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Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Cooperative Binding of Transcription Regulators

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Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...

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Related Experiment Video

Updated: Jul 1, 2026

Split-Ubiquitin Based Membrane Yeast Two-Hybrid (MYTH) System: A Powerful Tool For Identifying Protein-Protein Interactions

Split-Ubiquitin Based Membrane Yeast Two-Hybrid (MYTH) System: A Powerful Tool For Identifying Protein-Protein Interactions

Published on: February 2, 2010

Introduction of 6-formylcytidine into a Myb binding sequence.

A Kittaka¹, T Kuze, M Amano

¹School of Pharmaceutical Sciences, Showa University, Tokyo, Japan.

Nucleosides & Nucleotides

|January 20, 2000

Summary

This summary is machine-generated.

Introducing 6-formylcytidine into oligonucleotide duplexes significantly reduces their binding affinity to Myb protein. This modified nucleoside substitution also lowers the duplex melting temperature (Tm), impacting DNA-protein interactions.

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Split-Ubiquitin Based Membrane Yeast Two-Hybrid (MYTH) System: A Powerful Tool For Identifying Protein-Protein Interactions

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CD Spectroscopy to Study DNA-Protein Interactions

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Published on: February 10, 2022

Area of Science:

Molecular Biology
Biochemistry
Nucleic Acid Chemistry

Background:

The Myb protein is a crucial transcription factor involved in various cellular processes.
Oligonucleotide-based therapeutics require stable and specific DNA-protein interactions.
Understanding the impact of modified nucleosides on DNA structure and function is essential.

Purpose of the Study:

To investigate the effect of incorporating 6-formylcytidine (f6C) as a thymidine substitute in a Myb binding site.
To evaluate the impact of this modification on oligonucleotide duplex stability and Myb protein binding affinity.

Main Methods:

Synthesis of a 23-mer oligonucleotide duplex containing 6-formylcytidine in place of thymidine within the Myb recognition sequence (3'-TTGAC-5').
Determination of duplex melting temperature (Tm) using thermal denaturation analysis.
Assessment of Myb protein binding affinity via electrophoretic mobility shift assays (EMSA).

Main Results:

The modified duplex with 6-formylcytidine exhibited a melting temperature (Tm) of 67°C, which was 6°C lower than the native duplex.
Electrophoretic mobility shift assays demonstrated that the binding affinity of the modified 23-mer to the Myb protein was almost completely abolished.

Conclusions:

Substitution of thymidine with 6-formylcytidine in the Myb binding sequence significantly destabilizes the oligonucleotide duplex.
The 6-formylcytidine modification drastically impairs the binding of the oligonucleotide to the Myb protein, suggesting potential implications for gene regulation studies.