Seven-Base-Pair Inverted Repeats in DNA Form Stable Hairpins in Vivo in Saccharomyces cerevisiae

INVESTIGATIONS

Seven-Base-Pair Inverted Repeats in DNA Form Stable Hairpins in Vivo in Saccharomyces cerevisiae

D. K. Nag and T. D. Petes
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280

Palindromic sequences in single-stranded DNA and RNA have the potential for intrastrand base pairing, resulting in formation of ``hairpin'' structures. We previously reported a genetic method for detecting such structures in vivo in the yeast Saccharomyces cerevisiae. Below, we describe evidence indicating that a 14-base-pair palindrome (7 bp per inverted repeat) is sufficient for formation of a hairpin in vivo.

This article has been cited by other articles:

F. W. Stahl and H. M. Foss
But See KITANI (1978)
Genetics, March 1, 2008; 178(3): 1141 - 1145.
[Full Text] [PDF]

T. J. Getz, S. A. Banse, L. S. Young, A. V. Banse, J. Swanson, G. M. Wang, B. L. Browne, H. M. Foss, and F. W. Stahl
Reduced Mismatch Repair of Heteroduplexes Reveals "Non"-interfering Crossing Over in Wild-Type Saccharomyces cerevisiae
Genetics, March 1, 2008; 178(3): 1251 - 1269.
[Abstract] [Full Text] [PDF]

L. E. Jensen, P. A. Jauert, and D. T. Kirkpatrick
The Large Loop Repair and Mismatch Repair Pathways of Saccharomyces cerevisiae Act on Distinct Substrates During Meiosis
Genetics, July 1, 2005; 170(3): 1033 - 1043.
[Abstract] [Full Text] [PDF]

H. Wang, Y. Yang, M. J. Schofield, C. Du, Y. Fridman, S. D. Lee, E. D. Larson, J. T. Drummond, E. Alani, P. Hsieh, et al.
DNA bending and unbending by MutS govern mismatch recognition and specificity
PNAS, December 9, 2003; 100(25): 14822 - 14827.
[Abstract] [Full Text] [PDF]

J. D. Merker, M. Dominska, and T. D. Petes
Patterns of Heteroduplex Formation Associated With the Initiation of Meiotic Recombination in the Yeast Saccharomyces cerevisiae
Genetics, September 1, 2003; 165(1): 47 - 63.
[Abstract] [Full Text] [PDF]

S. E. Corrette-Bennett, N. L. Mohlman, Z. Rosado, J. J. Miret, P. M. Hess, B. O. Parker, and R. S. Lahue
Efficient repair of large DNA loops in Saccharomyces cerevisiae
Nucleic Acids Res., October 15, 2001; 29(20): 4134 - 4143.
[Abstract] [Full Text] [PDF]

H. M. Kearney, D. T. Kirkpatrick, J. L. Gerton, and T. D. Petes
Meiotic Recombination Involving Heterozygous Large Insertions in Saccharomyces cerevisiae: Formation and Repair of Large, Unpaired DNA Loops
Genetics, August 1, 2001; 158(4): 1457 - 1476.
[Abstract] [Full Text] [PDF]

J. A. Clikeman, S. L. Wheeler, and J. A. Nickoloff
Efficient Incorporation of Large (>2 kb) Heterologies Into Heteroduplex DNA: Pms1/Msh2-Dependent and -Independent Large Loop Mismatch Repair in Saccharomyces cerevisiae
Genetics, April 1, 2001; 157(4): 1481 - 1491.
[Abstract] [Full Text]

J. Li and M. D. Baker
Use of a Small Palindrome Genetic Marker to Investigate Mechanisms of Double-Strand-Break Repair in Mammalian Cells
Genetics, March 1, 2000; 154(3): 1281 - 1289.
[Abstract] [Full Text]

A. Nicholson, M. Hendrix, S. Jinks-Robertson, and G. F. Crouse
Regulation of Mitotic Homeologous Recombination in Yeast: Functions of Mismatch Repair and Nucleotide Excision Repair Genes
Genetics, January 1, 2000; 154(1): 133 - 146.
[Abstract] [Full Text]

K. J. Hillers and F. W. Stahl
The Conversion Gradient at HIS4 of Saccharomyces cerevisiae. I. Heteroduplex Rejection and Restoration of Mendelian Segregation
Genetics, October 1, 1999; 153(2): 555 - 572.
[Abstract] [Full Text] [PDF]

