In vitro selection of DNAs with an increased propensity to form small circles

Gabriel Rosanio, Jonathan Widom, Olke C Uhlenbeck*

*Corresponding author for this work

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

A protocol was devised to select for DNA molecules that efficiently form circles from a library of 126 base pair DNAs containing 90 randomized base pairs. After six rounds of selection, individual molecules from the library showed 20- to 100-fold greater j-factors compared with the starting library, validating the selection protocol. High-throughput sequencing revealed a sinusoidal pattern of enrichment and de-enrichment of A/T dinucleotides in the random region with a 10.4 base pair period associated with the helicity of DNA. A similar, but more moderate pattern of C/G dinucleotides was offset by precisely half a helical turn. While C/G dinucleotide enrichments were evenly distributed, A/T dinucleotide enrichments displayed a preference to cluster in individual DNA molecules. The most highly enriched 10 base pair sequences in the random region contained adjacent blocks of A/T and C/G trinucleotides present in some, but not all, rapidly cyclizing molecules. The phased dinucleotide enrichments closely match those present in accurately mapped yeast nucleosomes, confirming the importance of DNA bending in nucleosome formation. However, at certain sites the nucleosomal DNAs show dinucleotide enrichments that differ substantially from the cyclization data. These discrepancies can often be correlated with sequence specific contacts that form between histones and DNA.

Original languageEnglish (US)
Pages (from-to)303-320
Number of pages18
JournalBiopolymers
Volume103
Issue number6
DOIs
StatePublished - Jan 1 2015

Fingerprint

DNA
Base Pairing
Molecules
Nucleosomes
Libraries
Cyclization
In Vitro Techniques
Histones
Yeast
Yeasts
Throughput

Keywords

  • SELEX
  • bending
  • cyclization
  • flexibility
  • sequence-dependent

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

Cite this

Rosanio, Gabriel ; Widom, Jonathan ; Uhlenbeck, Olke C. / In vitro selection of DNAs with an increased propensity to form small circles. In: Biopolymers. 2015 ; Vol. 103, No. 6. pp. 303-320.
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In vitro selection of DNAs with an increased propensity to form small circles. / Rosanio, Gabriel; Widom, Jonathan; Uhlenbeck, Olke C.

In: Biopolymers, Vol. 103, No. 6, 01.01.2015, p. 303-320.

Research output: Contribution to journalArticle

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