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INTRODUCTION
Formaldehyde was first applied as a denaturing agent in a polyacryl-
amide-gel electrophoretic system by Boedtker (l), who tried to achieve
a conformation-independent molecular weight determination of RNA.
Later, this method was criticized by Staynov et al. (2) on the basis of
a possible cross-linking of RNA by formaldehyde. These authors proposed
a method for the determination of the molecular weight of RNA by electro-
phoresis in polyacrylamide gels containing formamide, which has also
been applied to DNA fractionation (3,4).
In this work, we investigate the possibility of denaturing and electro-
phoresing DNA in polyacrylamide or agarose gels in the presence of
formaldehyde, using restriction nuclease DNA fragments as standards.
332
Copyright 0 1977 by Academic Press, Inc.
All rights of reproduction m any form reserved. ISSN 0003-2697
ELECTROPHORESIS OF DENATURED DNA 333
10
1 2 3 4 5 6 7 8 9 10 11 12
DISTANCE MIGRATED (CM)
FIG. 1. Log of chain length versus mobility plot of bacteriophage PM2 single-stranded
DNA fragments, obtained with Hemophilus injfuenzae restriction nuclease III, in a 2.5%
polyacrylamide gel containing formaldehyde. Closed circles, fragments isolated in the
laboratory of Dr. Zachau; open circles, fragments isolated in the laboratory of Dr. Van
Holde.
104
3 4 5 6 I 8 9
DISTANCE MIGRATED (Ct.41
FIG. 2. Log of chain length versus mobility plot of the same fragments as in Fig. 1
and high molecular weight ribosomal RNAs from different species, electrophoresed in a 1.5%
agarose gel containing formaldehyde. Symbols as in Fig. 1.
I
2 4 6 0 10 12 14
DISTANCE MIGRATED (CM)
2 4 6 a 10 12 14
DISTANCE MIGRATED (CM)
TABLE I
Nucleotides Nucleotides
Fraction determined calculated”
number (a) (b) b-a
1 140 180 40
2 305 360 55
3 500 540 40
4 680 720 40
5 860 900 40
6 1020 1080 60
7 1200 1260 60
than those calculated on the basis of an 180-base pair repeat. The difference
probably reflects the more advanced digestion of the “spacer” DNA,
which has been estimated to about 40 base pairs on the average (4).
Indeed, Fig. 3 shows the presence of some amount of DNA moving faster
than the “monomer.”
Another example is given in Fig. 4, which presents the electrophoretic
200
100
90
G 80
E 70
F 60
zd 50
z 40
10
3 4 5 6 7 8 9 10 11 12 13
DISTANCE MIGRATED (CM)
FIG. 5. Log of chain length versus mobility plot of the fragments in Fig. 4. The chain
lengths are assigned by analogy with the values given by No11 (3).
338 YANEVA, MLADENOVA AND DESSEV
ACKNOWLEDGMENTS
We wish to thank Dr. Zachau from the University of Miinchen and Dr. Van Holde
from the University of Oregon for the generous gifts of fragments of PM2 DNA.
REFERENCES
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ELECTROPHORESIS OF DENATURED DNA 339
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