J. A. Nickoloff, D. B. Sweetser, J. A. Clikeman, G. J. Khalsa, and S. L. Wheeler
Multiple Heterologies Increase Mitotic Double-Strand Break-Induced Allelic Gene Conversion Tract Lengths in Yeast
Genetics, October 1, 1999; 153(2): 665 - 679.
[Abstract] [Full Text] [PDF]

S. E. Corrette-Bennett, B. O. Parker, N. L. Mohlman, and R. S. Lahue
Correction of Large Mispaired DNA Loops by Extracts of Saccharomyces cerevisiae
J. Biol. Chem., June 18, 1999; 274(25): 17605 - 17611.
[Abstract] [Full Text] [PDF]

H. Moore, P. W. Greenwell, C.-P. Liu, N. Arnheim, and T. D. Petes
Triplet repeats form secondary structures that escape DNA repair in yeast
PNAS, February 16, 1999; 96(4): 1504 - 1509.
[Abstract] [Full Text] [PDF]

D. T. Kirkpatrick, M. Dominska, and T. D. Petes
Conversion-Type and Restoration-Type Repair of DNA Mismatches Formed During Meiotic Recombination in Saccharomyces cerevisiae
Genetics, August 1, 1998; 149(4): 1693 - 1705.
[Abstract] [Full Text] [PDF]

C. A. Bill, W. A. Duran, N. R. Miselis, and J. A. Nickoloff
Efficient Repair of All Types of Single-Base Mismatches in Recombination Intermediates in Chinese Hamster Ovary Cells: Competition Between Long-Patch and G-T Glycosylase-Mediated Repair of G-T Mismatches
Genetics, August 1, 1998; 149(4): 1935 - 1943.
[Abstract] [Full Text] [PDF]

D. G. Taghian, H. Hough, and J. A. Nickoloff
Biased Short Tract Repair of Palindromic Loop Mismatches in Mammalian Cells
Genetics, March 1, 1998; 148(3): 1257 - 1268.
[Abstract] [Full Text] [PDF]

Evidence for Independent Mismatch Repair Processing on Opposite Sides of a Double-Strand Break in Saccharomyces cerevisiae
Genetics, January 1, 1998; 148(1): 59 - 70.

J. C. Connelly, E. S. de Leau, E. A. Okely, and D. R. F. Leach
Overexpression, Purification, and Characterization of the SbcCD Protein from Escherichia coli
J. Biol. Chem., August 8, 1997; 272(32): 19819 - 19826.
[Abstract] [Full Text] [PDF]

E Alani, N W Chi, and R Kolodner
The Saccharomyces cerevisiae Msh2 protein specifically binds to duplex oligonucleotides containing mismatched DNA base pairs and insertions.
Genes & Dev., January 15, 1995; 9(2): 234 - 247.
[Abstract] [PDF]

				T. J. Getz, S. A. Banse, L. S. Young, A. V. Banse, J. Swanson, G. M. Wang, B. L. Browne, H. M. Foss, and F. W. Stahl Reduced Mismatch Repair of Heteroduplexes Reveals "Non"-interfering Crossing Over in Wild-Type Saccharomyces cerevisiae Genetics, March 1, 2008; 178(3): 1251 - 1269. [Abstract] [Full Text] [PDF]

				L. E. Jensen, P. A. Jauert, and D. T. Kirkpatrick The Large Loop Repair and Mismatch Repair Pathways of Saccharomyces cerevisiae Act on Distinct Substrates During Meiosis Genetics, July 1, 2005; 170(3): 1033 - 1043. [Abstract] [Full Text] [PDF]

				H. Wang, Y. Yang, M. J. Schofield, C. Du, Y. Fridman, S. D. Lee, E. D. Larson, J. T. Drummond, E. Alani, P. Hsieh, et al. DNA bending and unbending by MutS govern mismatch recognition and specificity PNAS, December 9, 2003; 100(25): 14822 - 14827. [Abstract] [Full Text] [PDF]

				J. D. Merker, M. Dominska, and T. D. Petes Patterns of Heteroduplex Formation Associated With the Initiation of Meiotic Recombination in the Yeast Saccharomyces cerevisiae Genetics, September 1, 2003; 165(1): 47 - 63. [Abstract] [Full Text] [PDF]

				S. E. Corrette-Bennett, N. L. Mohlman, Z. Rosado, J. J. Miret, P. M. Hess, B. O. Parker, and R. S. Lahue Efficient repair of large DNA loops in Saccharomyces cerevisiae Nucleic Acids Res., October 15, 2001; 29(20): 4134 - 4143. [Abstract] [Full Text] [PDF]

