fluorescence microscopy of transcription on single combed DNA , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[8]  R. Sinden,et al.  Structure and dynamics of three-way DNA junctions: atomic force microscopy studies. , 2000, Nucleic acids research.

[9]  Olivier Hyrien,et al.  A simple and optimized method of producing silanized surfaces for FISH and replication mapping on combed DNA fibers. , 2008, BioTechniques.

[10]  C. Bustamante,et al.  Circular DNA molecules imaged in air by scanning force microscopy. , 1992, Biochemistry.

[11]  Olle Inganäs,et al.  Soft lithographic printing of patterns of stretched DNA and DNA/electronic polymer wires by surface-energy modification and transfer. , 2006, Small.

[12]  X. Michalet,et al.  High-resolution mapping of the X-linked lymphoproliferative syndrome region by FISH on combed DNA , 1998, Cytogenetic and Genome Research.

[13]  Benedetta Mennucci,et al.  What is solvatochromism? , 2010, The journal of physical chemistry. B.

[14]  H. W. Liu,et al.  Materials science communication effects of rca clean-up procedures on the formation of roughened poly-si electrodes for high-density drams' capacitors , 1997 .

[15]  G. Sotzing,et al.  White luminescence from multiple-dye-doped electrospun DNA nanofibers by fluorescence resonance energy transfer. , 2009, Angewandte Chemie.

[16]  H. Hansma.  Surface biology of DNA by atomic force microscopy. , 2001, Annual review of physical chemistry.

[17]  S. Smith,et al.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. , 1992, Science.

[18]  C. Stavrianos,et al.  The role of DNA in forensic odontology: Part II. , 2010 .

[19]  Daniel J. Müller,et al.  Atomic force microscopy: A forceful way with single molecules , 1999, Current Biology.

[20]  A Bensimon,et al.  Alignment and sensitive detection of DNA by a moving interface. , 1994, Science.

[21]  D. Pang,et al.  Combing DNA on CTAB-coated surfaces. , 2004, Biophysical chemistry.

[22]  R. Fraser.  The structure of deoxyribose nucleic acid. , 2004, Journal of structural biology.

[23]  N. Uyeda,et al.  Direct imaging of a double-strand DNA molecule. , 1981, Ultramicroscopy.

[24]  M. Castillejo,et al.  Gold coating of micromechanical DNA biosensors by pulsed laser deposition , 2012 .

[25]  B. Finlayson‐Pitts,et al.  Substrate changes associated with the chemistry of self-assembled monolayers on silicon. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[26]  Michelle D. Wang,et al.  Stretching of single collapsed DNA molecules. , 2000, Biophysical journal.

[27]  A. Aurias,et al.  Color bar coding the BRCA1 gene on combed DNA: A useful strategy for detecting large gene rearrangements , 2001, Genes, chromosomes & cancer.

[28]  D E Wemmer,et al.  Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications. , 1992, Nucleic acids research.

[29]  Jennifer N. Cha,et al.  Amplified protein detection and identification through DNA-conjugated M13 bacteriophage. , 2012, ACS nano.

[30]  C. Zhu,et al.  A convenient method of aligning large DNA molecules on bare mica surfaces for atomic force microscopy. , 1998, Nucleic acids research.

[31]  Honggu Chun,et al.  Multi-order dynamic range DNA sensor using a gold decorated SWCNT random network. , 2011, ACS nano.

[32]  W. Li,et al.  Surface-engineered gold nanorods: promising DNA vaccine adjuvant for HIV-1 treatment. , 2012, Nano letters.

[33]  Philip LeDuc,et al.  Dynamics of individual flexible polymers in a shear flow , 1999, Nature.