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Abstract

Fragmentation of synthetic oligonucleotides under the influence of biotin was investigated using 3-hydroxypicolinic acid (3-HPA) as a matrix-assisted laser desorption/ionization (MALDI) matrix. Addition of biotin into the sample enhanced fragmentation of the oligonucleotide between bases. However, when the biotin was tagged to the 5′-terminus of the oligonucleotide, enhancements were observed not only in desorption/ionization efficiency but also in the fragmentation of molecular ions. The fact that the protonation/deprotonation process occurs on the tagged biotin is a possible reason for the enhancement in desorption/ionization. Site-specific backbone cleavage fragmentation patterns were observed. The sequences of oligonucleotides can be obtained from their fragment ions. The direct sequencing of a 5′-biotin-tagged 25-mer is demonstrated.

Keywords

matrix-assisted laser desorption/ionization time-of-flight mass spectrometry DNA sequencing biotin

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References

Sanger

Nicklen

and Coulson

A.R.

, Proc. Natl. Acad. Sci. USA 74, 5463 (1977).

Maxam

A.M.

and Gilbert

, Proc. Natl. Acad. Sci. USA 74, 560 (1977).

Taranenko

N.I.

Allman

S.L.

Golovlev

V.V.

Taranenko

N.V.

Isola

N.R.

and Chen

C.H.

, Nucl. Acids Res. 26, 2488 (1998).

Isola

N.R.

Allman

S.L.

Golovlov

V.V.

and Chen

C.H.

, Anal. Chem. 71, 2266 (1999).

Puapaiboon

Jai-Nhuknan

Cowan

J.A.

, Anal. Chem. 72, 3338 (2000).

Shuette

J.M.

Pieles

Maleknia

S.D.

Srivatsa

G.S.

Cole

L.D.

Moser

H.E.

and Afeyan

N.B.

, J. Pharm. Biomed. Anal. 13, 1195 (1995).

Bentzley

C.M.

Jonhston

M.V.

and Larson

B.S.

, Anal. Biochem. 258, 31 (1998).

Grotjahn

Blocker

and Frank

, Biomed. Mass Spectrom. 12, 514 (1985).

Cerny

R.L.

Tomer

K.B.

Gross

M.L.

and Grotjahn

, Anal. Biochem. 165, 175 (1987).

10.

McLuckey

S.A.

Vaidyanathan

and Habibi-Goudarzi

S.J.

, J. Mass Spectrom. 30, 1222 (1995).

11.

McLuckey

S.A.

and Habibi-Goudarzi

S.J.

, Am. Chem. Soc. 115, 12085 (1993).

12.

Little

D.P.

Chorush

R.A.

Speir

J.P.

Senko

M.W.

Kelleher

N.L.

and McLafferty

F.W.

, J. Am. Chem. Soc. 116, 4893 (1994).

13.

McLafferty

F.W.

, Acc. Chem. Res. 27, 379 (1994).

14.

Nordhoff

Karas

Cramer

Hahner

Hillenkamp

Lezius

Kirpekar

Kristiansen

Muth

Meier

and Engels

J.W.

, J. Mass Spectrom. 30, 99 (1995).

15.

Pomerantz

S.C.

McCloskey

J.A.

Tarasow

and Eaton

B.E.

, J. Am. Chem. Soc. 119, 8361 (1997).

16.

Rozrnski

and McCloskey

J.A.

, Anal. Chem. 71, 1454 (1999).

17.

Pomerantz

S.C.

Rozenski

Zhang

and McCloskey

J.A.

, Anal. Chem. 68, 1989 (1996).

18.

Edwards

J.R.

Itagaki

and Ju

, Nucl. Acids Res. 29, 104 (2001).

19.

Zhu

Y.F.

Taranenko

N.I.

Allman

S.L.

Taranenko

N.V.

Martin

S.A.

Haff

L.A.

and Chen

C.H.

, Rapid Commun. Mass Spectrom. 11, 897 (1997).

20.

Zhu

Parr

G.P.

Fitzgerald

M.C.

Nelson

C.M.

and Smith

L.M.

, J. Am. Chem. Soc. 117, 6048 (1995).

21.

Nordhoff

Karas

Cramer

Hahner

Hillenkamp

Kirpekar

Kezius

Muth

Meier

and Engels

J.W.

, J. Mass Spectrom. 30, 99 (1995).

22.

K.J.

Shaler

T.A.

and Becker

C.H.

, Anal. Chem. 66, 1637 (1994).

23.

Kirpekar

Nordhoff

Kristiansen

Roepstorff

Hahner

and Hillenkamp

, Rapid Commun. Mass Spectrom. 9, 525 (1995).

24.

Sheneider

and Chait

, Nucl. Acids Res. 23, 1570 (1995).

25.

Tang

Zhu

and Smith

L.M.

, Anal. Chem. 69, 302 (1997).

26.

Britt

P.F.

Hurst

G.B.

and Buchanan

M.V.

, J. Mass Spectrom. 31, 661 (1996).

Biotin-Enhanced Fragmentation for Direct Deoxyribo-Nucleic Acid Sequencing Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

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