				H. M. Kearney, D. T. Kirkpatrick, J. L. Gerton, and T. D. Petes Meiotic Recombination Involving Heterozygous Large Insertions in Saccharomyces cerevisiae: Formation and Repair of Large, Unpaired DNA Loops Genetics, August 1, 2001; 158(4): 1457 - 1476. [Abstract] [Full Text] [PDF]

				J. A. Clikeman, S. L. Wheeler, and J. A. Nickoloff Efficient Incorporation of Large (>2 kb) Heterologies Into Heteroduplex DNA: Pms1/Msh2-Dependent and -Independent Large Loop Mismatch Repair in Saccharomyces cerevisiae Genetics, April 1, 2001; 157(4): 1481 - 1491. [Abstract] [Full Text]

				J. Li and M. D. Baker Use of a Small Palindrome Genetic Marker to Investigate Mechanisms of Double-Strand-Break Repair in Mammalian Cells Genetics, March 1, 2000; 154(3): 1281 - 1289. [Abstract] [Full Text]

				A. Nicholson, M. Hendrix, S. Jinks-Robertson, and G. F. Crouse Regulation of Mitotic Homeologous Recombination in Yeast: Functions of Mismatch Repair and Nucleotide Excision Repair Genes Genetics, January 1, 2000; 154(1): 133 - 146. [Abstract] [Full Text]

				K. J. Hillers and F. W. Stahl The Conversion Gradient at HIS4 of Saccharomyces cerevisiae. I. Heteroduplex Rejection and Restoration of Mendelian Segregation Genetics, October 1, 1999; 153(2): 555 - 572. [Abstract] [Full Text] [PDF]

				J. A. Nickoloff, D. B. Sweetser, J. A. Clikeman, G. J. Khalsa, and S. L. Wheeler Multiple Heterologies Increase Mitotic Double-Strand Break-Induced Allelic Gene Conversion Tract Lengths in Yeast Genetics, October 1, 1999; 153(2): 665 - 679. [Abstract] [Full Text] [PDF]

				S. E. Corrette-Bennett, B. O. Parker, N. L. Mohlman, and R. S. Lahue Correction of Large Mispaired DNA Loops by Extracts of Saccharomyces cerevisiae J. Biol. Chem., June 18, 1999; 274(25): 17605 - 17611. [Abstract] [Full Text] [PDF]

				H. Moore, P. W. Greenwell, C.-P. Liu, N. Arnheim, and T. D. Petes Triplet repeats form secondary structures that escape DNA repair in yeast PNAS, February 16, 1999; 96(4): 1504 - 1509. [Abstract] [Full Text] [PDF]

				D. T. Kirkpatrick, M. Dominska, and T. D. Petes Conversion-Type and Restoration-Type Repair of DNA Mismatches Formed During Meiotic Recombination in Saccharomyces cerevisiae Genetics, August 1, 1998; 149(4): 1693 - 1705. [Abstract] [Full Text] [PDF]

				C. A. Bill, W. A. Duran, N. R. Miselis, and J. A. Nickoloff Efficient Repair of All Types of Single-Base Mismatches in Recombination Intermediates in Chinese Hamster Ovary Cells: Competition Between Long-Patch and G-T Glycosylase-Mediated Repair of G-T Mismatches Genetics, August 1, 1998; 149(4): 1935 - 1943. [Abstract] [Full Text] [PDF]

				D. G. Taghian, H. Hough, and J. A. Nickoloff Biased Short Tract Repair of Palindromic Loop Mismatches in Mammalian Cells Genetics, March 1, 1998; 148(3): 1257 - 1268. [Abstract] [Full Text] [PDF]

				Evidence for Independent Mismatch Repair Processing on Opposite Sides of a Double-Strand Break in Saccharomyces cerevisiae Genetics, January 1, 1998; 148(1): 59 - 70.

				J. C. Connelly, E. S. de Leau, E. A. Okely, and D. R. F. Leach Overexpression, Purification, and Characterization of the SbcCD Protein from Escherichia coli J. Biol. Chem., August 8, 1997; 272(32): 19819 - 19826. [Abstract] [Full Text] [PDF]

				E Alani, N W Chi, and R Kolodner The Saccharomyces cerevisiae Msh2 protein specifically binds to duplex oligonucleotides containing mismatched DNA base pairs and insertions. Genes & Dev., January 15, 1995; 9(2): 234 - 247. [Abstract] [PDF]