3'-O-modified nucleotides as reversible terminators for pyrosequencing.
Pyrosequencing is a method used to sequence DNA by detecting the pyrophosphate (PPi) group that is generated when a nucleotide is incorporated into the growing DNA strand in polymerase reaction. However, this method has an inherent difficulty in accurately deciphering the homopolymeric regions of the DNA templates. We report here the development of a method to solve this problem by using nucleotide reversible terminators. These nucleotide analogues are modified with a reversible chemical moiety capping the 3'-OH group to temporarily terminate the polymerase reaction. In this way, only one nucleotide is incorporated into the growing DNA strand even in homopolymeric regions. After detection of the PPi for sequence determination, the 3'-OH of the primer extension products is regenerated through different deprotection methods. Using an allyl or a 2-nitrobenzyl group as the reversible moiety to cap the 3'-OH of the four nucleotides, we have synthesized two sets of 3'-O-modified nucleotides, 3'-O-allyl-dNTPs and 3'-O-(2-nitrobenzyl)-dNTPs as reversible terminators for pyrosequencing. The capping moiety on the 3'-OH of the DNA extension product is efficiently removed after PPi detection by either a chemical method or photolysis. To sequence DNA, templates containing homopolymeric regions are immobilized on Sepharose beads, and then extension-signal detection-deprotection cycles are conducted by using the nucleotide reversible terminators on the DNA beads to unambiguously decipher the sequence of DNA templates. Our results establish that this reversible-terminator-pyrosequencing approach can be potentially developed into a powerful methodology to accurately determine DNA sequences.
Wu
Jian
J
Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
Zhang
Shenglong
S
Meng
Qinglin
Q
Cao
Huanyan
H
Li
Zengmin
Z
Li
Xiaoxu
X
Shi
Shundi
S
Kim
Dae Hyun
DH
Bi
Lanrong
L
Turro
Nicholas J
NJ
Ju
Jingyue
J
D001483:Base Sequence; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry; D008156:Luciferases / Q000737:chemistry; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009711:Nucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D010100:Oxygen / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013379:Substrate Specificity
D009711:Nucleotides; D008156:Luciferases; D004259:DNA-Directed DNA Polymerase; D010100:Oxygen