| Abstract: | Protein matrices such as 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid, SA) and a-cyano-4-hydroxycinnamic acid (CHCA) tend to yield homogeneous dried spots. However, well known MALDI matrices for single- and double-stranded DNA such as 3-hydroxy picolinic acid (HPA) and picolinic acid (PA) forms the crystals at the rim of their spots with uneven distribution of matrix and DNA. This inhomogeneous deposition of DNA-doped matrix crystals at the MALDI spot requires a search for sweet spots. It is important to obtain homogeneous MALDI spots that yield signals not only from the periphery but the entire spot for automated, high throughput MALDI-TOF analysis of short DNA fragments. We have investigated the characteristics of MALDI matrices for DNA and presented a method for improving the homogeneity of MALDI samples by using polymer substrates such as linear polyacrylamide (LPA), poly(ethylene oxide) (PEO), methyl cellulose (MC) and Nafion. |
