Biomod/2012/Titech/Nano-Jugglers/Methods/DNA hybridization

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Revision as of 05:49, 2 September 2012 by Kensuke Hoshi (talk | contribs) (New page: DNA design *Method ・ポリビーズと白金を結合させるDNAを5本設計した We designed five DNA strands. ・2本はポリスチレンビーズに結合させるためにamino...)
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DNA design

  • Method

・ポリビーズと白金を結合させるDNAを5本設計した We designed five DNA strands. ・2本はポリスチレンビーズに結合させるためにamino groupがついているDNAとその相補鎖と確認用のFAMがついたDNA Three DNA strands relate to “amino modified DNA and polystyrene conjugation”. One DNA strand is modified amino group to conjugate polystyrene-beads. The other one is a complementary strand, which is modified thiol group to conjugate platinum. Another DNA strand also is a complementary strand, which is modified FAM. ・2本はアゾベンゼンを組み込んだDNAとその相補鎖 Two DNA strands relate “SAM”. One DNA strand includes azobenzene to photo-control. Another DNA is a complementary strand, which is modified thiol group to conjugate gold. ・これらのDNAは論文*2を参考にNUPACK*1でシミュレーションし設計した We designed these DNA strands using NUPACK*1. And we referred to a part of a paper*2 and selected orthonormal sequence.

25.0℃ Na+濃度0.195M(1×SSCの濃度) の条件下で2次構造を形成しないDNAを選出した When we designed DNA strands, we fixed the temperature at 25.0℃ and the Na+ concentration at 0.195M. And we selected ssDNA strands, which didn’t form secondary structure.

  • 1) NUPACK nucleic acid package. http://www.nupack.org/
  • 2) Tetsuro Kitajima, Masahiro Takinoue, Ko-ichiroh Shohda, and Akira Suyama.: Design of Code Words for DNA Computers and Nanostructures with Consideration of Hybridization Kinetics. LNCS 4848, 119-129 (2008)
  • Result

・最終的に以下のようなDNAを設計した We designed five DNA strands. ・The DNA strands seqA_azo4_5thiol [ThiSS]AATXACXCCXAGXCC (X=Azobenzene) seqAc_5thiol [ThiSS]GGCTGGGTATT seqB_5thiol [ThiSS]CGTCTATTGCTTGTCACTTCCCC seqBc_5amino [AminoC6]GGGGAAGTGACAAGCAATAGACG seqBc_5FAM [6-FAM]GGGGAAGTGACAAGCAATAGACG (The DNA strands selected by us.)


  DNA design

  • Method
We designed five DNA strands.

Three DNA strands relate to “amino modified DNA and polystyrene conjugation”. One DNA strand is modified amino group to conjugate polystyrene-beads. The other one is a complementary strand, which is modified thiol group to conjugate platinum. Another DNA strand also is a complementary strand, which is modified FAM. Two DNA strands relate “SAM”. One DNA strand includes azobenzene to photo-control. Another DNA is a complementary strand, which is modified thiol group to conjugate gold. We designed these DNA strands using NUPACK*1. And we selected orthonormal sequence, referring to a paper*2. When we designed DNA strands, we fixed the temperature at 25.0℃ and the Na+ concentration at 0.195M. And we selected DNA strands, which didn’t form secondary structure.

  • 1) NUPACK nucleic acid package. http://www.nupack.org/
  • 2) Tetsuro Kitajima, Masahiro Takinoue, Ko-ichiroh Shohda, and Akira Suyama.: Design of Code Words for DNA Computers and Nanostructures with Consideration of Hybridization Kinetics. LNCS 4848, 119-129 (2008)
  • Result

We designed five DNA strands. ・The DNA strands

seqA_azo4_5thiol [ThiSS]AATXACXCCXAGXCC (X=Azobenzene)
seqAc_5thiol [ThiSS]GGCTGGGTATT
seqB_5thiol [ThiSS]CGTCTATTGCTTGTCACTTCCCC
seqBc_5amino [AminoC6]GGGGAAGTGACAAGCAATAGACG
seqBc_5FAM [6-FAM]GGGGAAGTGACAAGCAATAGACG

(The DNA strands selected by us.)

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