Sequence-Dependent Fluorescence of Cy3-and Cy5-Labeled Double-Stranded DNA

被引:61
|
作者
Kretschy, Nicole [1 ]
Sack, Matej [1 ]
Somoza, Mark M. [1 ]
机构
[1] Univ Vienna, Inst Inorgan Chem, Fac Chem, Althanstr 14 UZA 2, A-1090 Vienna, Austria
基金
奥地利科学基金会;
关键词
PHOTOINDUCED ELECTRON-TRANSFER; CYANINE DYE; OLIGONUCLEOTIDES; STACKING; DYNAMICS; CY3; PHOTOPHYSICS; ENHANCEMENT; ABSORPTION; EFFICIENCY;
D O I
10.1021/acs.bioconjchem.6b00053
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured the fluorescence intensity of Cy3 and Cy5 bound to the S' end of all 1024 possible double-stranded DNA Smers. The fluorescence intensity was also determined for these dyes bound to the 5' end of fixed-sequence double-stranded DNA with a variable sequence 3' overhang adjacent to the dye. The labeled DNA oligonucleotides were made using light-directed, in situ microarray synthesis. The results indicate that the fluorescence intensity of both dyes is sensitive to all five bases or base pairs, that the sequence dependence is stronger for double- (vs single-) stranded DNA, and that the dyes are sensitive to both the adjacent dsDNA sequence and the 3'-ssDNA overhang. Purine-rich sequences result in higher fluorescence. The results can be used to estimate measurement error in experiments with fluorescent-labeled DNA, as well as to optimize the fluorescent signal by considering the nucleobase environment of the labeling cyanine dye.
引用
收藏
页码:840 / 848
页数:9
相关论文
共 50 条
  • [1] Sequence-Dependent Enhancement of Cy3 Fluorescence on DNA
    Harvey, Billie J.
    Claudia, Perez
    Levitus, Marcia
    BIOPHYSICAL JOURNAL, 2010, 98 (03) : 582A - 582A
  • [2] DNA sequence-dependent enhancement of Cy3 fluorescence
    Harvey, Billie Jo
    Perez, Claudia
    Levitus, Marcia
    PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 2009, 8 (08) : 1105 - 1110
  • [3] DNA sequence-dependent enhancement of Cy3 fluorescence
    Billie Jo Harvey
    Claudia Perez
    Marcia Levitus
    Photochemical & Photobiological Sciences, 2009, 8 : 1105 - 1110
  • [4] Sequence-dependent photophysical properties of Cy3-labeled DNA
    Levitus, Marcia
    REPORTERS, MARKERS, DYES, NANOPARTICLES, AND MOLECULAR PROBES FOR BIOMEDICAL APPLICATIONS II, 2010, 7576
  • [5] Photostability of Cy3 and Cy5-labeled DNA in the presence of metallic silver particles
    Malicka, J
    Gryczynski, I
    Fang, JY
    Kusba, J
    Lakowicz, JR
    JOURNAL OF FLUORESCENCE, 2002, 12 (3-4) : 439 - 447
  • [6] Photostability of Cy3 and Cy5-Labeled DNA in the Presence of Metallic Silver Particles
    Joanna Malicka
    Ignacy Gryczynski
    Jiyu Fang
    Jozef Kusba
    Joseph R. Lakowicz
    Journal of Fluorescence, 2002, 12 : 439 - 447
  • [7] Sequence-Dependent Cy3-DNA Interactions: Effects On Fluorescence Properties
    Harvey, Billie
    Levitus, Marcia
    BIOPHYSICAL JOURNAL, 2009, 96 (03) : 401A - 401A
  • [8] Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA
    Lietard, Jory
    Ameur, Dominik
    Somoza, Mark M.
    RSC ADVANCES, 2022, 12 (09) : 5629 - 5637
  • [9] Comparison of the Sequence-Dependent Fluorescence of the Cyanine Dyes Cy3, Cy5, DyLight DY547 and DyLight DY647 on Single-Stranded DNA
    Kretschy, Nicole
    Somoza, Mark M.
    PLOS ONE, 2014, 9 (01):
  • [10] Sequence-dependence of Cy3 and Cy5 dyes in 3ʹ terminally-labeled single-stranded DNA
    Tadija Kekić
    Jory Lietard
    Scientific Reports, 12